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Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure ( Camelina sativa )
... The collinearity of major wild relative genomes with C. sativa subgenomes was revealed later (Chaudhary et al., 2020), together with major evolutionary trajectories and karyotype changes that were identified or confirmed . Phylogenetic relationships between representatives of the genus were also studied, but their results differed, depending on the chosen method and the investigated region of Camelina distribution (Brock et al., 2018;Čalasan et al., 2019;Brock et al., 2022a;Brock et al., 2022b). However, not all aspects of Camelina genus evolution and hexaploid species divergence have been investigated yet. ...
... 1.62 Mya (estimated dating for most recent common ancestor of Camelina spp.) (Brock et al., 2022a) (Figure 1). The basal status of C. laxa and its significant genetic differences from other Camelina sp. have also been confirmed by numerous studies (Hutcheon et al., 2010;Kagale et al., 2014;Brock et al., 2018;Mańdakováet al., 2019;Chaudhary et al., 2020;Martin et al., 2022). ...
... Most studies show that C. hispida was the next species to diverge from the genus along with others (Hutcheon et al., 2010;Kagale et al., 2014;Brock et al., 2018;Mańdakováet al., 2019;Brock et al., 2022a;Martin et al., 2022). Instead, results of Čalasan et al. (2019) showed that C. hispida belongs to the same clade as C. sativa and Camelina alyssum, which is most likely caused by the abovedescribed "subgenomic bias" of the analyzed ETS sequences. ...
Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop.
... Camelina sativa (L.) Crantz (Brassicaceae; Cruciferae) is now considered an important and promising oilseed and biofuel crop (Vollmann & Eynck, 2015;Brock et al., 2018Brock et al., , 2020Blume et al., 2020aBlume et al., , 2022Zanetti et al., 2021). Because of that, taxa of the genus Camelina Crantz are currently the focus of large-scale and diverse research projects covering various aspects of taxonomy, morphology, biogeography, phylogeog-raphy, phylogeny, genetics, evolution, biochemistry, and biotechnology of C. sativa and its wild relatives and possible progenitors (Martin et al., 2017;Brock et al., 2018Brock et al., , 2020Brock et al., , 2022aŽerdoner Čalasan et al., 2019;Luo et al., 2019;Mandáková et al., 2019;Chaudhary et al., 2020;Blume et al., 2020b, etc.). ...
... Camelina sativa (L.) Crantz (Brassicaceae; Cruciferae) is now considered an important and promising oilseed and biofuel crop (Vollmann & Eynck, 2015;Brock et al., 2018Brock et al., , 2020Blume et al., 2020aBlume et al., , 2022Zanetti et al., 2021). Because of that, taxa of the genus Camelina Crantz are currently the focus of large-scale and diverse research projects covering various aspects of taxonomy, morphology, biogeography, phylogeog-raphy, phylogeny, genetics, evolution, biochemistry, and biotechnology of C. sativa and its wild relatives and possible progenitors (Martin et al., 2017;Brock et al., 2018Brock et al., , 2020Brock et al., , 2022aŽerdoner Čalasan et al., 2019;Luo et al., 2019;Mandáková et al., 2019;Chaudhary et al., 2020;Blume et al., 2020b, etc.). These projects continue the tradition of early studies of the evolution of crops and weeds using Camelina as a model taxon (Zinger, 1909;Tedin, 1925;Sinskaja, 1928;Sinskaja & Beztuzheva, 1931). ...
... This name is now usually considered to be a synonym of C. microcarpa. The reason why Dorofeyev (2019) In addition to its wide acceptance in floras, manuals and numerous other publications, C. microcarpa was, and still is in, the focus of recent molecular phylogenetic, phylogeographic, and genetic studies aimed at a better understanding of the origin and evolution of an important crop species, C. sativa, and its improvement as an significant oilseed and biofuel crop (Brock et al., 2018(Brock et al., , 2020Žerdoner Čalasan et al., 2019;Mandáková & Lysak, 2022). ...
The long-forgotten and taxonomically problematic name Camelina armeniaca Desv. is one of the earliest speciesʼ names published in Camelina (Brassicaceae; Cruciferae). Because of that, the issue of its proper taxonomic application was important for the nomenclatural stability of taxa belonging to the C. sativa - C. microcarpa aggregate and containing the important oilseed and biofuel crop C. sativa and its wild relatives and progenitors. The name Camelina armeniaca is lectotypified here with the specimen P00652666 from the Tournefort Herbarium (Herbarium Tournefortianum No. 1634) in P, following the direct reference in the protologue. Judging from the morphological characters of the lectotype, taxonomically, it represents a morphotype of C. sativa sensu lato, probably most closely matching C. caucasica (C. sativa var. caucasica) from a morphological viewpoint. Contrary to the recent listing of C. armeniaca in synonymy (!) of C. microcarpa in several main biodiversity databases (such as GBIF, POWO, etc.), we conclude that C. armeniaca is definitely not conspecific with C. microcarpa. Because of that, nomenclatural conservation of the latter name against the earlier one is unnecessary, as well as a possible proposal to reject the name C. armeniaca. We prefer to treat C. armeniaca as a taxonomic synonym of C. sativa. A corrected typification (lectotypification and epitypification) of the name C. sativa var. caucasica is also provided.
... This dearth of diversity is likely largely attributable to the loss of landrace and cultivar diversity following 20th-century declines in camelina cultivation. Abandonment of camelina farming is also almost certainly a key factor in the near disappearance of the species as an agricultural weed and the apparent absence of feral populations in modern times (Brock et al., 2018); this decline is strikingly evident in the precipitous drop in C. sativa herbarium collections made after the mid-20th century (Martin et al., 2017). Additional contributing factors in the decline of weedy and feral camelina populations likely include improved techniques for removing weed seeds in flax harvests (Mirek, 1997) and increased herbicide use in European agriculture. ...
... Camelina sativa is an allohexaploid species (2n = 6x = 40), and only recently have studies uncovered its phylogenetic relationships to wild Camelina species (Brock et al., 2018;Mandáková et al., 2019;Žerdoner Čalasan et al., 2019;Chaudhary et al., 2020). Using genome-wide SNP markers, Brock et al. (2018) determined phylogenetic relationships in the genus and provided genetic evidence that C. sativa is derived from the wild hexaploid species C. microcarpa. ...
... Camelina sativa is an allohexaploid species (2n = 6x = 40), and only recently have studies uncovered its phylogenetic relationships to wild Camelina species (Brock et al., 2018;Mandáková et al., 2019;Žerdoner Čalasan et al., 2019;Chaudhary et al., 2020). Using genome-wide SNP markers, Brock et al. (2018) determined phylogenetic relationships in the genus and provided genetic evidence that C. sativa is derived from the wild hexaploid species C. microcarpa. In complementary work, Mandáková et al. (2019) utilized comparative chromosome painting and genomic in situ hybridization to elucidate a nearly identical chromosome structure and common macroevolutionary origin for the subgenomes of C. sativa and C. microcarpa (Mandáková et al., 2019). ...
Premise:
Camelina (gold-of-pleasure or false flax) is an ancient oilseed crop with emerging applications in the production of sustainable, low-input biofuels. Previous domestication hypotheses suggested a European or western Asian origin, yet little genetic evidence has existed to assess the geographical origin for this crop, and archaeological data have not been systematically surveyed.
Methods:
We utilized genotyping-by-sequencing of 185 accessions of C. sativa and its wild relatives to examine population structure within the crop species and its relationship to populations of its wild progenitor, C. microcarpa; cytotype variation was also assessed in both species. In a complementary analysis, we surveyed the archaeological literature to identify sites with archaeobotanical camelina remains and assess the timing and prevalence of usage across Europe and western Asia.
Results:
The majority of C. microcarpa sampled in Europe and the United States belongs to a variant cytotype (2n = 38) with a distinct evolutionary origin from that of the crop lineage (2n = 40). Populations of C. microcarpa from Transcaucasia (South Caucasus) are most closely related to C. sativa based on cytotype and population structure; in combination with archaeological insights, these data refute prior hypotheses of a European domestication origin.
Conclusions:
Our findings support a Caucasus, potentially Armenian, origin of C. sativa domestication. We cannot definitively determine whether C. sativa was intentionally targeted for domestication in its own right or instead arose secondarily through selection for agricultural traits in weedy C. sativa, as originally proposed by Vavilov for this species.
... ex DC. In a previous study, we employed genome-wide ddRADseq markers to assess phylogenetic relationships in the genus; this work confirmed the traditional morphologically-based species delimitations and documented the domestication origin of cultivated C. sativa from the wild hexaploid species, C. microcarpa (Brock et al. 2018). However, many unanswered questions remain on phylogenetic relationships in the genus and the domestication origin of C. sativa. ...
... The long branch length with high support (100% ML bootstrap support) and relatively diverged chloroplast genome suggests that C. anomala is indeed a distinct species, yet little is known about its current distribution, ploidy, or if it is extant in the wild. Our findings refute a previous hypothesis that C. anomala is basal to the Camelina genus [35], and instead we add to previous reports of C. laxa as being the most basal species in the genus [15,36]. The feature of siliques in C. anomala should thus be considered an evolutionarily derived trait for this species, as the rest of the genus all have silicle fruits. ...
... Seven species of Camelina were collected from the field in Turkey, Georgia, Armenia, Ukraine, United States, from the USDA GRIN and PGRC germplasm collections, and from herbarium specimens located at MO and G. Most samples in this study were previously described in Brock et al. 2018 andBrock et al. 2020. GPS coordinates and approximate localities for collections can be found in Supplemental Table 1. ...
The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.
... Genomic and cytological evidence indicate that this allopolyploidization event occurred prior to C. sativa's domestication from its wild progenitor, the hexaploid species C. microcarpa Andrz. ex DC [16,17]. With similar genome sizes and welldocumented interfertility [18,19], crosses between C. microcarpa and C. sativa could increase genetic diversity in the crop and introduce traits for agronomic improvement. ...
... With similar genome sizes and welldocumented interfertility [18,19], crosses between C. microcarpa and C. sativa could increase genetic diversity in the crop and introduce traits for agronomic improvement. Camelina microcarpa has been estimated to harbor roughly twice the genetic diversity of C. sativa [17], which further suggests that this wild species could be valuable for breeding programs. However, little is known about C. microcarpa and its potential for agricultural improvement, especially regarding seed oil composition. ...
... The genus comprises~7-8 species in total [15,20]. Several additional species-rank entities were recognized in the past, often based on minor morphological differences (see historical overviews in: [21,22]; see also [17], and references therein), and some authors continue to recognize numerous narrowly-defined species (e.g., [23]). ...
Background
Camelina sativa (gold-of-pleasure) is a traditional European oilseed crop and emerging biofuel source with high levels of desirable fatty acids. A twentieth century germplasm bottleneck depleted genetic diversity in the crop, leading to recent interest in using wild relatives for crop improvement. However, little is known about seed oil content and genetic diversity in wild Camelina species.
Results
We used gas chromatography, environmental niche assessment, and genotyping-by-sequencing to assess seed fatty acid composition, environmental distributions, and population structure in C. sativa and four congeners, with a primary focus on the crop’s wild progenitor, C. microcarpa. Fatty acid composition differed significantly between Camelina species, which occur in largely non-overlapping environments. The crop progenitor comprises three genetic subpopulations with discrete fatty acid compositions. Environment, subpopulation, and population-by-environment interactions were all important predictors for seed oil in these wild populations. A complementary growth chamber experiment using C. sativa confirmed that growing conditions can dramatically affect both oil quantity and fatty acid composition in Camelina.
Conclusions
Genetics, environmental conditions, and genotype-by-environment interactions all contribute to fatty acid variation in Camelina species. These insights suggest careful breeding may overcome the unfavorable FA compositions in oilseed crops that are predicted with warming climates.
... Camelina microcarpa has been of interest in studies of Camelina diversity as it is believed to be the closest extant relative to domesticated C. sativa and could help in understanding the domestication process in Camelina species, as well as providing novel variation (Brock et al. 2018). The collections of C. microcarpa species in different genebanks suggest that it has a diverse range of origin including the Mediterranean region, Armenia (Brock et al. 2018), Germany, Poland, Czechia, Slovakia and Georgia (Martin et al. 2017;Smejkal 1971). ...
... Camelina microcarpa has been of interest in studies of Camelina diversity as it is believed to be the closest extant relative to domesticated C. sativa and could help in understanding the domestication process in Camelina species, as well as providing novel variation (Brock et al. 2018). The collections of C. microcarpa species in different genebanks suggest that it has a diverse range of origin including the Mediterranean region, Armenia (Brock et al. 2018), Germany, Poland, Czechia, Slovakia and Georgia (Martin et al. 2017;Smejkal 1971). Diversity studies, analyses of genome size and chromosome number along with the success of hybridization efforts between C. microcarpa and C. sativa (Séguin-Swartz et al. 2013;Martin et al. 2019) suggested the close relationship between these two species (Brock et al. 2018;Martin et al. 2017). ...
... The collections of C. microcarpa species in different genebanks suggest that it has a diverse range of origin including the Mediterranean region, Armenia (Brock et al. 2018), Germany, Poland, Czechia, Slovakia and Georgia (Martin et al. 2017;Smejkal 1971). Diversity studies, analyses of genome size and chromosome number along with the success of hybridization efforts between C. microcarpa and C. sativa (Séguin-Swartz et al. 2013;Martin et al. 2019) suggested the close relationship between these two species (Brock et al. 2018;Martin et al. 2017). However, not all the results were so encouraging with varying levels of hybridization success depending on the genotype (Séguin-Swartz et al. 2013). ...
Camelina sativa (L.) Crantz an oilseed crop of the Brassicaceae family is gaining attention due to its potential as a source of high value oil for food, feed or fuel. The hexaploid domesticated C. sativa has limited genetic diversity, encouraging the exploration of related species for novel allelic variation for traits of interest. The current study utilised genotyping by sequencing to characterise 193 Camelina accessions belonging to seven different species collected primarily from the Ukrainian-Russian region and Eastern Europe. Population analyses among Camelina accessions with a 2n = 40 karyotype identified three subpopulations, two composed of domesticated C. sativa and one of C. microcarpa species. Winter type Camelina lines were identified as admixtures of C. sativa and C. microcarpa. Eighteen genotypes of related C. microcarpa unexpectedly shared only two subgenomes with C. sativa, suggesting a novel or cryptic sub-species of C. microcarpa with 19 haploid chromosomes. One C. microcarpa accession (2n = 26) was found to comprise the first two subgenomes of C. sativa suggesting a tetraploid structure. The defined chromosome series among C. microcarpa germplasm, including the newly designated C. neglecta diploid née C. microcarpa, suggested an evolutionary trajectory for the formation of the C. sativa hexaploid genome and re-defined the underlying subgenome structure of the reference genome.
... The latter region is also speculated to represent the area of origin not only of Camelina, but of the whole Brassicaceae family (Hedge, 1976). Interspecific and intergeneric hybridisation is a common phenomenon in Camelina (Julié-Galau et al., 2014;Séguin-Swartz et al., 2013) and together with subtle morphological character differences between species and numerous cytotypes, these make the taxonomy of Camelina notoriously difficult (Brock et al., 2018). Additionally, several contradictory cytotypes have been reported for this species group (Francis and Warwick, 2009;Koch et al., 2018;Martin et al., 2017), possibly due to a high hybridisation potential which further confounds accurate taxonomic inference. ...
... Fast-evolving rRNA operon regions such as the internal transcribed spacers 1 and 2 (ITS) (Schultz, 2005;Suh et al., 1993) have failed to delimitate the species in question, further preventing the recovery of true evolutionary relationships between the species (Brock et al., 2018). Until now, no study has investigated other nuclear regions that could be useful as a barcode for species level taxonomic identification within the Camelina clade. ...
... Until now, no study has investigated other nuclear regions that could be useful as a barcode for species level taxonomic identification within the Camelina clade. Species delineation and their evolutionary relationships have been tackled successfully in a recent study using a double digest restriction site associated sequencing (ddRADSeq) approach, recovering distinct and highly supported clades that were congruent with morphologically assigned species names (Brock et al., 2018). However, not all Camelina species were taken into account. ...
Stretching 8000 km from the Pannonian basin and the Danube delta in the West to the Manchuria region in the East and reaching up to 1000 km in width, the Eurasian steppe belt is the vastest steppe region worldwide. However, our knowledge about the temporal and spatial patterns of floral origin and evolution of the Eurasian Steppe is limited and inconclusive. Case studies on typical steppe flora may help us close such gaps. The study subject of this project was Camelina – a taxon which occupies open dry habitats in temperate zones of Eurasia. To infer the evolutionary history of this genus, maximum likelihood optimisation in RAxML and Bayesian Inference approach were carried out, based on the nuclear external transcribed spacer region. Furthermore, we performed a secondarily calibrated time estimation analysis using Bayesian optimisation in BEAST to infer potential influence of climatic shifts and paleogeographic events on the distribution patterns of Camelina and carried out an ancestral area reconstruction analysis using a Bayesian Binary Method. Our study resulted in a well-supported phylogeny that corresponds with the species morphology and uncovered several genetically distinct inter- and intraspecific lineages which appear to correlate geographically. Time divergence estimation argue for the diversification of Camelina to have taken place in the Middle East around the transition from Pliocene to Pleistocene (3-2 mya), and its historical biogeography to have been under a strong influence of several glacial periods and their palaeoclimatic and palaeoenvironmental consequences. Its young age also explains the subtle morphological character differences among species and high interspecific hybridisation potential. We further discuss the rediscovery of wild Camelina sativa populations and propose the external transcribed spacer as a ribotype identifying region for young and rapidly evolving core eudicot lineages.
... Another layer of explanation regarding the contrasting behaviors between the two species relies on their respective breeding history. Intense breeding in rapeseed has fruitfully increased seed yield and quality (Wang et al., 2017;Snowdon and Iniguez Luy, 2012) while, camelina did not undergo the same selection pressure (Brock et al., 2018;Luo et al., 2019). Indeed, few varietal selection and domestication efforts have been undertaken in this species since it was largely replaced by rapeseed in the 1950 s (Brock et al., 2018;Luo et al., 2019). ...
... Intense breeding in rapeseed has fruitfully increased seed yield and quality (Wang et al., 2017;Snowdon and Iniguez Luy, 2012) while, camelina did not undergo the same selection pressure (Brock et al., 2018;Luo et al., 2019). Indeed, few varietal selection and domestication efforts have been undertaken in this species since it was largely replaced by rapeseed in the 1950 s (Brock et al., 2018;Luo et al., 2019). As a result, traits of resistance to biotic and abiotic stresses were not counter selected in camelina by contrast with rapeseed which genetic pools have been drastically eroded (Esquinas-Alcázar, 2005;Ibrahim and El Habbasha, 2015;Moser, 2010;Soorni et al., 2021). ...
... Forced hybridization between GM crops and their closely-related species has been one of the first steps for assessing the potential gene flow, and this approach has been applied to C. sativa and its closelyrelated species (Julié-Galau et al., 2014;Martin et al., 2015Martin et al., , 2017Martin et al., , and 2019Séguin-Swartz et al., 2013;Tepfer et al., 2020;Zhang and Auer, 2020a). Camelina sativa, an allohexaploid (2n = 40) domesticated from the widespread weed, Camelina microcarpa (hexaploidy, 2n = 40) (Brock et al., 2018(Brock et al., , 2022, has several closely-related wild relatives, including Camelina alyssum (hexaploid, 2n = 40) and Camelina rumelica (tetraploid, 2n = 26). Others including diploid Camelina laxa (2n = 12), Camelina hispida (2n = 14), and Camelina neglecta (2n = 12) have restricted ranges in the Irano-Turanian floristic regions (Al-Shehbaz, 2012;Brock et al., 2018Brock et al., , 2019Canadian Food Inspection Agency, 2018). ...
... Camelina sativa, an allohexaploid (2n = 40) domesticated from the widespread weed, Camelina microcarpa (hexaploidy, 2n = 40) (Brock et al., 2018(Brock et al., , 2022, has several closely-related wild relatives, including Camelina alyssum (hexaploid, 2n = 40) and Camelina rumelica (tetraploid, 2n = 26). Others including diploid Camelina laxa (2n = 12), Camelina hispida (2n = 14), and Camelina neglecta (2n = 12) have restricted ranges in the Irano-Turanian floristic regions (Al-Shehbaz, 2012;Brock et al., 2018Brock et al., , 2019Canadian Food Inspection Agency, 2018). According to Mandáková et al. (2019) and Mach (2019), the genomes of diploid Camelina species originated from an ancestral n = 7 genome. ...
Pre-release risk assessment of genetically modified (GM) Camelina sativa (L.) Crantz requires a careful evaluation of the reproductive compatibility with its closely-related Camelina species. Camelina rumelica Velen. is a naturalized weed occurring in C. sativa production region in the northwestern China. In this study, a large number of reciprocal crosses was conducted between the tetraploid C. rumelica and hexaploid C. sativa. The F1 hybrids were produced by the tetraploid C. rumelica (♀) × hexaploid C. sativa (♂) at the rate of one hybrid for 217 ovules pollinated, and one hybrid for 220 ovules pollinated in the reciprocal direction. All F1 hybrids required vernalization treatment to induce timely flowering and showed the significant lower pollen viability (< 2%) compared to the parental lines. Despite that the F1 failed to backcross with the parental lines, selfed seeds (F2) were obtained from F1 hybrids plants. The F2 hybrids showed some degree of restored pollen viability (about 20%) and successfully produced seeds by both backcrossing and self-pollination. A similar pattern was observed in the field, with F1 hybrids showing self-compatibility and reduced seed production potential. It is worthwhile to mention that all F1 and F2 plants grew well both in the greenhouse and field conditions, but with the significant lower seed production ability. A portion of selfed F2 seeds from naturally shattering persisted in the soil seedbank during summer period and subsequently germinated in late fall. By contrast, other F2 seeds may have been dormant in the soil seedbank and germinated the following spring. These altered life-cycle related traits in hybrids generates the novel ecological concerns on the persistence and population dynamics of transient hybrids in the seedbank. In summary, this study provided the evidence that the tetraploid C. rumelica and hexaploid C. sativa, which have the sympatric distributions and overlapped flowering periods, gene flow between them probably could occur. Although the rate was relatively low (about 0.5%), the introgression of life-cycle related traits into C. sativa population could alter its key life-cycle traits and raise the concerns on the soil seedbank persistence and invasiveness of transient hybrid in C. sativa production region in the northwestern China.
... The similarity between C. sativa and Arabidopsis thaliana [41,42] makes A. thaliana a useful reference for the development of genetic and genomic tools in C. sativa [34]. The genus Camelina has up to 11 species, revealing taxonomic dissimilarity with its center of diversity in Eurasia (Russia or Ukraine) [43][44][45]. Among 11 species, five species, namely C. sativa, C. microcarpa, C. rumelica, C. alyssum, and C. hispida, are found in Europe and three species, namely C. sativa, C. microcarpa, and C. alyssum, are found in the USA and Canada [11]. ...
... Morphologically, C. sativa and C. microcarpa are very similar except for the smaller seed size of C. microcarpa [51]. This phenotypic similarity suggests that C. sativa could potentially be the domesticated form of C. microcarpa [43]. Greater variations in chromosome counts within species might arise from intraspecific ploidy variations or inaccurate records suggesting past taxonomic misidentification [52]. ...
Camelina sativa (L.) Crantz. is an annual oilseed crop within the Brassicaceae family. C. sativa has been grown since as early as 4000 BCE. In recent years, C. sativa received increased attention as a climate-resilient oilseed, seed meal, and biofuel (biodiesel and renewable or green diesel) crop. This renewed interest is reflected in the rapid rise in the number of peer-reviewed publications (>2300) containing “camelina” from 1997 to 2021. An overview of the origins of this ancient crop and its genetic diversity and its yield potential under hot and dry growing conditions is provided. The major biotic barriers that limit C. sativa production are summarized, including weed control, insect pests, and fungal, bacterial, and viral pathogens. Ecosystem services provided by C. sativa are also discussed. The profiles of seed oil and fatty acid composition and the many uses of seed meal and oil are discussed, including food, fodder, fuel, industrial, and medical benefits. Lastly, we outline strategies for improving this important and versatile crop to enhance its production globally in the face of a rapidly changing climate using molecular breeding, rhizosphere microbiota, genetic engineering, and genome editing approaches.
... As a "low-input and environment-friendly" oil crop grown around the world, the camelina has been planted in many countries in Europe and the Middle East in addition to China [1]. Compared with other commercialized oil crops, C. sativa has several prominent agronomic traits, such as a short life cycle (80-100 days), strong tolerance to abiotic stresses (salt, drought, cold, etc.), and high resistance to common pests and diseases that infect many cruciferous crops [2][3][4][5]. Camelina seeds accumulate high levels of oil (36% 47%) and protein (30%) as well as a variety of natural active ingredients. Its seed oil contains 90% unsaturated fatty acids, of which omega-3 fatty acids constitute 40% or more of the total. ...
... Author details 1 Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Jinzhong, Shanxi, China, 2 College of Biological Science and Technology, Jinzhong University, Jinzhong, Shanxi, China ...
Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.
Results: A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.
Conclusions: The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in twelve tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.
... De algemene opvatting is dat zulke gewassen begonnen zijn als onkruid tussen andere gewassen en uiteindelijk een eigen status als cultuurgewas verwierven. Een studie van de genetische eigenschappen van de Camelina groep toont aan dat het cultuurgewas hexaploïed is, dat wil zeggen drie sets chromosomen heeft (Brock et al. 2018). Andere soorten zijn diploïed, de meest normale status van planten, maar er zijn ook enkele tetraploïed. ...
... Camelina microcarpa komt voor in de steppegordel van Oost-Europa en Centraal-Azië (Larina & Budrevskaya 2004). De toeschrijving wordt mede ondersteund door het feit dat de genetische variabiliteit van Camelina microcarpa groter is dan die van het cultuurgewas (Brock et al. 2018). Door voortdurende, al dan niet bewuste, selectie van zaaigoed hebben cultuurgewassen gewoonlijk een kleinere genetische variatie dan de wilde soorten. ...
Abstract
Cultivation of gold of pleasure (Camelina sativa [L.] Crantz) started in the Netherlands
in the Pre-Roman Iron Age, from 800 BC onwards. Its progenitor is Camelina microcarpa
DC, a wild plant native to the steppes of Central Asia and adjacent Eastern
Europe. Gold of pleasure is a so-called secondary crop, i.e. a plant that started as a
weed and subsequently evolved into an oil crop on its own. Why the crop plant quite
suddenly gained importance in the Iron Age is unclear. Unfamiliarity with the plant,
climate change and/or a new technical use for its oil, all may have played a role. After
the Iron Age cultivation of gold of pleasure decreased, until it recently came into use
as biofuel.
... Andrz) -вид однорічної озимої трав'янистої рослини, який належить до роду Рижій (Camelina Crantz) родини капустяних (Brassicaceae). Згідно з даними, рижій дрібноплодий має різне походження, включаючи Середземноморський регіон, Вірменію, Німеччину, Польщу, Чехію, Словаччину та Грузію (Brock, 2018;Martin, 2017). ...
... Phylogenetic and genetic diversity analyses was performed by Brock et al., (2018) "-omics" enable camelina as a candidate model oil plant to study lipid metabolism regulation and genetic improvement (Yuan & Li, 2020). ...
... Camelina sativa is a crop that belongs to the Brassicaceae family and is further known as false flax or gold of pleasur (Brock et al., 2018). Since it can be grown in different soils and climates, in summer or even in winter in temperate regions, it is a very compatible crop with harsh and different climatic conditions. ...
This research was conducted for the first time in Iran on Camelina Sohail seed meal with the aim of investigating its physicochemical properties and its nutritional and anti-nutritive compounds for the possibility of using it in animal and poultry feed. The prepared samples were related to four temperate regions of Iran, i.e. Ilam, Kermanshah, Fars, and Hamedan (cold temperate), which were obtained by two methods of solvent extraction and cold pressing. In general, the examined characteristics included qualitative, physicochemical, and anti-nutritional composition (glucosinolates). The results obtained included the appearance of flour, pellets or flakes, yellow to brown color, specific taste and smell, and camellia flour free of unacceptable factors (all unacceptable factors in any amount of camellia flour). Maximum moisture content was 10 g/100 g, total ash was a maximum of 7 g/100 g, acid insoluble ash was a maximum of 1 g/100 g, and crude protein was a minimum of 35 g/100 g. The total gram content of glucosinolate, which was measured by the new HPLC analysis method, was 30 mmol/kg, and the content of urea nitrogen and free ammonia was obtained. In general, all the results obtained were in accordance with the national standard of Iranian animal feed-Camelina food-specifications and test methods.
... Camelina sativa is a crop that belongs to the Brassicaceae family and is further known as false flax or gold of pleasur (Brock et al., 2018). Since it can be grown in different soils and climates, in summer or even in winter in temperate regions, it is a very compatible crop with harsh and different climatic conditions. ...
This research was conducted for the first time in Iran on Camelina Sohail seed meal with the aim of investigating its physicochemical properties and its nutritional and anti-nutritive compounds for the possibility of using it in animal and poultry feed. The prepared samples were related to four temperate regions of Iran, i.e. Ilam, Kermanshah, Fars, and Hamedan (cold temperate), which were obtained by two methods of solvent extraction and cold pressing. In general, the examined characteristics included qualitative, physicochemical, and anti-nutritional composition (glucosinolates). The results obtained included the appearance of flour, pellets or flakes, yellow to brown color, specific taste and smell, and camellia flour free of unacceptable factors (all unacceptable factors in any amount of camellia flour). Maximum moisture content was 10 g/100 g, total ash was a maximum of 7 g/100 g, acid insoluble ash was a maximum of 1 g/100 g, and crude protein was a minimum of 35 g/100 g. The total gram content of glucosinolate, which was measured by the new HPLC analysis method, was 30 mmol/kg, and the content of urea nitrogen and free ammonia was obtained. In general, all the results obtained were in accordance with the national standard of Iranian animal feed-Camelina food-specifications and test methods.
... Camelina sativa is a crop that belongs to the Brassicaceae family and is further known as false flax or gold of pleasur (Brock et al., 2018). Since it can be grown in different soils and climates, in summer or even in winter in temperate regions, it is a very compatible crop with harsh and different climatic conditions. ...
This research was conducted for the first time in Iran on Camelina Sohail seed meal with the aim of investigating its physicochemical properties and its nutritional and anti-nutritional composition for the possibility of using it in animal and poultry feed. The prepared samples were related to four temperate regions of Iran, i.e. Ilam, Kermanshah, Fars, and Hamedan (cold temperate), which were obtained by two methods of solvent extraction and cold pressing. In general, the examined characteristics included qualitative, physicochemical, and anti-nutritional composition (glucosinolates). The results obtained included the appearance of flour, pellets or flakes, yellow to brown color, specific taste and smell, and camellia flour free of unacceptable factors (all unacceptable factors in any amount of camellia flour). Maximum moisture content was 10 g/100 g, total ash was a maximum of 7 g/100 g, acid insoluble ash was a maximum of 1 g/100 g, and crude protein was a minimum of 35 g/100 g. The gram content of total glucosinolate was 30 mmol/kg and the nitrogen content of urea and free ammonia. In general, all the obtained results were in accordance with the national standard of Iran's animal feed-Camelina food specifications and test methods.
... The uptake and assimilation of sulfate resources that are available in the environment produce essential sulfur (S) metabolites that are crucial for development and stress responses, which is critical for plants and microbes [4]. The soil sulfate content can be modified by various factors, such as the dissimilation of soil microbes, model plant [32,33]. Moreover, C. sativa is becoming more important as a biofuel [34,35]. ...
Sulfate transporters (SULTRs) are responsible for the uptake of sulfate (SO42−) ions in the rhizosphere by roots and their distribution to plant organs. In this study, SULTR family members in the genomes of two oilseed crops (Camelina sativa and Brassica napus) were identified and characterized based on their sequence structures, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. In total, 36 and 45 putative SULTR genes were recognized in the genomes of C. sativa and B. napus, respectively. SULTR proteins were predicted to be basophilic proteins with low hydrophilicity in both studied species. According to the observed phylogenetic relationships, we divided the SULTRs into five groups, out of which the SULTR 3 group showed the highest variation. Additionally, several duplication events were observed between the SULTRs. The first duplication event occurred approximately five million years ago between three SULTR 3.1 genes in C. sativa. Furthermore, two subunits were identified in the 3D structures of the SULTRs, which demonstrated that the active binding sites differed between C. sativa and B. napus. According to the available RNA-seq data, the SULTRs showed diverse expression levels in tissues and diverse responses to stimuli. SULTR 3 was expressed in all tissues. SULTR 3.1 was more upregulated in response to abiotic stresses in C. sativa, while SULTR 3.3 and SULTR 2.1 were upregulated in B. napus. Furthermore, SULTR 3 and SULTR 4.1 were upregulated in response to biotic stresses in B. napus. Additionally, the qPCR data showed that the SULTRs in C. sativa were involved in the plant’s response to salinity. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones, such as ABA and MeJA. Therefore, it seems likely that SULTR genes in C. sativa have been more heavily influenced by evolutionary processes and have acquired further diversity. The results reveal new insights of the structures and functions of SULTRs in oilseed crops. However, further analyses, related to functional studies, are needed to uncover the role of SULTRs in the plants’ development and growth processes, as well as in their response to stimuli.
... The high percentage of oils present in its seeds makes it a very suitable and interesting resource for the production of biofuels [25][26][27][28][29], and for the food industry [30]. Studies are also being carried out to explore its possible use in animal and human feed because of the protein richness of seed meal [31][32][33][34][35] and the great nutritional value of its seed oil [36,37]. ...
Camelina sativa (L.) Crantz is a promising oilseed crop that has increased worldwide attention because of its agronomic characteristics and potential uses. From an agricultural point of view, this plant can grow in different environments, providing a good yield with low input requirements. In addition, camelina seeds contain a high percentage of oil (36–47%) and protein (24–31%), making them interesting for food or energy industries. Nevertheless, its cultivation is not widespread in Europe, particularly in Spain. In the present context of global change and the search for new sustainable crops, we are conducting two pilot projects aiming to confirm that camelina is a good option for oilseed crops in semi-arid climates (especially in central Spain, Madrid) and to find new profitable varieties for farmers. To reach our objective we have used nine new varieties, recently developed, to characterize and compare their seed oil content, and their seed and straw chemical composition. Finally, with our preliminary results, we determine which varieties present better properties to be used in future agricultural research or breeding programs. These results are part of a larger study that we are carrying out.
... Like most angiosperms, many Brassicaceae species have been identified as polyploids, ranging from paleopolyploids with remnants of older hybridization events to relatively young neopolyploids such as Camelina sativa, where the progenitor species have yet to be confirmed. The whole genome sequencing of C. sativa has confirmed the hexaploid nature of its genome and facilitated a number of studies deciphering the relationships among Camelina species (Brock et al., 2018); however, without knowledge of the progenitor genomes, our understanding of the formation and evolution of C. sativa is innately limited. There are several lower ploidy species of Camelina viz. ...
Camelina neglecta is a diploid species from the genus Camelina, which includes the versatile oilseed Camelina sativa. These species are closely related to Arabidopsis thaliana and the economically important Brassica crop species, making this genus a useful platform to dissect traits of agronomic importance, while providing a tool to study evolution of polyploids. A highly contiguous chromosome level genome sequence of C. neglecta with an N50 size of 29.1 Mb was generated utilizing Pacific Biosciences long read sequencing followed by chromosome conformation phasing. Comparison of the genome with that of C. sativa shows remarkable coincidence with subgenome 1 of the hexaploid, with only one major chromosomal rearrangement separating the two. Synonymous substitution rate analysis of the predicted 34,061 genes suggested subgenome 1 of C. sativa directly descended from C. neglecta around 1.2 mya. Higher functional divergence of genes in the hexaploid as evidenced by the greater number of unique orthogroups, and differential composition of resistant gene analogs, might suggest an immediate adaptation strategy after genome merger. The absence of genome bias in gene fractionation among the subgenomes of C. sativa in comparison to C. neglecta, and the complete lack of fractionation of meiosis specific genes attests to the neopolyploid status of C. sativa. The assembled genome will provide a tool to further study genome evolution processes in the Camelina genus and potentially allow the identification and exploitation of novel variation for Camelina crop improvement.
... Саме тому його молекулярно-генетичні дослідження можуть сприяти як з'ясуванню процесів еволюції різних видів роду Camelina, так і допомогти прояснити роль різних популяцій цього виду в окультуренні C. sativa. Це також дозволить залучити нові алельні варіанти до селекції рижію посівного, який є історично важливою олійною культурою Європи та останнім часом привернув увагу як потенційне джерело біопалива [1], але його сорти вирізняються недостатньою генетичною різноманітністю [2]. ...
Aim. The aim of this research was to compare the efficiency of DNA isolation methods from herbarium specimens of Camelina microcarpa Andrz. Ex DC., further modification of these methods to increase DNA yield, and determine the method that would provide the best yield of isolated DNA. Methods. Modifications of the DNA isolation methods using the DNeasy Plant Mini Kit (QIAgen) and the CTAB method were used. PCR was performed using degenerate primers for method of β-tubulin intron length polymorphism (TBP). Amplicons were fractionated in polyacrylamide gel followed by visualization by silver nitrate staining. Results. DNA was successfully extracted from C. microcarpa herbarium specimens sampled with leaf parts and seeds, using the modified by CTAB method, and our modified methods using DNeasy Plant Mini Kit (QIAgen). Conclusions. The study revealed that the most effective method tested was the DNeasy Plant Mini Kit (QIAgen) No. 2. Prolongation of the cell lysis stage had the best effect on the increase of DNA yield. We found that the success of DNA isolation was influenced not so much by the age of the herbarium specimen as by the methods of drying and storing the plants in the collection.
... Camelina has a sufficient number of multicopy lincRNA gene families, allowing us to monitor the impact of WGD events on lincRNA expression. Camelina is an allohexaploid containing three subgenomes similar to those of its two progenitor species, C. hispida and a C. neglecta-like autotetraploid (Brock et al., 2018 referred to here as the C. hispida, C. neglecta, and C. neglecta [like] subgenomes). In Camelina, C. hispida mRNA paralogs are typically more highly expressed relative to those from the other two subgenomes, and thus it is considered to be the dominant subgenome (Chaudhary et al., 2020). ...
Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tbp of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used Nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our dataset with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our dataset. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
... As illustrated in the Fig 1, C. sativa (2n=40), is an ancient oilseed crop with a new found application as an aviation biofuel and omega-3 rich feedstock. The genus Camelina, represented by seven or eight species (Brock et al., 2019), belongs to one of the most karyo logically variable crucifer genera, with chromosome numbers ranging from 2n = 12 to 40 (2n = 12, 14, 16, 26, 28, 32, 36, 38 and 40) and a threefold genome size variation (Hutcheon et al., 2010;Brock et al., 2018). ...
Camelina sativa-an oil seed flowering plant that originated in North Europe and Central Asia is known by many names: gold-of-pleasure, false flax, wild flax and German sesame. Belongs to the Family Cruciferae, genus Camelina and it includes several species. Camelina has several favorable agronomic characteristics, it can be cultivated both in winter and spring season, having a remarkable capacity to adapt and resist to difficult climate conditions and pests.Camelina sativa contains 30-48% oil and 33-47% protein and adequate micronutrients with unique properties for industrial and nutritional applications. In addition, Camelina is a promising oilseed crop for production of edible oil, seed meal for animal feed rations and/or biodiesel feedstock. The high amounts of unsaturated fatty acids (about 90%) make camelina oil fast-drying which can be used for making polymers, varnishes, paints, cosmetics and dermatological products. Camelina sativa seed meal consisting of up to 50% crude protein-can be sold asan ingredient for cattle and chicken feed, adding further value to producing camelina. Overall, Camelina oil, due to its composition, has multiple uses in various industries: feed technology, biodiesel production, biopolymer industry, cosmetic industry (skin-conditioning agent), in food products due to its high omega-3 fatty acid content and low erucic acid content and as milk fat substitution.
... Camelina seeds' oil content ranges from 30% to 49% of their dry weight [12], and is characterized for its high amount of unsaturated fatty acids (>90%): 14-16% oleic acid (C18:1), 15-23% linoleic acid, (C18:2), 31-40% linolenic acid (C18:3), and 12-15% eicosenoic acid (C20:1) [13]. Camelina seeds also contain a relatively high level of proteins (23-27%) [14] making them a potential source of animal feed [15][16][17]. In addition to its food, feed, and nutritional applications, camelina oil can be used for biofuel production, in particular jet fuel [17]. ...
Camelina (Camelina sativa (L.) Crantz) is an emerging industrial crop from the Brassicaceae family, with its seed oil and cake being used for food, feed, and fuel applications. In this study, the relationships between economically important agronomic traits including seed yield (SY), days to maturity (DM), 1000-seed weight (TSW), seed protein content (PC), seed oil content (OC), and fatty acid composition in 136 doubled haploid (DH) camelina lines were investigated under rain-fed conditions in two consecutive years. There was prominent diversity among the studied DH lines for the agronomic traits such as seed yield, erucic acid, omega3, protein content, etc. Based on the Pear-son correlation analysis of the data, SY was positively correlated with DM and OC, and negatively correlated with TSW, PC, and linolenic acid (C18:3) content. The positive relationships of the main characteristics, relevant to industrial applications, suggest the feasibility of developing new higher-yielding camelina cultivars with high seed oil content. The high seed yield of some camelina lines (DH044 and DH075) during the two growing seasons showed the potential of the lines. On the other hand, the contrasting genotypes for key traits in this study promised a favorable source to develop the superior breeding lines with higher seed yield and food/nonfood traits. Therefore, it can be concluded that the diversity of camelina DH lines traits is crucial for developing new cultivars. Furthermore , the present study reports some significant correlations among the DH lines, which may be useful for the current and future camelina breeding program.
... Camelina is known to consist of 6-11 species as reported in the literature (Brock et al., 2018). However, there are only 6-7 species, which match the ploidy and chromosome number. ...
Camelina sativa (L.) Crantz is an oilseed crop with favorable potentials for biodiesel production, such as the high plant yield, high oil content in the seed, high net energy ratio, and low oil production cost. This review paper deals with the present state and perspectives of biodiesel production from camelina oil. First, important issues of camelina seed pretreatment and biodiesel production are reviewed. Emphasis is given to different biodiesel technologies that have been used so far worldwide, the economic assessment of the camelina oil biodiesel (COB) production, the camelina-based biorefineries for the integrated biodiesel production, the COB life cycle analysis, and impact human health and ecosystem. Finally, the perspectives of COB production from the techno-economic and especially genetic engineering points of view are discussed.
... Brock et. al(Brock et al. 2018) created a 618 phylogeny using data from ddRADseq for 48 specimens from gene bank material and field 619 collections from Turkey, Jordan, and Armenia for C. sativa, C. microcarpa hexaploids, C. 620 rumelica, C. laxa and C. hispida. In the maximum likelihood consensus tree generated from this 621 data, C. laxa was basal to the other species. ...
Plant evolution has been a complex process involving hybridization and polyploidization. As a result, understanding the origin and evolution of a plant's genome is often challenging even once a published genome is available. The oilseed crop, Camelina sativa from the Brassicaceae, has a fully sequenced allohexaploid genome with potentially three unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for four diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora and C. laxa using a combination of long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the fully sequenced chloroplasts in order to examine the evolutionary relationships within Camelina and Camelineae. We conclude that the genome of C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 was more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential genetic resources for crop improvement.
... Camelina originated in vast regions across southeast Europe and southwest Asia (Brock et al., 2018). Previous studies suggested that domesticated camelina, which includes primarily spring types, has limited genetic diversity and therefore may limit the potential of crop improvement (Chaudhary et al., 2020;Ghamkhar et al., 2010;Manca et al., 2013;Singh et al., 2015;Vollmann et al., 2005). ...
Camelina [Camelina sativa (L.) Crantz] is an oilseed crop in the Brassicaceae family that is currently being developed as a source of bioenergy and healthy fatty acids. To facilitate modern breeding efforts through marker‐assisted selection and biotechnology, we evaluated genetic variation among a worldwide collection of 222 camelina accessions. We performed whole‐genome resequencing to obtain single nucleotide polymorphism (SNP) markers and to analyze genomic diversity. We also conducted phenotypic field evaluations in two consecutive seasons for variations in key agronomic traits related to oilseed production such as seed size, oil content (OC), fatty acid composition, and flowering time. We determined the population structure of the camelina accessions using 161,301 SNPs. Further, we identified quantitative trait loci (QTL) and candidate genes controlling the above field‐evaluated traits by genome‐wide association studies (GWAS) complemented with linkage mapping using a recombinant inbred line (RIL) population. Characterization of the natural variation at the genome and phenotypic levels provides valuable resources to camelina genetic studies and crop improvement. The QTL and candidate genes should assist in breeding of advanced camelina varieties that can be integrated into the cropping systems for the production of high yield of oils of desired fatty acid composition. Genome resequencing and population structure analyses are used to assess genetic diversity. QTL mapping is conducted to identify regions associated with seed traits in camelina. Genomic resources and candidate genes are provided to improve camelina seed traits.
... Defining the relationships between the camelina species may help to identify species that are potential novel sources of allelic variation for introgression into C. sativa [51]. So far, little genetic diversity exists in currently available C. sativa cultivars limiting the effectiveness of traditional breeding programs [52][53][54]. ...
‘Genome editing’ is intended to accelerate modern plant breeding enabling a much faster and more efficient development of crops with improved traits such as increased yield, altered nutritional composition, as well as resistance to factors of biotic and abiotic stress. These traits are often generated by site-directed nuclease-1 (SDN-1) applications that induce small, targeted changes in the plant genomes. These intended alterations can be combined in a way to generate plants with genomes that are altered on a larger scale than it is possible with conventional breeding techniques. The power and the potential of genome editing comes from its highly effective mode of action being able to generate different allelic combinations of genes, creating, at its most efficient, homozygous gene knockouts. Additionally, multiple copies of functional genes can be targeted all at once. This is especially relevant in polyploid plants such as Camelina sativa which contain complex genomes with multiple chromosome sets. Intended alterations induced by genome editing have potential to unintentionally alter the composition of a plant and/or interfere with its metabolism, e.g., with the biosynthesis of secondary metabolites such as phytohormones or other biomolecules. This could affect diverse defense mechanisms and inter-/intra-specific communication of plants having a direct impact on associated ecosystems. This review focuses on the intended alterations in crops mediated by SDN-1 applications, the generation of novel genotypes and the ecological effects emerging from these intended alterations. Genome editing applications in C. sativa are used to exemplify these issues in a crop with a complex genome. C. sativa is mainly altered in its fatty acid biosynthesis and used as an oilseed crop to produce biofuels.
... Camelina sativa is an oilseed member of Brassicaceae, which has gained great attention due to its high potential for biofuel production (Ahmadizadeh et al., 2020b;Murphy, 2016). Also, C. sativa is resistant to doughtiness, salinity and coldness and many pathogens (Brock et al., 2018). A study on C. sativa seed yield response to various fertilizers showed that maximum predicted seed yield was obtained without using Pi fertilizer (Solis et al., 2013). ...
Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.
... Southeast Europe and Southwest Asia are believed to be the center of the origin of camelina, even if one study evoked the Russian-Ukrainian area as a camelina genetic diversity hotspot (Ghamkhar et al. 2010). In these native regions, camelina could be found both cultivated or as a weed, but the increasing use of herbicides over time has decreased the presence of wild camelina in cultivated fields (Brock et al. 2018). Wild camelina may represent a valuable source of genetic diversity for this species in future breeding programs in Europe. ...
Promoting crop diversification in European agriculture is a key pillar of the agroecological transition. Diversifying crops generally enhances crop productivity, quality, soil health and fertility, and resilience to pests and diseases and reduces environmental stresses. Moreover, crop diversification provides an alternative means of enhancing farmers’ income. Camelina ( Camelina sativa (L.) Crantz) reemerged in the background of European agriculture approximately three decades ago, when the first studies on this ancient native oilseed species were published. Since then, a considerable number of studies on this species has been carried out in Europe. The main interest in camelina is related to its (1) broad environmental adaptability, (2) low-input requirements, (3) resistance to multiple pests and diseases, and (4) multiple uses in food, feed, and biobased applications. The present article is a comprehensive and critical review of research carried out in Europe (compared with the rest of the world) on camelina in the last three decades, including genetics and breeding, agronomy and cropping systems, and end-uses, with the aim of making camelina an attractive new candidate crop for European farming systems. Furthermore, a critical evaluation of what is still missing to scale camelina up from a promising oilseed to a commonly cultivated crop in Europe is also provided (1) to motivate scientists to promote their studies and (2) to show farmers and end-users the real potential of this interesting species.
... As a "low-input and environment-friendly" oil crop worldwide, camelina has been planting in many countries including Europe, Middle East and China [1]. Compared with other commercialized oil crops, C. sativa has several prominent agronomic traits, such as short life cycle (80-100 days), strong tolerance to abiotic stress (salt, drought, cold, etc.), and highly resistance to common pests and diseases infected in many cruciferous crops [2][3][4][5]. Camelina seeds accumulate high levels of oil (36% 47%) and protein (30%) as well as a variety of natural active ingredients. The seed oil contains 90% of unsaturated fatty acids of which omega-3 fatty acids are 40% or more. ...
Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.
Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.
Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.
... As a "low-input and environment-friendly" oil crop worldwide, camelina has been planting in many countries including Europe, Middle East and China [1]. Compared with other commercialized oil crops, C. sativa has several prominent agronomic traits, such as short life cycle (80-100 days), strong tolerance to abiotic stress (salt, drought, cold, etc.), and highly resistance to common pests and diseases infected in many cruciferous crops [2][3][4][5]. Camelina seeds accumulate high levels of oil (36% 47%) and protein (30%) as well as a variety of natural active ingredients. The seed oil contains 90% of unsaturated fatty acids of which omega-3 fatty acids are 40% or more. ...
Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina.
Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress.
Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.
... As a "low-input and environment-friendly" oil crop grown around the world, the camelina has been planted in many countries in Europe and the Middle East in addition to China [1]. Compared with other commercialized oil crops, C. sativa has several prominent agronomic traits, such as a short life cycle (80-100 days), strong tolerance to abiotic stresses (salt, drought, cold, etc.), and high resistance to common pests and diseases that infect many cruciferous crops [2][3][4][5]. Camelina seeds accumulate high levels of oil (36%~47%) and protein (30%) as well as a variety of natural active ingredients. Its seed oil contains 90% unsaturated fatty acids, of which omega-3 fatty acids constitute 40% or more of the total. ...
Background
WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.
Results
A total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.
Conclusions
The present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.
... Genomic DNA was extracted using the CTAB protocol of Brock, Dönmez, Beilstein, & Olsen (2018), which was modified from Webb & Knapp (1990). Genotyping-by-sequencing (GBS) libraries were prepared following Poland & Rife (2012), using a double digest of Pst I andMsp I. Samples were sequenced on three lanes of the Illumina HiSeq 2500 platform with 1x100 reads at the Roy J. Carver Biotechnology Center at the University of Illinois Champaign-Urbana. ...
... These hypothetical crosses would explain the varied chromosome counts documented in numerous camelina publications. The hypothetical crossing scenario is further supported by a recent publication [81] where the genetic diversity of the camelina genus was assessed across 54 accessions representing five species through RADseq, ITS sequencing, and flow cytometry. Results of the investigation infer that an (n = 6 + 7 + 7) hybridization is possible. ...
Camelina sativa (L.) Crntz. is a hardy self-pollinated oilseed plant that belongs to the Brassicaceae family; widely grown throughout the northern hemisphere until the 1940s for production of vegetable oil but was later displaced by higher-yielding rapeseed and sunflower crops. However, interest in camelina as an alternative oil source has been renewed due to its high oil content that is rich in polyunsaturated fatty acids, antioxidants as well as its ability to grow on marginal lands with minimal requirements. For this reason, our group decided to screen the existing (2011) National Genetic Resources Program (NGRP) center collection of camelina for its genetic diversity and provide a phenotypic evaluation of the cultivars available. Properties evaluated include seed and oil traits, developmental and mature morphologies, as well as chromosome content. Selectable marker genes were also evaluated for potential use in biotech manipulation. Data is provided in a raw uncompiled format to allow other researchers to analyze the unbiased information for their own studies. Our evaluation has determined that the NGRP collection has a wide range of genetic potential for both breeding and biotechnological manipulation purposes. Accessions were identified within the NGRP collection that appear to have desirable seed harvest weight (5.06 g/plant) and oil content (44.1%). Other cultivars were identified as having fatty acid characteristics that may be suitable for meal and/or food use, such as low (<2%) erucic acid content, which is often considered for healthy consumption and ranged from a high of 4.79% to a low of 1.83%. Descriptive statistics are provided for a breadth of traits from 41 accessions, as well as raw data, and key seed traits are further explored. Data presented is available for public use.
... La cameline [Camelina sativa (L.) Crantz] est une culture oléagineuse annuelle de la famille des Brassicacées (Zubr, 1997). Historiquement cultivée en Europe du Nord pour son huile, comme en témoignent des études archéologiques (Larsson, 2013;Pollmann, 2014;Effenberger, 2018), elle a peu à peu disparu au profit d'autres cultures oléagineuses plus compétitives, comme le colza, le tournesol ou le lin (Karg, 2012;Brock et al., 2018). Depuis la fin des années 1990, on observe un regain d'intérêt pour cette culture, justifié par ses caractéristiques agronomiques et industrielles intéressantes (Putnam et al., 1993;Vollmann et al., 1996;Bonjean and Le Goffic, 1999;Zanetti et al., 2013). ...
L’introduction d’espèces de diversification, voie incontournable pour assurer la transition agroécologique, pose aujourd’hui une question majeure : comment produire de manière économe les connaissances nécessaires sur ces espèces orphelines de recherche ? Nous avons proposé et mis en œuvre une démarche articulant production de connaissances et conception, et combinant différents dispositifs multi-acteurs, pour accompagner l’introduction d’une nouvelle espèce dans les systèmes de culture. Ce travail s’appuie sur le cas de la cameline, introduite soit en culture principale soit en double culture dans les systèmes de culture de l’Oise, en vue du développement d’une bioraffinerie oléagineuse. Nous avons d’abord articulé un atelier multi-acteurs -regroupant agriculteurs, conseillers, chercheurs, ingénieurs en R&D agricole et industriels- et des essais de modalités de conduite de la cameline en double culture, conçus, gérés et évalués par des agriculteurs dans leur ferme. Cette approche a permis d’identifier des trous de connaissances et de produire des connaissances utiles pour la conception (ex : des règles de décision pour la conduite de la cameline). En parallèle, nous (chercheurs) avons conçu et évalué, au sein d’un réseau multi-local et pluriannuel de parcelles agricoles, trois itinéraires techniques de la cameline de printemps sans herbicide, en comparaison à l’itinéraire technique classiquement recommandé. Nos résultats montrent que l’augmentation de la densité de semis de cameline ou l’association de la cameline avec une autre espèce (orge ou pois) sont des leviers agroécologiques efficaces pour maîtriser les adventices dans la culture de cameline.De plus, le diagnostic de la variabilité du rendement, de la teneur en huile des graines, et de leur composition en acides gras, réalisé au sein de ce même réseau d’essais, a permis d’identifier (i) les principaux facteurs responsables (ex : le statut azoté de la culture pour le rendement), et (ii) les conditions environnementales (ex : fourniture d’azote minéral par le sol) et les pratiques (ex : association d’espèces) déterminant ces facteurs. La formalisation de ces connaissances, leur confrontation à la littérature scientifique, ainsi que leur partage et leur mise en discussion au cours de différents dispositifs d’échanges multi-acteurs au champ et en salle ont conduit à élargir la gamme des modalités d’insertion et de conduite de la cameline, conçues par les agriculteurs et adaptées à leurs conditions individuelles, lors d’un atelier de conception.Enfin, nous discutons en quoi cette combinaison originale de dispositifs multi-acteurs, permet (i) de produire à moindre coût des connaissances situées et génériques, utiles pour la conception, et (ii) d’outiller à la fois l’agriculteur-concepteur, le conseiller agricole et le chercheur, pour accompagner la diversification des systèmes de culture d’une région.
... Although further studies are required to analyse the exact nature and mechanisms associated with the observed meiotic defects (e.g. Friebe et al., 2005), their wide occurrence does not support the assumption that C. sativa was domesticated from C. microcarpa (Brock et al., 2018), or that it was from C. microcarpa genotypes that would be quite different from those used in this study. Considering the meiotic abnormalities we observed in the C. microcarpa × C. sativa F 1 s, it is also surprising that Mandáková et al. (2019) observed no differences in chromosome structure between C. sativa and the C. microcarpa accession they studied. ...
Background and aims:
Camelina (Camelina sativa, Brassicaceae) has attracted interest in recent years as a novel oilseed crop, and an increasing number of studies have sought to enhance camelina's yield potential or to modify the composition of its oil. The ability of camelina to cross hybridize with its wild relative, C. microcarpa, is of interest as a potential source of genetic variability for the crop.
Methods:
Manual crosses were performed between the crop C. sativa and its wild relative C. microcarpa: F1 and F2 progenies were obtained. Cytology was used to study meiosis in the parents and F1s and to evaluate pollen viability. Flow cytometry was used to estimate nuclear DNA amounts, and FAME analysis was used to evaluate the lipid composition of F3 seeds.
Key results:
The F1 plants obtained by interspecific crosses presented severe abnormalities at meiosis, low pollen viability, and produced very few F2 seeds. The F2s presented diverse phenotypes, in some cases severe developmental abnormalities. Many F2s were aneuploid. F2s produced highly variable numbers of F3 seeds, and certain F3 seeds presented atypical lipid profiles.
Conclusions:
Considering the meiotic abnormalities observed and the probability of aneuploidy in the F2 plants, the C. microcarpa accessions used in this study would be difficult to use as sources of genetic variability for the crop.
... Furthermore, camelina seeds present a natural high omega-3 https://doi.org/10.1016/j.agsy.2019.102717 Received 15 August 2019; Received in revised form 27 September 2019; Accepted 5 October 2019 fatty acids content, which makes it an attractive crop for feedstock industries by providing animal meals with a protein-rich ingredient (Brock et al., 2018). Many studies have reported the applications of camelina for animal feed, mainly in fish (Hixson et al., 2016) and poultry (Ciurescu et al., 2016) production. ...
The molecular genetic diversity of Ukrainian little-pod false flax (Camelina microcarpa Andrz. ex DC.) was assessed using two methods: tubulin-based polymorphism (TBP), which is based on length polymorphism of the first intron of β-tubulin genes, and microsatellite sequences (SSR — simple sequence repeats). The study was aimed to investigate the genetic diversity among the analyzed little-pod false flax accessions and determine the comparative effectiveness of the employed molecular methods. Furthermore, the suitability of prioritizing the TBP method for the analysis of herbarium specimens, considering the limited plant material and potential DNA damage caused by long-term storage, was demonstrated.
Common carp is the first domesticated fish species in the world, which is the main fish candidate for being cocultured with rice in paddy fields. There are several strains of rice field-domesticated common carp in China, such as Qingtian (paddy-field) carp, Congjiang Carp, Wuyi Carp etc. Unfortunately, their geographical origins were unclear and the adaptability to rice field of these common carp varieties have not yet been well studied. Here we used 2b-RAD simplified genome sequencing to obtain 108,813 SNP markers from two paddy-field carp populations (Qingtian and Wuyi Mountain) and eight wild carp populations to explore the phylogenetic relationship and differences between the Qingtian paddy field carp and the other neighboring wild and domesticated carp populations. Compared with the wild carp populations, the levels of nucleotide diversity of the two paddy-field carp populations were lower. The neighbor-joining (NJ) tree, principal component analysis (PCA), and population structure analysis all showed three clusters of the carp populations: Qingtian paddy-field carps as one of the clusters, paddy-field carps from Wuyi Mountain areas the second and all the wild common carp populations the third. Qingtian paddy-field carps were clearly separated from other populations, which was consistent with the population differentiation index (Fst) analysis. All these analyses indicated that Qingtian paddy-field carps showed the closest relationship with the Oujiang wild carp population (OJ), and less close to all other populations, providing clear evidence of the geographical origin of Qingtian paddy-field carp from Oujiang River. With wild carps as the control group and paddy-field carps as the selection group, 180 genes with a selection signature were obtained. The gene ontology (GO) classification and enrichment analysis showed that the genes with a selection signature were enriched in the pathway related to signal transduction function. We can thus conclude that Qingtian paddy field carp of the Asia first GIAHS rice-fish coculture system were originated from the domestication from the local Oujiang wild common carp population, which showed a clear genetic adaptive evolution in genes with function in signal transduction. These findings will help us to further disclose the domestication effects on fish that leading us better understanding the adaptive mechanism of fish to the rice field environment.
Sulfate transporters (SULTRs) are responsible for the uptake of the sulfate (SO4 2−) ions in the rhizosphere by the roots and their distribution in plant organs. In this study, SULTR family members in the genome of the two oilseed crops, Camelina sativa, and Brassica napus, were identified and characterized based on their sequence structure, duplication events, phylogenetic relationships, phosphorylation sites, and expression levels. Herein, 36 and 45 putative SULTR genes were recognized from the genome of C. sativa, and B. napus, respectively. SULTR proteins were predicted as basophilic proteins with low hydrophilicity in both studied species. According to phylogenetic relationships , we divided SULTRs into five groups, in which SULTRs 3 showed highest variation. Besides, several duplication events were observed between SULTRs. The first duplication event was predicted approximately five million years ago between three SULTRs 3.1 in C. sativa. Two subunits were indicated in the 3D structure of SULTRs that the active binding sites differed between C. sativa and B. napus. According to available RNA-seq data, SULTRs showed diverse expression in tissues and response to stimuli. SULTRs 3 showed an expression in all tissues. SULTRs 3.1 were more up-regulated in response to abiotic stresses in C. sativa, while SULTRs 3.3, and SULTRs 2.1 showed an upregulation in B. napus. Furthermore, SULTRs 3 and SULTRs 4.1 showed an upregulation in response to biotic stresses in B. napus. Based on the distribution of cis-regulatory elements in the promoter region, we speculated that SULTRs might be controlled by phytohormones such as ABA, and MeJA. Therefore, it seems that SULTR genes in C. sativa have been more influenced by evolutionary processes and have acquired more diversity.
Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant’s genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with three unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa’s formation, we sequenced and assembled chromosome level draft genomes for four diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa’s sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa’s sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa’s sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa’s genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.
Hexaploid camelina (Camelina sativa; 2n = 6x = 40) is an important oilseed crop closely related to Arabidopsis. Compared to other polyploid crops, the origin of the three camelina subgenomes has begun to be unveiled only recently. While phylogenomic studies identified the diploid C. hispida (2n = 2x = 14) as the paternal genome of C. sativa, the maternal donor genome remained unknown. Because the chromosomes assigned to a putative maternal genome resembled those of diploid C. neglecta (2n = 12), a tetraploid C. neglecta-like genome (2n = 4x = 26) was hypothesized to be the likely maternal ancestor of the hexaploid crop. Here we report the chromosome-level structure of the predicted tetraploid Camelina genome identified among genotypes previously classified together as C. microcarpa and referred to here as C. intermedia. Detailed cytogenomic analysis of the tetraploid genome revealed high collinearity with two maternally inherited subgenomes of hexaploid C. sativa. The identification of the missing donor tetraploid genome provides new insights into the reticulate evolutionary history of the Camelina polyploid complex and allows us to postulate a comprehensive evolutionary model for the genus. The herein elucidated origin of the C. sativa genome opens the door for subsequent genome modifications and resynthesis of the allohexaploid camelina genome.
In plants, phosphate transporters (PHTs) are responsible for distributing phosphorus in cells and organs. PHO1 genes, as a sub-group of PHT gene family, have been characterized in several plant species, however, these genes have not been widely characterized based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we characterized PHT proteins in C. sativa based on sequence structure, physicochemical properties, gene expression, promoter elements, and post-translational modifications via in silico manner. Our finding revealed that PHO1 proteins and their homologs are more diverse based on their physicochemical properties such as isoelectric point, molecular weight, GRAVY value, and exon-intron number(s) than other PHTs. Besides, the expression profile of PHT genes in C. sativa based on available RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The in silico tissue specific expression revealed high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHO1 genes play various functions in C. sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.
In plant species, variation in levels of clonality, ploidy and interspecific hybridization can interact to influence geographic patterns of genetic diversity. These factors commonly vary in plants that specialize on saline habitats (halophytes) and may play a role in how they adapt to salinity variation across their range. One such halophyte is the turfgrass and emerging genomic model system seashore paspalum (Paspalum vaginatum Swartz). To investigate how clonal propagation, ploidy variation, and interspecific hybridization vary across ecotypes and local salinity levels in wild P. vaginatum, we employed genotyping‐by‐sequencing, cpDNA sequencing and flow cytometry in 218 accessions representing >170 wild collections from throughout the coastal southern United States plus USDA germplasm. We found that the two morphologically distinct ecotypes of P. vaginatum differ in their adaptive strategies. The fine‐textured ecotype is diploid and appears to reproduce in the wild both sexually and by clonal propagation; in contrast, the coarse‐textured ecotype consists largely of clonally‐propagating triploid and diploid genotypes. The coarse‐textured ecotype appears to be derived from hybridization between fine‐textured P. vaginatum and an unidentified Paspalum species. These clonally propagating hybrid genotypes are more broadly distributed than clonal fine‐textured genotypes and may represent a transition to a more generalist adaptive strategy. Additionally, the triploid genotypes vary in whether they carry one or two copies of the P. vaginatum subgenome, indicating multiple evolutionary origins. This variation in subgenome composition shows associations with local ocean salinity levels across the sampled populations and may play a role in local adaptation.
Background: WRKY gene family is one of the largest transcription factor families and WRKY proteins (WRKYs) have the complex biological functions to regulate plant metabolic processes. Although the WRKY genes were identified in many species and the functions were verified, there were no reports of Camelina sativa WRKY genes.
Results: In this investigation, a total of 202 CsWRKY genes were identified and encoded 242 CsWRKYs. The CsWRKYs were further classified into three major groups according to their structure and phylogeny. The comprehensive analysis showed the characteristic sequences of CsWRKYs were conserved in the evolutionary process. In addition, the 137 segmental duplication events were the major force to expand the CsWRKY members in evolution. Compared with other reported plant species, CsWRKYs family as the largest WRKY gene family had maximum members. Furthermore, expression profiling indicated that different CsWRKY members exhibited differently in shoots and roots, and some CsWRKY genes were also up-regulated to varying degrees under salt stress in shoots.
Conclusions: In this research, a detailed overview of CsWRKY family genes and expression patterns offered precious information for understanding the potential evolutionary process and the biological functions of CsWRKY genes, which was useful for the further characteristic research of CsWRKY genes and the development of high-quality Camelina sativa varieties.
The movement of genes between crops and closely-related weeds has the potential to create economic and environmental problems. Camelina sativa (L.) Crantz is a promising oilseed crop and minor weed in North America, but ecological risk assessment is needed to predict crop-weed gene flow. In this study, reciprocal crosses between C. sativa cultivars and 17 Brassicaceae species in the genera Arabidopsis, Arabis, Barbarea, Camelina, Cardamine, Erysimum, and Lepidium were performed. F1 hybrids were formed between C. sativa cultivars and three species: Camelina alyssum (Mill.) Thell., Camelina microcarpa Andrz. Ex DC., and Capsella bursa-pastoris (L.) Medik. None of the other Brassica species formed hybrid offspring. F1 hybrids from C. sativa × C. alyssum showed the same pollen viability and fecundity as the parents, while hybrids from C. sativa × C. microcarpa had reduced pollen viability, silicle (pod) number and seed production. Intergeneric F1 hybrids from Camelina sativa × Capsella bursa-pastoris were sterile and this correlated with large decreases in pollen viability and number of ovules/flower. In addition, the SSR markers could be applied to identify progenies in C. sativa breeding programs as well as auxiliarily assess possibility of gene flow between C. sativa and weedy relatives. Principle coordinate analysis (PCoA) made from SSR markers clearly divided into 12 species into five groups of species. Especially, C. sativa was classified into one group with those two interfertile C. microcarpa, and C. alyssum but distinctly separated from Camelina hispida var. grandiflora (Boiss.) Hedge, Camelina laxa C. A. Mey and Camelina rumelica Velen. This division among the Camelina species was consistent with their capacity to produce fertile F1 hybrids with C. sativa. The hybridization results suggest that gene flow is likely between cultivated C. sativa and the North American weeds C. alyssum and C. microcarpa.
We present version 6 of the DnaSP (DNA Sequence Polymorphism) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyse large datasets, such as those generated by high-throughput sequencing (HTS) technologies. Among other features, DnaSP 6 implements: i) modules for reading and analysing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, ii) faster methods scalable for HTS data, and iii) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.
Interest on the genus Camelina has recently increased due to the biofuel, or jet fuel, potential of the oil extracted from seeds of the cultivated species Camelina sativa (L.) Crantz. While our knowledge on C. sativa is constantly augmenting, only few studies have been performed on the other species of the genus, which could be a potentially useful material for the genetic improvement of C. sativa. The genus Camelina consists of 11 species, but only six (C. sativa, C. microcarpa, C. alyssum, C. rumelica, C. hispida and C. laxa) could be retrieved from germplasm banks to carry out genomic fingerprinting studies based on the use of the cTBP molecular marker. Each species, with the exception of C. alyssum that is proposed to be a subspecies of C. sativa, shows a distinct cTBP profile resulting from multiple DNA length polymorphisms present in the second intron of the members of the β-tubulin gene family. In contrast to the high level of genetic diversity detected among the six Camelina species, low variability is observed among and within the accessions of the same species, except for C. hispida that is characterized by an intra-accession high number of cTBP polymorphic bands. In addition, cTBP is also able to identify incorrectly classified accessions and provide information on the ploidy level of each species.
Camelina (Camelina sativa (L.) Crantz) is a Brassicaceae oilseed crop with valuable agronomic and biotechnological attributes that make it an attractive renewable feedstock for biofuels and bio-based materials. Camelina seeds contain 30–40 % oil and can achieve oil yields per hectare that surpass established oilseed crops such as soybean. Camelina is also productive under conditions of limited rainfall and low soil fertility. As a short season, frost tolerant oilseed, Camelina is amenable to double cropping systems and fallow year production. Simple, non-labor intensive Agrobacterium-based transformation methods have recently been described for Camelina that can be used in combination with breeding to rapidly improve seed quality and agronomic traits to advance Camelina as a production platform for biofuels and industrial feedstocks in geographical regions such as the North American Great Plains that currently have little oilseed production for edible vegetable oils.
Camelina sativa is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana. C. sativa represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of C. sativa surprisingly mirrors those of economically important amphidiploid Brassica crop species from lineage II as well as wheat and cotton. The three genomes of C. sativa show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of C. sativa presents significant consequences for breeding and genetic manipulation of this industrial oil crop.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
Omega-3 (also called n-3) long-chain polyunsaturated fatty acids (≥C20; LC-PUFAs) are of considerable interest, based on clear evidence of dietary health benefits and the concurrent decline of global sources (fish oils). Generating alternative transgenic plant sources of omega-3 LC-PUFAs, i.e. eicosapentaenoic acid (20:5 n-3, EPA) and docosahexaenoic acid (22:6 n-3, DHA) has previously proved problematic. Here we describe a set of heterologous genes capable of efficiently directing synthesis of these fatty acids in the seed oil of the crop Camelina sativa, while simultaneously avoiding accumulation of undesirable intermediate fatty acids. We describe two iterations: RRes_EPA in which seeds contain EPA levels of up to 31% (mean 24%), and RRes_DHA, in which seeds accumulate up to 12% EPA and 14% DHA (mean 11% EPA and 8% DHA). These omega-3 LC-PUFA levels are equivalent to those in fish oils, and represent a sustainable, terrestrial source of these fatty acids. We also describe the distribution of these non-native fatty acids within C. sativa seed lipids, and consider these data in the context of our current understanding of acyl exchange during seed oil synthesis.
Two new finds of Camelina seeds prove the presence of the plant in middle Neolithic and Chalcolithic western France nearly 3000 years before widespread cultivation in France.
The beginnings of agriculture throughout the Fertile Crescent are still not completely understood, par-ticularly at the eastern end of the Fertile Crescent in the area of modern Iran. Archaeobotanical samples from Epi-palaeolithic/PPNA Körtik Tepe in southeastern Turkey and from the Pre-Pottery Neolithic sites of Chogha Golan and East Chia Sabz in south western Iran were studied in order to define the status of cultivation at these sites. Preliminary results show the presence of abundant wild progenitor species of crops at the Iranian sites before 10600 cal. B.P., and very few wild progenitor species at Körtik Tepe dated to 11700–11250 cal. B.P. The Iranian sites also indicate size increase of wild barley grain across a sequence of 400 years through either cultivation or changing moisture conditions.
Can. J. Plant Sci. 89: 791-810. This paper summarizes biological information on three cruciferous weed species: Camelina alyssum, C. microcarpa and C. sativa. Camelina sativa, which had been gathered or cultivated as an oil seed for many centuries in Europe, was the first to reach North America as a weed, towards the mid-19th century, gradually spreading across the prairies, mainly in crops, to British Columbia and the Northwest Territory. The most common of the three species in North America, C. microcarpa, arrived in the late 19th century, and subsequently appeared at numerous crop and uncultivated sites across the country, probably in cargo as the railways expanded. Camelina alyssum appeared in the early 20th century at restricted sites on the prairies, mostly in Saskatchewan. All three species have diminished in importance as crop weeds in western Canada over the past few decades. This reduction could be related to increased weed control by herbicides. Herbicide-resistant biotypes have recently been reported in C. microcarpa. Camelina sativa has attracted renewed interest as an oil crop, because of an adaptation to various climatic conditions, low nutrient requirements and resistance to disease and pests. In Europe, where it is now widely grown, it has shown considerable potential in the food, animal feed, nutraceutical, paint, dye, cosmetic and biofuel industries. In North America, it is being grown on a trial basis mainly for its potential as a biofuel in Alberta, Saskatchewan, the Maritime Provinces, and the northern United States of America.
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.
The evolutionary transition from outcrossing to self-fertilization (selfing) through the loss of self-incompatibility (SI) is one of the most prevalent events in flowering plants, and its genetic basis has been a major focus in evolutionary biology. In the Brassicaceae, the SI system consists of male and female specificity genes at the S-locus and of genes involved in the female downstream signaling pathway. During recent decades, much attention has been paid in particular to clarifying the genes responsible for the loss of SI. Here, we investigated the pattern of polymorphism and functionality of the female specificity gene, the S-locus receptor kinase (SRK), in allotetraploid Arabidopsis kamchatica. While its parental species, A. lyrata and A. halleri, are reported to be diploid and mainly self-incompatible, A. kamchatica is self-compatible. We identified five highly diverged SRK haplogroups, found their disomic inheritance and, for the first time in a wild allotetraploid species, surveyed the geographic distribution of SRK at the two homeologous S-loci across the species range. We found intact full-length SRK sequences in many accessions. Through interspecific crosses with the self-incompatible and diploid congener A. halleri, we found that the female components of the SI system, including SRK and the female downstream signaling pathway, are still functional in these accessions. Given the tight linkage and very rare recombination of the male and female components on the S-locus, this result suggests that the degradation of male components was responsible for the loss of SI in A. kamchatica. Recent extensive studies in multiple Brassicaceae species demonstrate that the loss of SI is often derived from mutations in the male component in wild populations, in contrast to cultivated populations. This is consistent with theoretical predictions that mutations disabling male specificity are expected to be more strongly selected than mutations disabling female specificity, or the female downstream signaling pathway.
Analyses of charred remains and impressions of chaff in pisé (mudbrick) from the Neolithic sites of Aratashen and Aknashen
(sixth millennium cal b.c.) situated in the Ararat valley in Armenia demonstrate that naked barley and possible naked (free-threshing) wheat together
with emmer and hulled barley were common. Two lesser known crucifers, Camelina microcarpa (false flax) and Alyssum desertorum (alyssum) were found in the form of crop processing residues. These were frequent in the pisé, indicating their use perhaps
as an oil source. Lens culinaris (small-seeded lentil) and Vicia ervilia (bitter vetch) were recovered both as carbonized seeds and from crop processing residues in the pisé. False flax and bitter
vetch were less common than alyssum and lentil. Two charred pips of Vitis vinifera (wild vine) were recovered, suggesting the early use of vines in the region. Flotation samples alone would have provided
limited data; examination of crop processing residues used for tempering pisé provided important evidence of the plant economy
at these two sites.
There is renewed interest in the crucifer Camelina sativa (false flax, camelina, gold of pleasure) as an alternative oilseed crop because of its potential value for food, feed, and industrial applications. This species is adapted to canola-growing areas in many regions of the world and is generally considered to be resistant to many diseases. A review of the literature indicates that C. sativa is highly resistant to alternaria black spot and blackleg of crucifers. Genotypes resistant to sclerotinia stem rot, brown girdling root rot, and downy mildew can be found among C. sativa accessions, raising the possibility of developing cultivars resistant to these diseases. However, C. sativa is susceptible to clubroot, white rust, and aster yellows disease. Until resistant cultivars or effective management practices have been developed, the susceptibility of C. sativa to these diseases will limit the cultivation of the crop in areas where these diseases are prevalent.
Biological invasions are a major ecological and socio-economic problem in many parts of the world. Despite an explosion of research in recent decades, much remains to be understood about why some species become invasive whereas others do not. Recently, polyploidy (whole genome duplication) has been proposed as an important determinant of invasiveness in plants. Genome duplication has played a major role in plant evolution and can drastically alter a plant's genetic make-up, morphology, physiology and ecology within only one or a few generations. This may allow some polyploids to succeed in strongly fluctuating environments and/or effectively colonize new habitats and, thus, increase their potential to be invasive.
We synthesize current knowledge on the importance of polyploidy for the invasion (i.e. spread) of introduced plants. We first aim to elucidate general mechanisms that are involved in the success of polyploid plants and translate this to that of plant invaders. Secondly, we provide an overview of ploidal levels in selected invasive alien plants and explain how ploidy might have contributed to their success.
Polyploidy can be an important factor in species invasion success through a combination of (1) 'pre-adaptation', whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the 'evolution of invasiveness'. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.
The crucifer oilseed plant false flax (Camelina sativa subsp. sativa) possesses numerous valuable agronomic attributes that make it attractive as an alternative spring-sown crop for tight crop rotations. The oil of false flax is particularly rich in polyunsaturated C18-fatty acids, making it a valuable renewable feedstock for the oleochemical industry. Because of the minimal interest in the crop throughout the 20th century, breeding efforts have been limited. In this study, a genetic map for C. sativa was constructed, using amplified fragment length polymorphism (AFLP) markers, in a population of recombinant inbred lines that were developed, through single-seed descent, from a cross between 'Lindo' and 'Licalla', 2 phenotypically distinct parental varieties. Three Brassica simple sequence repeat (SSR) markers were also integrated into the map, and 1 of these shows linkage to oil-content loci in both C. sativa and Brassica napus. Fifty-five other SSR primer combinations showed monomorphic amplification products, indicating partial genome homoeology with the Brassica species. Using data from field trials with different fertilization treatments (0 and 80 kg N/ha) at multiple locations over 3 years, the map was used to localize quantitative trait loci (QTLs) for seed yield, oil content, 1000-seed mass, and plant height. Some yield QTLs were found only with the N0 treatment, and might represent loci contributing to the competitiveness of false flax in low-nutrient soils. The results represent a starting point for future marker-assisted breeding.
To estimate the evolutionary history of the mustard family (Brassicaceae or Cruciferae), we sampled 113 species, representing 101 of the roughly 350 genera and 17 of the 19 tribes of the family, for the chloroplast gene ndhF. The included accessions increase the number of genera sampled over previous phylogenetic studies by four-fold. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the Shimodaira-Hasegawa test (S-H test) to compare the phylogenetic results with the most recent tribal classification for the family. The resultant phylogeny allowed a critical assessment of variations in fruit morphology and seed anatomy, upon which the current classification is based. We also used the S-H test to examine the utility of trichome branching patterns for describing monophyletic groups in the ndhF phylogeny. Our phylogenetic results indicate that 97 of 114 ingroup accessions fall into one of 21 strongly supported clades. Some of these clades can themselves be grouped into strongly to moderately supported monophyletic groups. One of these lineages is a novel grouping overlooked in previous phylogenetic studies. Results comparing 30 different scenarios of evolution by the S-H test indicate that five of 12 tribes represented by two or more genera in the study are clearly polyphyletic, although a few tribes are not sampled well enough to establish para- or polyphyly. In addition, branched trichomes likely evolved independently several times in the Brassicaceae, although malpighiaceous and stellate trichomes may each have a single origin.
Camelina sativa is a re-emerging low-input oilseed crop that may provide economical vegetable oils for industrial applications. It is desirable to increase the monounsaturated oleic acid (cis-9-octadecenoic acid, 18:1), and to decrease polyunsaturated fatty acids (PUFA), linoleic (cis, cis-9,12-octadecadienoic acid, 18:2) and α-linolenic (all-cis-9,12,15-octadecatrienoic acid, 18:3) acids, in camelina oils to improve oxidative stability. 18:1 desaturation is mainly controlled by the microsomal oleate desaturase (FAD2; EC 1.3.1.35) encoded by the FAD2 gene. Three FAD2 genes, designated CsFAD2-1 to 3, were identified in camelina. Functional expression of these genes in yeast confirmed that they all encode microsomal oleate desaturases. Although the three CsFAD2 genes share very high sequence similarity, they showed different expression patterns. Expression of CsFAD2-1 was detected in all tissues examined, including developing seed, flower, as well as in vegetable tissues such as leaf, root, and stem. Transcripts of CsFAD2-2 and CsFAD2-3 were mainly detected in developing seeds, suggesting their major roles in storage oil desaturation in seed. The introns of the three CsFAD2 genes, which showed greater sequence variations, may provide additional resources for designing molecular markers in breeding. Furthermore, the roles of CsFAD2 in PUFA synthesis were demonstrated by mutant analysis and by antisense gene expression in camelina seed.
Camelina (Camelina sativa L.) is a promising sustainable alternative energy crop belonging to the Brassicaceae (mustard) family. Camelina has several favorable agronomic characteristics which give it potential to significantly enhance domestic biofuels production. With high seed oil content as well as high yield of oil per hectare, camelina can be efficiently processed into high quality renewable fuels such as biodiesel (fatty acid methyl esters) as well as renewable diesel and jet fuels using existing technologies. This review summarizes the attributes of camelina along with conversion of the lipid fraction into advanced renewable biofuels.
Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD) 2 and fatty acid elongase (FAE) 1, which revealed unexpected complexity in the C. sativa genome.
In C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome.
There is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general development of C. sativa should consider and, when possible take advantage of, the implications of polyploidy.
Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms. However, there are important differences in the genomic organization of retrotransposons in plants compared to some other eukaryotes, including their often-high copy numbers, their extensively heterogeneous populations, and their chromosomal dispersion patterns. Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons. This review describes the structure, genomic organization, expression, regulation, and evolution of retrotransposons, and discusses both their contributions to plant genome evolution and their use as genetic tools in plant biology.
Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15 % below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15 % more DNA than 2C chicken nuclei (with >2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75 % above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57 % above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined.
Mechanical chopping of plant tissues in the presence of mithramycin released intact nuclei representative of the cells within the tissues. The amount of nuclear DNA in the homogenates of monocotyledonous and dicotyledonous plants was accurately and rapidly determined by flow microfluorometry, and the distribution of nuclei involved in the cell cycle was charted for tissues selected from different physical locations or developmental stages.
Camelina sativa is an alternative oilseed crop that can be used as a potential low-cost biofuel crop or a source of health promoting omega-3 fatty acids. Currently, the fatty acid composition of camelina does not uniquely fit any particular uses, thus limit its commercial value and large-scale production. In order to improve oil quality and other agronomic characters, we have developed an efficient and simple in planta method to generate transgenic camelina plants. The method included Agrobacterium-mediated inoculation of plants at early flowering stage along with a vacuum infiltration procedure. We used a fluorescent protein (DsRed) as a visual selection marker, which allowed us to conveniently screen mature transgenic seeds from a large number of untransformed seeds. Using this method, over 1% of transgenic seeds can be obtained. Genetic analysis revealed that most of transgenic plants contain a single copy of transgene. In addition, we also demonstrated that transgenic camelina seeds produced novel hydroxy fatty acids by transforming a castor fatty acid hydroxylase. In conclusion, our results provide a rapid means to genetically improve agronomic characters of camelina, including fatty acid profiles of its seed oils. Camelina may serve as a potential industrial crop to produce novel biotechnology products.
The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization.
Availability: Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2).
Contact:jombart@biomserv.univ-lyon1.fr
Supplementary information:Supplementary data are available at Bioinformatics online.