Long-lived species of trees, especially conifers, often display weak patterns of reproductive isolation, but clear patterns of local adaptation and phenotypic divergence. Discovering the evolutionary history of these patterns is paramount to a generalized understanding of speciation for long-lived plants. We focus on two closely related yet phenotypically divergent pine species, Pinus pungens and P. rigida, that co-exist along high elevation ridgelines of the southern Appalachian Mountains. In this study, we performed historical species distribution modeling (SDM) to form hypotheses related to population size change and gene flow to be tested in a demographic inference framework. We further sought to identify drivers of divergence by associating climate and geographic variables with genetic structure within and across species boundaries. Population structure within each species was absent based on genome-wide RADseq data. Signals of admixture were present range-wide, however, and species-level genetic differences associated with precipitation seasonality and elevation. When combined with information from contemporary and historical species distribution models, these patterns are consistent with a complex evolutionary history of speciation influenced by Quaternary climate. This was confirmed using inferences based on the multidimensional site frequency spectrum, where demographic modeling inferred recurring gene flow since divergence (2.74 million years ago) and population size reductions that occurred during the last glacial period (~ 35.2 thousand years ago). This suggests that phenotypic and genomic divergence, including the evolution of divergent phenological schedules leading to partial reproductive isolation, as previously documented for these two species, can happen rapidly, even between long-lived species of pines.
Sweet chestnut is a valuable species, highly managed for centuries for nut and wood production, whose genetic structure was affected by translocations. In this study, we selected a total of 51 genetically different clonal varieties from Galicia (NW of the Iberian Peninsula), Central Iberian Peninsula, France and Italy that were genotyped at 9 microsatellites. Almost all Galician varieties include at least two accessions with the same genotype. Several datasets of reference samples, from 29 natural or naturalized populations, were used to classify them into several groups. Genetic distances among varieties showed its cultivation area. Almost all Galician varieties cultivated in orchards were grouped in a single cluster except to ‘Famosa’, ‘Longal’, ‘Garrida’ and ‘Presa’ that were classified to the Central Iberian group and ‘Luguesa’ and ‘Carrelao’ to the French-Italian varieties. The Bayesian analysis with reference samples identified a group of varieties that could be autochthonous in Galicia because they were assigned to the Atlantic or the Cantabrian cluster. Other varieties from the Galician inner mountains that belong to the Mediterranean cluster could be translocated because this gene pool was found previously in several populations in the Iberian and Italian Peninsulas. Additionally, a large number of hybrid varieties between the Western Mediterranean cluster and the Atlantic or the Cantabrian cluster were found. Further analysis indicated that these Mediterranean varieties could be originated in Mercurín, in Central Iberian or Italian Peninsulas, and that ‘Luguesa’ and ‘Puga de Afora’ could be translocated from France or Italy. The results provided in this work provide a valuable information for a more efficient use of sweet chestnut genetic resources.
Pollen dispersal patterns and male reproductive success are crucial factors for seed orchard management. Information on pedigree reconstruction is also important for backward selection in selecting potential superior paternal clones in an open-pollinated seed orchard. The breeding without breeding (BwB) strategy has been shown to be helpful in avoiding expensive and laborious controlled mating, and in achieving genetic gain without making any artificial crosses. Although it is known that the efficiency of BwB depends on the scale of evaluated materials and the accuracy of paternity assignment, empirical data regarding the application of this strategy for various seed orchard designs are limited. In this study, we performed paternity analysis of 360 progenies derived from a 15-year-old hybrid larch test plantation (Larix gmelinii var. japonica × L. kaempferi), with candidate male parents (L. kaempferi) located within 50 m of 11 mother trees (L. gmelinii var. japonica) from an open-pollinated seed orchard. We then examined the pollen dispersal pattern within the seed orchard using molecular marker data and statistical modeling. We were able to assign 59 fathers to 57% of all progenies by paternity analysis using SSRs within a 50-m radius, and the mean distance of pollen dispersal was 42.2 m. We evaluated the performance of 17 paternal clones with at least four progenies based on the volume genetic gain of the progeny. As a result, the top two superior clones (average volume genetic gain: 32%) are expected to be candidates for producing new F1 cultivars.
Millions of lodgepole pine seedlings are planted each year to replace losses due to harvest or large-scale natural disturbances such as fires and forest pests. In Canada, replacement seeds and seedlings used for reforestation are often regulated by explicit policies. For example, in the province of Alberta, seedlings must be grown from seeds collected within a strictly defined zone that includes the harvested area where the seedlings will be planted. Thus, traceability along the entire reforestation chain of custody, from seed collection to seedling outplanting, is vital to ensure policy compliance. Here, we report a case study in which we used genomic tools to determine if seedlings were sown from a contaminated seed source. The 165,000 seedlings under scrutiny were scheduled for deployment the same year in which the seeds were sown, necessitating fast processing to make decisions on deployment. The scenario was made more complex by the fact that most of the potentially contaminated seed sources represented wild-collected genetic material in close geographic proximity to each other, rather than pedigree genetic material. With genotyping data obtained from a high-density single nucleotide polymorphism array analyzed with clustering analyses, kinship estimations, and genetic assignment tests, we were able to determine the probable seed source of this suspect group of seedlings and make data-guided recommendations on whether these seedlings could be confidently deployed onto the landscape without violating policy guidelines. This case study demonstrates the unique utility of molecular markers to confidently assign seedlings to a non-pedigree parent seed source originating within a limited geographic range, thereby ensuring traceability within a reforestation pipeline.
A large proportion of the western marginal range for common ash (Fraxinus excelsior L.) is located on the island of Ireland. However, the molecular diversity of common ash in Ireland has only been studied in a limited number of populations and using mainly non-standard chloroplast and nuclear simple sequence repeat (SSR) markers. This has prevented direct comparisons with studies on the rest of the species’ range across Europe. Here, four chloroplast and six nuclear SSR markers were used to infer the genetic diversity from 347 trees sampled across 20 populations. Results confirmed that, like Britain, Ireland is dominated by one main haplotype (H04) which originates from an Iberian glacial refugium. The occurrence of a second, rarer haplotype (H13) that also occurs as a rare haplotype in Britain but nowhere else, suggests at least some post-glacial recolonisation from the east. Chloroplast allelic richness was similar to Norway, which constitutes the species’ northern marginal range, but lower than in Britain and the European average. Nuclear allelic richness was also comparable with Norway, but Irish common ash differed in a complete absence of sub-population structure and geographic variability at both the chloroplast and nuclear level. Analysis of nuclear genetic structure indicated that common ash in Ireland mainly comprises one genetic group which is likely part of a single, western European meta-population. However, a less frequent genetic cluster is hypothesised to represent a mix of non-native alleles from imported plantation ash. Finally, conservation recommendations and the consequences of a uniform and low genetic diversity are discussed in the context of ash dieback disease, which was present in all populations sampled here.
The objective of this study was to better understand the underlying gene action in eucalyptus, under different plantation densities, for a different set of traits: growth, bark thickness, ecophysiological, and wood chemical property traits. We estimated the magnitude and relative proportion of the various genetic variance components using a eucalyptus genotype by spacing (G × S) interaction experiment. A clonally replicated progeny test including 888 clones belonging to 64 full-sib families of Eucalyptus urophylla × Eucalyptus grandis hybrid was used to estimate genetic parameters using genomic information to assess relationship matrix. Two densities (833 and 2500 trees/ha) were used representing contrasted environments in terms of individual tree available resource. Results showed that for height and circumference, additive-by-spacing (A × S) interaction variance increased from 18 to 55 months old, while dominance-by-spacing (D × S) interaction variance decreased. For bark thickness, specific leaf area, nitrogen, calcium, and magnesium, A × S interaction variance was preponderant. For wood chemical properties, except with Klason lignin, genetic additive effects strongly interacted with spacing compared to non-additive effects.
The genetic architecture of resistance for witches’ broom disease of cacao (WBD) was reexamined in an F2 population (Sca-6 × ICS-1), addressing symptom-specificity and possible genetic basis for the differences in disease scores from terminal and cushion brooms. A high-density genetic linkage map was constructed with 494 individuals and 2968 SNPs, obtaining 10 linkage groups comprising 1595 centiMorgans. The trees were evaluated under field conditions with high WBD pressure from 2015 to 2019, with low spatial autocorrelation tested by Moran’s I. Five WBD symptoms and one tree growth trait were mapped, resulting in 23 minor-effects QTLs, primarily arranged in clusters and distributed in all linkage groups except 4 and 6, indicating that WBD has a polygenic inheritance. Terminal and cushion brooms shared a genomic region in linkage group 9, suggesting pleiotropy. In these conditions, the ICS-1 grandparent contributed with more QTLs than Sca-6 to WBD resistance, indicating that the resistance pattern has changed and confirming the susceptible parent’s importance. Few QTLs were identified in the same or proximal loci comparing the 5-year, annual, or biennial periods. Several candidate genes such as glutathione peroxidases, threonine-serine receptors, and endochitinases were potentially associated with WBD resistance. These findings strongly suggest that WBD resistance is more complex than previously postulated, and future directions are presented and suggested to investigate further and improve the insights into WBD resistance.
A clonal trial, including 124 hybrid poplars, was planted in the center of Chile in 2014 and Septoria canker was detected in 2016. We propose a new approach to analyzing the relationship between fungi attack and growth. As an example, we report the analysis of the diameter of trees growing in the presence of Septoria canker for three consecutive years. We modeled two linear models. The original (reduced) model of the trial and an alternative (full) model added the level of attack effect. We compared variances of additive random effects and their interaction with the level of fungi attack, genetic parameters (heritability and environmental variances), and BLUPs of the clonal values. The focus was on modeling the intra-clonal covariation that depends on the interaction between the genetic and micro-environmental effects. Our results show that the most severe fungi attack occurred in trees with the largest growth in diameter. Including the level of attack effect into the full model produced significant changes in the estimation of genetic parameters at age 5. We observed a genotype-by-micro-environment interaction at ages 3 and 4. We conclude that including the level of Septoria attack in the modeling of genetic parameters for diameter growth of poplar hybrids is a way to correct the prediction of the clonal value of each hybrid planted in a trial. Using a full model that included the pathogen effect allowed a better prediction (BLUP) of the clonal worth.
Recently, a candidate gene (CJt020762) for MALE STERILITY 1 (MS1) in Cryptomeria japonica has been identified, which made it possible to perform accurate selection of trees with mutant alleles (ms1–1 or ms1–2). Marker-assisted selection (MAS) is an effective method for drastically reducing the time required for a breeding cycle; however, a larger sample size for selection increases the labor and cost of analysis. In this study, firstly, we developed an efficient and low-cost marker selection method using bulk DNA extracted from a mixture of needle tissues from several individual trees. The time required for the extraction of bulk DNA, the accuracy of target peak identification in fragment analysis, and the numbers of samples required to identify trees with ms1 were compared for 3-, 5-, 7-, and 10-individual mixed bulk DNA samples. The results showed that MAS using 10-individual mixed bulk DNA samples was the most efficient and lowest cost for selecting trees with ms1. The accuracy of genotyping using 10-individual mixed bulk DNA samples was verified by conducting a blind test consisting of sample preparation, extraction of bulk DNA, and genotyping under blind conditions (i.e., all researchers were unaware of the correct genotype of the samples). Next, we tried selecting trees with ms1 from 866 breeding materials by MAS using 10-individual mixed bulk DNA samples. We successfully selected nine previously untested trees that were heterozygous for MS1. Finally, we showed that the use of bulk DNA in MAS enabled significant reductions in labor and cost by comparing the approaches using bulk DNA samples with single-individual (non-bulk) DNA samples, although it should be noted that the efficiency of selection depends on the proportion of samples with a target allele.
The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for example is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic diversity, population differentiation and linkage disequilibrium (LD) across the highly disjunct native range of the Australian forest tree Eucalyptus globulus, using 203,337 SNPs genotyped in 136 trees spanning seven races. We found support for four broad genetic groups, with moderate FST, high allelic diversity and genome-wide LD decaying to an r² of 0.2 within 4 kb on average. These results are broadly similar to those reported previously in Eucalyptus species and support the ‘ring’ model of migration proposed for E. globulus. However, two of the races (Otways and South-eastern Tasmania) exhibited a much slower decay of LD with physical distance than the others and were also the most differentiated and least diverse, which may reflect the effects of selective sweeps and/or genetic bottlenecks experienced in their evolutionary history. We also show that FST and rates of LD vary within and between chromosomes across all races, suggestive of recombination outcomes influenced by genomic features, hybridization or selection. The results obtained from studying this species serve to illustrate the genomic effects of population disjunction and further contribute to the characterisation of genomes of woody genera.
Lignin biosynthesis occurs via the phenylpropanoid pathway and is regulated by transcription factors (TFs) including R2R3-MYB family members. In this study, we functionally characterized the R2R3-MYB TF VcMYB4a from blueberry (Vaccinium corymbosum) in lignin biosynthetic pathway. Phylogenetic analysis indicated that VcMYB4a clusters in a subclade with other TFs that act as transcriptional repressors of lignin and phenolic acid biosynthesis. Furthermore, lignin accumulation appeared to be negatively correlated with VcMYB4a expression during fruit development. Heterologous expression of VcMYB4a repressed lignin accumulation in Arabidopsis. Overexpression of VcMYB4a decreased lignin content in blueberry calli, whereas inhibition of VcMYB4a expression increased lignin accumulation in blueberry leaves. Finally, the transcriptome sequencing showed that overexpressing VcMYB4a in blueberry calli downregulated the expression of Vc4CL (Vc4CL5 and Vc4CL7), VcCOMT (VcCOMT1 and VcCOMT2), and VcCAD (VcCAD1 and VcCAD9) genes involved in lignin biosynthetic pathway. The heterologously expressing VcMYB4a in Arabidopsis downregulated the expression of genes, including AtC4H, At4CL (At4CL1 and At4CL5), AtCAD (AtCAD5 and AtCAD9), and AtCOMT1. The promoter sequences of these genes all contain MYB binding sites, and VcCAD9 and AtCAD9 genes have the most MYB binding sites. At the same time, VcCAD9 is more closely related to AtCAD9 than other CAD homologs from blueberry and Arabidopsis according to phylogenetic analysis. These findings suggested that VcMYB4a functions as a repressor of lignin biosynthesis by downregulating expression of 4CL, COMT, and CAD family members, especially CAD9 homologs. Our studies provide prospects for breeding new blueberry varieties with high lignin contents.
Date palm (Phoenix dactylifera L.), a monocotyledonous species of the Arecaceae family, is widely cultivated in the arid regions of the Middle East and North Africa. Considering the prolonged generation cycle, the dioecious nature of date palm trees, and high heterozygosity, the traditional breeding approaches in date palm are lengthy and laborious, and numerous crosses and back-crosses all have led to intangible advancement in date palm breeding. In recent years, the powerful potential of biotechnology has been considered for resolving fundamental difficulties associated with date palm breeding. Plant tissue culture, an important application of biotechnology, is an essential tool for vegetative propagation and a prerequisite for genetic modification. Genomic studies and molecular tools are integrated with modern plant breeding programs for precise determination of genetic diversity, identification of desired traits, germplasm conservation, and genetic drift control. This technology clarifies how the genome works in a specific evolutionary or environmental condition, determines relationships between genes, identifies the role of coding and non-coding parts of the genome, and identifies key points in regulating evolutionary processes and responding to plant internal and external factors. A comprehensive and clear picture of functional genomics pave the way for plant genetic engineering to improve the desired traits. This review surveys the recent approaches and applications of biotechnology in date palm breeding.
In the present study, phenotypic correlations and direct and indirect effects were estimated in a breeding population of cacao involving 22 full-sib families from 14 reciprocals and 8 direct crosses to obtain information aiming to increase selection efficiency for higher production. Path analysis was used to obtain estimates at the family level, within families, and the individual level. High phenotypic correlation coefficients were found between the total number of pods per tree and frosty pod rot incidence, with bean dry weight per tree, at the family (r = 0.91 and − 0.84, p < 0.001) and individual levels (r = 0.89 and − 0.50, p < 0.001), respectively. Path analysis revealed that the total number of pods per tree had the highest positive direct effects (0.66 to 1.05) on bean dry weight per tree expression. Likewise, indirect effects via the total number of pods per tree were important to explain the significant association of the other variables with the bean dry weight yield per tree. Variations in the correlation significance and direct and indirect effect magnitudes were observed among sample size, families, reciprocal and direct crosses, years, and bimonthly. However, beyond the influence of these, the total number of pods per tree had the greatest effects on production. These results suggest that indirect selection on the total number of pods per tree would improve selection efficiency for high bean yield in these breeding populations, accelerating and reducing costs than using a larger number of traits. The low heritability associated with the number of pods per tree might be beneficial in the second step of the selection process, considering other yield components of higher heritability as bean dry weight per pod. Also, extrapolation of the results should be done with care, considering that genetic parameter estimates are strictly valid for the population and environment studied, especially here that the number of parents used is a small sample (although important) of the parents used in cacao breeding programs.
Crataegus bretschneideri C. K. Schneid. is one of the species cultivated in China. Due to its unclear taxonomic classification status, the conservation and utilization of this germplasm resource have been limited. In this study, we analyzed the chloroplast genomes and nuclear sequences to reveal the taxonomic relationships among C. bretschneideri and related species. We assembled the chloroplast genomes of C. bretschneider and related species and varieties, including C. maximowiczii C. K. Schneid., C. maximowiczii var. ninganensis S. Q. Nie & B. J. Jen., C. pinnatifida Bunge, and C. pinnatifida var. major N. E. Br. The lengths of the chloroplast genomes ranged from 159,644 bp (C. bretschneideri) to 159,947 bp (C. pinnatifida var. major). The five Crataegus chloroplast genomes had similar features and possessed 86 to 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes which were arranged in the same order. Eight mutation hotspot regions, including matk, psaB, accD, petA, clpP, trnD-GUC, psbH-petB, and trnN-GUU-trnR-ACG could be used as potential molecular markers for further studies of Crataegus genetic diversity. Phylogenetic analyses based on 17 chloroplast genomes of Crataegus and Amelanchier indicated that C. bretschneideri was related to C. maximowiczii and C. maximowiczii var. ninganensis. However, the phylogenetic trees constructed by nuclear sequences of 36 Crataegus accessions reflected a closer relationship between C. bretschneideri and C. pinnatifida. Furthermore, divergence time estimation suggested that C. bretschneideri and C. maximowiczii diverged in the late Miocene and that speciation of C. pinnatifida occurred during the middle to late Miocene. These findings revealed that C. bretschneideri is an independent species and may be of hybrid origin.
Although spatial analysis of population genetic structure has been one of the most important ways to infer microevolutionary processes, these studies are usually focused on neutral dynamics and limited dispersal, interpreted under the theoretical reasoning of isolation-by-distance. More recently, however, there has been a growing interest on how environmental variation is also involved in population differentiation, both by direct effects of local adaptation and other processes related to environmentally or ecologically constrained dispersal. Here we evaluated patterns of genetic population structure and isolation-by-ecology, or environment (IBE), in Eugenia dysenterica DC (Myrtaceae), a fruit tree species of economic potential interest and widely distributed throughout the Central Brazil and endemic to the Cerrado biome (Neotropical savannas). We analyzed population structure using nuclear SSR markers for 736 individuals sampled from 23 localities (local population) and disentangled the effects of genetic molecular variation, estimated by pairwise FST (matrix G) and geographical distances (matrix S) into Grinnelian niche of populations (matrix E), based on climate and soil data. Spatial patterns in eigenvectors of G and E reveal northwest-southeast gradients, coherent with geographic range shifts after the Last Glacial Maximum. We used different forms of Mantel regression and correlation and redundancy analyses, as well as simulations of isolation-by-distance, to show that there is a significant partial correlation between G and E taking S into account, thus supporting the IBE process for E. dysenterica, in addition to other processes related to spatially constrained gene flow.
Facultative clonality is extremely common in plants, but the relative emphasis on sexual versus asexual reproduction varies both between and within species, which in turn may influence individual fitness and population persistence. Tilia cordata is a temperate, entomophilous canopy tree that is partially clonal. Favourably warm climatic conditions have been linked with successful sexual reproduction in the species with clonality being suggested as the reason for population persistence in colder periods. Despite this the extent, character and structure of asexual reproduction in the species have never been described, nor has its relationship with climate. Fine-scale spatial genetic structure was assessed in 23 stands across a latitudinal gradient. The proportion of individuals that are of clonal origin has a wide range with a mean of ~43%. Genetic diversity is high, with even mostly clonal stand possessing several distinct genotypes. A beta regression model shows that historic summer temperatures and density of recent recruits are predictors of the proportion of clonal recruitment. Clonal reproduction is less important in stands that experience higher temperatures during flowering while stands with more saplings have more clones. Additional factors likely affect the balance between the two reproductive modes. The climatic relationship suggests a trend towards a higher proportion of recruitment from seed in a warming climate, although factors such as herbivory may prevent this.
Knowledge of post-zygotic hybrid incompatibility is essential to understand speciation. Although the genes and molecular mechanisms involved in hybrid incompatibility are being elucidated in model plants and crops, the information on woody non-model plants is lacking. In the seedlings of a cross between the most famous ornamental cherry cultivar Cerasus × yedoensis ‘Somei-yoshino’ and its closely related wild species Cerasus itosakura, we discovered a hybrid incompatibility characterized by a phenotype in which growth stops after the expansion of the first true leaves and the seedling eventually dies. To elucidate the molecular mechanisms related to this seedling necrosis, we performed a comprehensive expressed gene analysis on normal-growth and necrotic weak-growth (SW) hybrid seedlings. The RNA-seq results showed over 1500 differentially expressed genes (DEGs) specified for the SW. Numerous genes associated with plant defense response, such as pathogenesis-related genes, and several receptor-like protein kinases were included in SW-specific upregulated DEGs. The Gene Ontology enrichment analysis also showed the significant association of “defense response” in SW seedlings. These upregulated defense-related gene expressions were particularly observed in the hypocotyls. On the contrary, the reduction of photosynthesis-related gene expression and reduction in the gene expressions of cell division and cell cycle at specific parts of seedlings were also observed in the SW. Our results suggest that an upregulated defense-related gene expression suppresses the meristem growth and deviation, resulting in growth failure as an autoimmune response in hybrid cherry seedlings.
The genus Rosa comprises more than 150 species spread across three subgenera, Hesperhodos, Hulthemia, and Rosa, most of which have high economic and ecological values. Here, we report 31 complete plastomes that belong to the genus Rosa, with the aim of better understanding the evolution and divergence of genes of the plastome in this genus. A comparative analysis was conducted to characterize the chloroplast genomes of 12 taxa that cover all the sections in the three subgenera of Rosa. Further, complete chloroplast genome sequences revealed six hotspots of nucleotide polymorphism, including five intergenic regions and one coding sequence. In addition, a pairwise analysis revealed that R. stellata and R. berberifolia have the highest average genetic distances (Da) and nucleotide divergence (Dxy) compared with other species. Moreover, the lowest Da and Dxy was observed between R. gallica and R. canina, followed by R. multiflora and R. chinensis var. spontanea. The phylogenetic relationships within Rosa inferred from the 44 chloroplast genomes revealed the R. subg. Hesperhodos is the clade that diverged the earliest. Its successive clades were identified as R. subg. Huithemia and R. sect. Pimpinellifolia. The phylogenomic analysis also revealed rapid simultaneous diversification within the Rosa subgenus. Significant increases in Pi and dN for ycf1, dN/dS for ycf2 were observed across the genus. Finally, we found that most RNA editing sites identified in the genus are section-specific, suggesting that the subgenera or sections have a self-evolving lineage. Taken together, the plastome information is valuable for species identification, phylogenetic studies, molecular genetics and breeding Rosa species.
Polyploidy is defined as the presence of more than two complete chromosome sets in an organism and has frequently occurred throughout the history of angiosperms. Polyploidization is a process that typically results in instant speciation. Using Psidium cattleyanum, a natural polyploid complex with several cytotypes, we aim to test two hypotheses regarding speciation in polyploids: polyploidization promotes (1) interruption of gene flow and (2) intraspecific niche divergence. We analyzed 12 natural populations of P. cattleyanum, integrating population genetics data, accessed by microsatellite markers, and climatic niche analysis, using environmental niche modeling, to provide insights about polyploid speciation. We found strong genetic structure in populations and cytotypes and low environmental niche similarity between cytotypes. Genetic diversity declines with increasing ploidy levels which is probably associated with asexual reproduction. Our results corroborate that polyploidy is generating a reproductive barrier and is associated with niche divergence among cytotypes. Therefore, we infer future divergent lineages between cytotypes of P. cattleyanum and confirm the role of polyploidy as an evolutionary step in speciation in this group. Additionally, this study provides new information for the discussion about how polyploidy affects the genetic diversity of taxa and ecological niches.
Gene dispersal processes shape demographic and microevolutionary dynamics of tree species. Gene dispersal patterns can be studied by spatially explicit methods. Spatial genetic structure (SGS), summarized in the Sp statistic, provides indirect estimates of gene dispersal across generations for a known or assumed population effective density. Sp is modulated by exogenous and endogenous factors including the mating system that can be assessed using outcrossing rates (tm). Knowledge on tm and Sp are particularly important for the conservation of species in fragmented biomes such as seasonally dry tropical forests (SDTF). The main aim of this review was to evaluate putative drivers of Sp and tm, and their consequences for gene dispersal in tree species from SDTF. We reviewed 59 genetic studies on SDTF tree species published between 2000 and 2020 and extracted data on propagule dispersal, successional stages, seasonality, mating system, population density, landscape features, type of molecular markers, pairwise kinship in the first distance class (F1), Sp statistic, mean gene dispersal distance (σg), and multilocus outcrossing rates (tm). Sp was significantly associated with the mating system where Sp(outcrossing) > Sp(mixed-mating), and population density where Sp was higher in high-density populations. Outcrossing rate was significantly associated with the type of propagule dispersal, where tm was higher in populations of plants pollinated by wind, and in those with animal-mediated seed dispersal, tm(zoochory) > tm(anemochory) > tm(autochory), and with successional stage where tm(late-successional) > tm(pioneer). These factors are relevant to inform management actions in conservation and restoration projects. Thus, the knowledge on the determinants of gene dispersal processes can help to rescue SDTF through sustainable management.
Three screening trials of clonally replicated Acacia mangium seedlings were evaluated for survival and lesion length following inoculation with locally collected strains of Ceratocystis in Indonesia. Tolerance in the population was low with 6.7% of the 1033 clones represented by more than 4 ramets surviving repeated inoculations. Differences in tolerance among populations were slight; however, populations with consistently higher survival and shorter lesion lengths were from Papua New Guinea rather than Queensland. Estimates of the proportion of the experimental variation attributable to differences among parents (heritability) were low to moderate for both survival and lesion length. Estimates of the proportion of the experimental variation that was attributable to differences among clones (repeatability) were greater but typically similar to the heritability estimates, indicating that initial improvements from selection will primarily be derived from identifying tolerant parents. While genetic correlations among experiments were positive, estimates could not exclude the existence of host–pathogen interactions. Two validation trials of the tolerant clones were assessed 9 months after establishment; these trials verified that one-third of the clones identified in the nursery screening were also tolerant to Ceratocystis in field trials. The experiments confirmed that nursery screening may be used to quickly focus efforts on parents that produce more tolerant progeny, screening additional seedlings to increase selection intensity rather than using clonal replication to increase accuracy would lead to greater improvements in tolerance and field trials are required to verify disease tolerance at later ages.
Increasing [CO2] may influence commercial crop and timber yield. While selection of genotypes sensitive to elevated [CO2] (e[CO2]) appears possible in agricultural crops, there is limited evidence for genotype-by-CO2 (G × CO2) interactions in commercial tree species. We examined [CO2] responsiveness in 124 open-pollinated Eucalyptus globulus ssp. globulus (E. globulus) families with the aim of assessing whether G × CO2 interactions are detectable in seedlings for early-age screening. Plants were grown in ambient (a[CO2]; ~ 405 μmol mol⁻¹) and e[CO2] (640 μmol mol⁻¹) and harvested 25 days after germination. Total, shoot, and root dry weights were determined for each plant. Carbon isotopic discrimination against ¹³C (Δ¹³C) was determined at the family level. We observed highly significant (p < 0.0001) increases in mean total, shoot, and root dry weights. Mixed-model equations were used to estimate the main and interaction effects of the G × CO2 for each mass trait. The main effects from the mixed-model output ([CO2] and individual-tree effects) were significant for all traits. However, [CO2]-by-individual tree interactions were non-significant for all traits, indicating little G × CO2 interaction. A secondary aim was to examine the correlation between greenhouse and mature-age growth from breeding trials that use common families conducted under ambient [CO2]. These correlations were non-significant, suggesting early growth is not necessarily indicative of later-age responses. Our results suggest that while early growth of E. globulus is enhanced under e[CO2], genotypes respond relatively uniformly to e[CO2] and little opportunity exists for seedling-based selection at the population level based upon the response of plants during the first weeks of growth.
Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.
We evaluated differential expression of genes in leaf and xylem tissues for three Eucalyptus clones in the field using Illumina sequencing, under four contrasting fertilization regimes: a control combining nitrogen (N), phosphorus (P), and potassium (K) and three regimes with N, K, and P deficiency. The field results showed significantly better performance with a control fertilizing regime for height and circumference at 14 months, but no differences between clones. The number of up and down regulated DEG (differentially expressed genes) in pairwise clone comparisons was around 5900 for leaf and 6900 for xylem at FDR < 0.01. With fertilization treatment comparisons, DEG were only observed for N deficiency versus control with 45 up and down-regulated DEG for leaf and 1022 for xylem. The number of DEGs between fertilizer deficiency treatment and control varied greatly within each clone showing important clone by fertilization interaction. Gene ontology analysis showed that a great number of genes were related to stress, transport, and transcription factors. The co-expression analysis showed some significant correlations between complex network gene expression and tree growth induced by fertilization regime. For example, the co-expression of a 54 DEG network showed a significant correlation with tree height (0.84, P value: 1e⁻⁰⁴) and DBH (0.89, P value: 7e⁻⁰⁶) in the case of N deficiency versus control. Our results suggest that gene expression levels between different fertilization treatments and clones can provide a basis for future research on gene function in Eucalyptus under nutrient stress with the perspective of new development in Eucalyptus breeding.
Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of "Genomics and Adaptation in Forest Ecosystems" brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.
The online version contains supplementary material available at 10.1007/s11295-022-01542-1.
Acer L. (Sapindaceae) consists of approximately 200 species, with great ornamental and commercial values. However, due to a substantial divergence in inflorescence, leaf shape, and fruit shape during the process of long-term natural evolution, it is remarkably difficult to distinguish them by morphological features. Eight species with compound-leaved maples from Sect. Trifoliata, Pentaphylla, and Negundo play an important role in revealing the morphological variation of Acer. Hence, the complete chloroplast (cp) genomes of all eight compound-leaved maples native to Asia were characterized, and comparative genomic analysis was conducted to infer their phylogenetic relationships. A few differences were found in cp genome size and gene content among eight Acer species. The gene rps2 was only identified in A.griseum. The differences in the cp genome sequences among eight Acer species have been clearly demonstrated, where matK-rps16, trnE-trnT, ndhC-trnV, ccsA-ndhD, and ycf1-trnN were the most divergent regions. The phylogenetic analysis revealed that Acer was clustered into monophyly by 100% bootstrap values, with A.glabrum (Sect. Glabra) and A.pseudoplatanus (Sect. Palmata) as the most basic species. Except for A.henryi and A. negundo, seven compound-leaved maples and some simple-leaved maples were highly supported to cluster into one clade with A.sutchuenense as the primitive species of Sect. Trifoliata and A.pentaphyllum as a series (Ser. Pentaphylla) of Sect. Pentaphylla. Besides, it is speculated by plastid phylogeny reconstruction that A.cissifolium (Sect. Negundo) may have ancestral connections with A. triflorum (Sect. Trifoliata). Finally, we conjectured that compound-leaved maples may have evolved from simple-leaved maples.
In forest tree breeding programs, open-pollinated families are frequently used to estimate genetic parameters and evaluate genetic merit of individuals. However, the presence of selfing events not documented in the pedigree affects the estimation of these parameters. In this study, 194 open-pollinated families of Eucalyptus globulus Labill. trees were used to compare the precision of estimated genetic parameters and accuracies of predicted breeding values with the conventional pedigree-based model (ABLUP) and the pedigree-genomic single-step model (ssGBLUP). The available genetic information for pairwise parent-offspring allows us to estimate an actual populational selfing rate of 5.4%. For all the growth and disease resistance traits evaluated, the inclusion of selfing rate was effective in reducing the upward bias, between 7 and 30%, in heritability estimates. The predictive abilities for ssGBLUP models were always higher than those for ABLUP models. In both cases, a considerable reduction of predictive abilities was observed when relatedness between training and validation populations was removed. We proposed a straightforward approach for the estimation of the actual selfing rate in a breeding population. The incorporation of this parameter allows for more reliable estimation of genetic parameters. Furthermore, our results proved that ssGBLUP was effective for the accurate estimation of genetic parameters and to improve the prediction of breeding values in presence of selfing events, thus a valuable tool for genomic evaluations in Eucalyptus breeding programs.
Citrus is an economically important fruit crop growing worldwide, with enormous health benefits. However, conventional citrus breeding has been hindered by a variety of genetic factors, thereby becoming obsolete and insufficient. Citrus research mostly focused on botanical, taxonomic, and cytogenetics issues. Nowadays the knowledge base has strengthened with the plausible outcomes of commercially successful varietal releases. Unfortunately; this has been gradual with only a few success stories among citrus rootstocks and even fewer among scion cultivars. Recent advancements in genetics, molecular biology, biotechnology, and omics (genomics, transcriptomics, proteomics, and metabolomics) have expedited citrus breeding and genetics research. Linkage mapping, genetic diversity, phylogenetic relationships, mutation breeding, mapping, and the international citrus genome sequencing initiatives along with functional analysis have been comprehensively summarized in this review. While providing information on future avenues, this review provides novel mechanistic compiled up-to-date information based on the past and recent progress, facilitating their broader applications to accelerate citrus breeding.
Quambalaria shoot blight (QSB) has emerged recently as a severe disease of Corymbia calophylla (marri). In this study, QSB damage and growth were assessed in Corymbia calophylla trees at 4 and 6 years of age in two common gardens consisting of 165 and 170 open-pollinated families representing 18 provenances across the species' natural distribution. There were significant differences between provenances for all traits. The narrow-sense heritability for growth traits and QSB damage at both sites were low to moderate. The genetic correlation between QSB damage and growth traits was negative; fast-growing families were less damaged by QSB disease. Age-age genetic correlations for individual traits at four and six years were very strong, and the type-B (site-site) correlations were strongly positive for all traits. Provenances from cooler wetter regions showed higher resistance to QSB. The QSB incidence at 6 years was significantly correlated with environmental factors of the provenance's origin. The QSB incidence at years four and six was not correlated with the QSB expression in 3-month-old seedlings. Based on these results, selection for resistance could be undertaken using 4-year-old trees. There is potential for a resistance breeding program to develop populations of marri genetically diverse and resistant to QSB.
Polymethoxyflavones (PMFs) are bioactive flavonoids exclusively found in the genus citrus, and they show various health-promoting activities. Researchers have studied the biosynthesis of PMFs and focused on isolation and characterization of the responsible genes. However, our knowledge about the biosynthesis of PMFs is still limited. In this study, we aimed to reveal the loci for causative factors that are responsible for PMF accumulation. We investigated the frequency distributions of PMF accumulation in F1 hybrids derived from several patterns of parent combinations. The distribution patterns in F1 hybrids indicated that the major gene for PMF biosynthesis was recessive. We developed single-nucleotide polymorphism (SNP) markers by taking advantage of their high abundance in genomes. SNP genotyping was performed using high-resolution melting (HRM) analysis. We successfully mapped 119 SNP markers and were able to construct a linkage map consisting of nine linkage groups (LGs) with a total genetic distance of 1504.3 cM. Quantitative trait locus (QTL) analysis for PMF accumulation was carried out with the mapped SNP markers. We found three novel QTLs: two QTLs related to nobiletin accumulation in LG1 and LG8 and one QTL related to tangeretin accumulation in LG3. We found 27 candidate genes in QTL confidence intervals, which could be associated with the biosynthesis of PMFs and suggested that flavanone 3-hydroxylase, flavonoid 3′-monooxygenase, and O-methyltransferase could be the key enzymes responsible for PMF biosynthesis. Our results provide valuable information that contributes to the elucidation of the PMF biosynthetic pathway.
Given the difficulties for rapid biodiversity assessments in understudied regions, DNA barcoding appears as a suitable alternative. Still, this approach relies heavily on accurate reference sequence databases for correct taxonomic assignments. In this study, we evaluated the effectiveness of matK, rbcL, and ITS regions for the identification of Myrtaceae species with emphasis on the megadiverse genus Syzygium from Sumatra, Indonesia; and analyzed the applicability of species-tree inference for species assignment using barcode markers. ITS was the most variable barcode region (42.6% of variable sites), followed by matK (25.7%), and rbcL (14.9%). In terms of assignments of sequences using the BLAST algorithm, all markers were effective for genus-level attribution. For assignments at species rank, rbcL was able to attribute 30.15% of the samples at the species level, followed by matK (26.47%), and ITS (17.21%). These results are largely related to the availability of reference sequences for Myrtaceae in the databases since for the 27 species analyzed in this study, only 8 species had reference sequences for all three barcode regions available in GenBank. The species-tree inference based on the combination of matK, rbcL, and ITS markers recovered 41% of the species as monophyletic clades with strong node support. Due to its high level of differentiation, we recommend the ITS region as the most efficient barcode marker for the identification of Syzygium, and the traditional core-barcodes (matK + rbcL) as add-on barcodes.
Hedgerows are an important component of agricultural landscapes, but in recent years have increasingly faced threats such as habitat loss, land use change, climate change, invasive species, pests and plant pathogens. Given the potential importance of genetic diversity in countering these threats, and the spatial distribution of such diversity within and across natural populations, we analyzed levels and patterns of diversity in blackthorn ( Prunus spinosa ), a key component of many hedgerows. Twenty-one populations of blackthorn from a mixture of hedgerows and woodlands were genotyped for four nuclear and five chloroplast microsatellites. Three hundred twenty-one unique clonal genotypes were identified from 558 individuals analyzed, 207 of which were found in a single individual. With the exception of a single population that appears to have been planted recently from seed (Peatlands Park), all populations exhibited evidence of vegetative reproduction via suckering. Multi-ramet clones were highly spatially structured within populations, and ranged in size from < 1 to 258 m. These findings indicate that asexual reproduction is widespread in the populations of blackthorn studied. Although levels of clonality varied across study sites, there was clear spatial structuring of clones in each case. Such clonal organization should be taken into account in hedge management or where planting or replanting of hedgerows becomes necessary. Knowledge of the patterns and extent of spatial structuring of genotypes within potential source populations will allow the selection of genetically divergent material, rather than selection of clonal replicates of the same genotype.
We investigated the efficiency of genomic selection in a large clonal population (N = 2023) of Pinus taeda L. The study population comprised 58 families that were tested across eight locations in the southern USA. The clones were genotyped with the Pita50K SNP array. Whole-genome regression models were used to obtain genomic estimated breeding values (GEBVs). The predictive ability of SNP markers for commercially important traits were estimated using various cross-validation scenarios that address the family structure in the population. In the random cross-validation scenario (clonal varieties randomly assigned to either training or validation sets), the predictive ability of GEBVs for stem volume, stem straightness, and fusiform rust disease incidence was 0.43, 0.57, and 0.26, respectively. In the family cross-validation scenario (whole families randomly assigned to either training or validation sets), the predictive ability for stem volume dropped to 0.36, but the change for the other two traits was small. In the third scenario, the predictive ability of the GEBVs of clones in a new environment was 0.32 for stem volume, 0.40 for stem straightness, and 0.18 for fusiform rust disease incidence. The predictive ability of the models dropped for all three traits when the GEBVs of untested varieties (varieties excluded from the training population) were predicted across multiple environments (range of 0.06 to 0.40 across traits). This study highlights the importance of genetic relatedness between the model training and validation sets of a cloned population of P. taeda. The expected genetic gain was about twice the expected genetic gain achieved by a traditional breeding strategy, mainly due to a 50% shorter breeding cycle achieved through the implementation of genomic selection.
Climate change may lead to severe losses in agriculture, including wood production. To understand the effects of climate change on physiology and molecular aspects of wood formation, we grew plants of Eucalyptus grandis and E. globulus for 35 days under three temperatures (10–12 °C, 20–22 °C, and 33–35 °C) combined with two CO2 concentrations (390 and 700 ppm). Biochemical analyses and RNAseq in stems were carried out together with leaf gas exchange measurements. We analyzed in-depth cell wall biosynthesis genes and their regulation by several transcription factors, as well as genes associated with carbon partitioning, cell wall remodeling, and hormonal regulation. E. globulus, a species adapted to low temperature, was more responsive to the treatments than E. grandis. Gene expression was greatly affected by changes in temperature than in CO2. The most relevant processes affected by the treatments were related to stress, secondary metabolism, hormonal response, and signaling. Ethylene and auxin biosynthetic genes were upregulated in both species, but more intensely in E. globulus. High CO2 stimulated lignin biosynthesis genes and increased S-containing oligomers in E. globulus. Genes related to cell wall carbohydrates and lignin were strongly induced by temperature and CO2, respectively. Photosynthesis activity and transpiration were highest under high temperature and high temperature + high CO2 in both species. Our results show that responses of woody plants may be different regarding the temperature at eCO2.
Pear (Pyrus) is an important temperate fruit, which originates in the southwestern region of China and has more than 3000 year’s cultivation history. However, the historic routes of pear dissemination in China have not been fully elucidated. In this study, a total of 2,412,930 single nucleotide polymorphisms (SNPs) at a density of 4.74 SNP/kb were identified by resequencing. The SNP-based phylogenetic analysis revealed that 102 pear samples from 23 provinces in China were divided into two major clades and eight geographic groups, and these divisions were supported by results of a population structure analysis and principal component analysis (PCA). Combined with the results of population diversity and identity-by-descent (IBD) analysis, it was revealed that the dissemination direction of pear was from southwest to southeast and from south to north. In the southern region, the dispersal pattern of pear spreading from west to east was generally in line with the course of the Yangtze River and Pearl River. The southern pear spread by multiple routes to its north neighboring areas, and regions in the middle and lower reaches of the Yellow River played important roles in the further dissemination of pear in the northern region of China. Moreover, we identified comparative higher genetic diversity of Ussurian pear than other populations, which might be due to low degree of domestication and closely resembled the high diversity of its wild counterpart. Our study provides new information to further our understanding of pear evolution in China, while laying a foundation of data for population genetic research, germplasm protection, and utilization for pear breeding in the future.
Prunus subgenus Cerasus is a large and diverse genus. Its botanical classification has long been controversial and complicated. Molecular markers derived from the chloroplast genome may provide useful tools for phylogenetic resolution and taxonomic study in Prunus species. Thus, we compared chloroplast genomes of 23 Prunus species to identify sequences with high variation levels. The repeated sequences (RSs) and two types of sequence variation, comprising divergent homologous regions and short sequence repeats (SSRs), were identified. The species with the highest number of RSs was P. emarginata (60), whereas P. campanulata contained the highest amount of SSRs (70). In contrast, P. dictyoneura and P. yedoensis contained the lowest number of RSs (37) and SSRs (46), respectively. Out of these homologous SSRs, 11 were shared in the 23 species, and seven of them showed variations. A total of 203 homologous regions were identified. Out of these, 20 regions (19 IGSs and one intron) showed a high variation from 6.75 to 19.31%. The phylogenetic tree which was inferred based on 19 highly variable regions showed a topology similar to the one obtained using the whole chloroplast genome. We conclude that the seven variable SSRs and the 20 highly variable regions may potentially be convenient as molecular markers for phylogenetic and population genetics studies in subgenus Cerasus species. In addition, the molecular phylogenetic position of P. clarofolia was inferred based on the 19 highly variable regions.
Hazelnut (Corylus avellana L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in ex situ repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections. A total of 480 accessions were used: 430 from ex situ collections and 50 landraces maintained on-farm. SSR analysis identified 181 genotypes, that represented our whole hazelnut germplasm collection (WHGC). Four approaches (utilizing MSTRAT, Power Core, and Core Hunter’s single- and multi-strategy) based on the maximization (M) strategy were used to determine the best sampling method. Core Hunter’s multi-strategy, optimizing both allele coverage (Cv) and Cavalli-Sforza and Edwards (Dce) distance with equal weight, outperformed the others and was selected as the best approach. The final core collection (Cv-Dce30) comprised 30 entries (16.6% of genotypes). It recovered all SSR alleles and preserved parameter variations when compared to WHGC. Entries represented all six gene pools obtained from the population structure analysis of WHGC, further confirming the representativeness of Cv-Dce30. Our findings contribute towards improving the conservation and management of European hazelnut genetic resources and could be used to optimize future research by identifying a minimum number of accessions on which to focus.
The mitochondrial phylogeography of some conifers shows evidence of introgression from sympatric congeners, with mitochondrial lineages not always reflecting species. This suggests that unique mitochondrial haplotypes previously reported in the ponderosa pines (Pinus subsection Ponderosae) from the USA might be more widespread in taxa not yet sampled. Recent nuclear and plastome phylogenies placed Pinus ponderosa paraphyletic in relation to Ponderosae in Mexico and Central America and confirmed that sympatric Pinus jeffreyi is more closely related to the California big-cone pines (Pinus subsection Sabinianae). We describe a broad survey of the repeated motifs in nad1 intron 2 of Ponderosae and Sabinianae, which revealed that most of the 27 mitochondrial haplotypes were not exclusive to a taxon but showed strong geographic patterns. In surprising contrast to nuclear and plastid phylogenies that resolve a monophyletic P. jeffreyi, unidirectional mitochondrial capture by P. jeffreyi (Sabinianae) from P. ponderosa was observed in all 28 samples of Jeffrey pine. Confirming the paraphyly of P. ponderosa sensu lato, mitochondrial haplotypes found mostly west and those found mostly east of the Great Basin each have more similarity to haplotypes found in Mexican taxa than they have to each other. Two distinctive haplotypes that were terminal nodes on the network were confirmed to be endemic to the Great Basin, USA, suggesting that they arose in place and have been maintained in isolation. Altogether, our results indicate a history of complex and intriguing mitochondrial relationships among the ponderosa pine species, especially between P. ponderosa and P. jeffreyi.
Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for the organoleptic and nutraceutical properties of the juice and for the quality of the essential oils in the peel.
Herein, we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively, which agree well with an estimated genome size of 312 Mb. The analysis of the transposable element (TE) allowed the identification of 2878 regions on the primary and 2897 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of Citrus sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome.
In parallel, total RNA was extracted from fruit, flower, leaf, and root enabling the detection of 35,020 and 34,577 predicted transcripts on primary and alternative assemblies respectively. To further characterize the annotated transcripts based on their function, a gene ontology and a gene orthology analysis with other Citrus and Citrus-related species were carried out.
The availability of a reference genome is an important prerequisite both for the setup of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.
Optimal oil palm (Elaeis guineensis) crop yields rely on the purity of the tenera fruit form. The high yielding hybrid tenera fruit form is the consequence of heterozygosity for one of nine genetic variants within the SHELL gene. High-throughput genotyping allows cost-efficient screening prior to planting to decrease unintentional non-tenera palm cultivation. We present a paradigm for dramatically reducing non-tenera cultivation by SHELL genotyping a ~ 10% sampling of seeds per seed production fruit bunch. Identification and seed supply chain removal of bunches above a predetermined non-tenera threshold represent a new paradigm for applying SHELL genetic testing in the industry. In a demonstration involving 121,896 embryos from 1304 independent dura x pisifera controlled crosses from two independent seed production units, we found that 38.4% of bunches achieved a 100% pure tenera prediction rate. The remaining bunches (61.6%) had predicted non-tenera contamination ranging from 1.0 to 89.6%, with an overall average of 3.32% seeds per bunch. SHELL genotyping of expected tenera embryos identified rare aneuploid embryos, confirmed by whole genome sequencing-based heterozygosity and copy number analyses.
Shorea parvifolia (Dipterocarpaceae) is a widely distributed tree species which is important in terms of ecosystem functioning as well as forestry in Southeast Asia. During glacial periods, substantial precipitation decline is believed to have occurred in Southeast Asia, which considerably changed the distribution of the species. Repeated glacial and inter-glacial fluctuations were found to have influenced the genetic structure of the species, which is important to know for conservation and sustainable use. Leaf samples were collected from 18 populations covering most of the natural distribution of this species including the Malay Peninsula, Sumatra, and Borneo Islands. We investigated these samples using sequence data for eight chloroplast DNA (cpDNA) regions and 14 nuclear EST-SSR loci. The nucleotide diversity of cpDNA is higher in Malay Peninsula populations but the genetic diversity of nuclear DNA is higher in Borneo populations. The genetic structure revealed by nuclear DNA clearly separated Borneo populations from the rest, with an FST value of 0.150, while the genetic structure obtained from cpDNA was less pronounced (FST value = 0.136). Tajima’s D and Fu and Li’s D* for cpDNA showed statistical significance only in populations from Borneo. These results suggested that there has been recent population expansion of S. parvifolia in Borneo.
We aimed to test the extent to which plastid DNA gives incongruent phylogeographic patterns to nuclear DNA in a species of eucalypt, Eucalyptus behriana, a taxonomic group where chloroplast capture is a well-established phenomenon. Furthermore, we aimed to test the degree of influence chloroplast capture has on the observed patterns by broadly sampling co-occurring, related species. A genome skimming approach was used to sequence and assemble chloroplast genomes from population-level sampling of E. behriana, as well as samples of twenty-one other Eucalyptus section Adnataria species which co-occur with it. Phylogenetic analyses were first undertaken on just E. behriana to allow direct comparison to previously reported phylogeographic patterns based upon nuclear markers. A subsequent analysis including the related taxa was undertaken to investigate the degree of chloroplast capture and how this may be influencing the observed phylogeographic patterns. We found strong geographic structuring of plastid DNA relationships across the geographic range of E. behriana, with a basal divergence between the most northerly isolated population at West Wyalong and all other populations which does not match phylogeographic patterns based on nuclear markers. When outgroups were included, we found that E. behriana is highly polyphyletic with respect to all other species, starkly contrasting with the species well-supported monophylly based upon nuclear markers, and that chloroplast capture is so widespread that geographic patterns of the plastid genomes are consistent across species boundaries.
For continuous genetic gains over time, a balance between genetic gain and maintaining the genetic base must be a constant concern of forest breeders. This study aims at determining the best thinning strategies for a population of Eucalyptus dunnii, by incorporating the effects of environmental heterogeneity and competition in the analysis, as well as the best growth trait regarding precision and accuracy. The population studied consisted of 160 open-pollinated families. The survival and growth (height, HT; diameter at breast height, DBH; and volume, VOL) were evaluated 4 years after planting. The growth rate data were analyzed and compared by four mixed models. Selection and thinning strategies were simulated by varying the number of families, individuals within families, and selected individuals, considering the estimated genetic gains and the effective size. The species showed good survival (89.7%) and productive performance (mean annual increment = 42 m³ ha⁻¹ y⁻¹). The Spatial+Competition Model provided the best fit for DBH and VOL. The strategies that allow a balance between improvement (genetic gains) and genetic conservation (effective size) consist of keeping 36 to 50% of the individuals in the test (370 to 510 trees ha⁻¹), by reducing more intensively the number of individuals from the worst-performing families. The selection of 100 individuals with a restriction of at most one individual per family generates the largest number of effective size (Ne), with more than double the Ne obtained without restricting the individuals per family, with a small drop in genetic gain.
Malus baccata (L.) Borkh. and Malus toringo (Siebold) Siebold ex de Vriese of the genus Malus Mill. (Rosaceae) are wild crabapples occurring in temperate East Asia. Despite their horticultural importance as ornamental trees and the natural resources in apple breeding, their phylogenetic relationships have never been determined clearly owing to lack of resolution in previous studies. We characterized four complete chloroplast genomes of these two species and conducted various phylogenomic analyses comparatively to the previously reported plastomes of other wild Malus species. They were highly conserved in genomic structures and gene contents, containing 129 genes including 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Phylogenetic analysis of 23 representative Malus plastomes did not support the current classification of the major sections in Malus, revealing non-monophylies. The plastomes of M. toringo revealed two chloroplast types corresponding to their geographic distribution; M. toringo from China was more closely related to other sympatric species, while two conspecific M. toringo from Japan and Korea were in a sister relationship with M. baccata from Korea. We identified one positively selected gene (ndhD) and seven mutation hotspots (trnK-rps16, trnR-atpA, petN-psbM, trnT-psbD, psbZ-trnG, ndhC-trnV, and ycf1) and variable SSRs as potential useful plastid markers.
The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT(UGU)-L(UAA) IGS, trnL(UAA)intron, trnL(UAA)-F(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT(UGU)-L(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and hT > vT observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely “Ilex” and “Coccifera.” Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex.
N6-methyladenosine (m6A) plays an important role in the gene expression regulation. Previously, we found an ortholog of Arabidopsis LBD15 that showed xylem preferential expression and involved in leaf development in Poplar 84 K. In order to investigate whether m6A modification affects the function of LBD15, the m6A-immunoprecipitation sequence and the matched input RNA sequence for non-transgenic plants (CK) and the LBD15 overexpression (LBD15-oe) plants were compared and analyzed. As a result, 7,156 differential m6A peaks were identified, with 2,896 upregulated m6A peaks and 4,260 downregulated m6A peaks. Correlation analysis of differential expression genes and differential m6A peaks indicated that a total of 119 differently methylated genes showed a negative correlation with the differentially expressed genes. Among them, Nudix hydrolase, LRR receptor-like serine/threonine-protein kinase, tubulin, vacuole membrane protein KMS1, and MYB family transcription factor PHL11 may be involved in the posttranscriptional gene regulation in LBD15 overexpression plants. The expression of ten m6A-modified genes was validated by qRT-PCR. Our results will provide a basis for the further elucidation of the regulatory mechanism of m6A modification and the epigenetic regulation of LBD15.
The unique adaptation of Eucalyptus benthamii to low temperatures coupled to fast growth and versatile wood quality has made it a valued plantation species in frost-prone areas worldwide, but little is known on its quantitative genetic parameters for key industrial traits. We used GBLUP additive (GA), additive-dominant (GAD), single-step (HBLUP), and pedigree-based predictive models to estimate lignin, extractives, carbohydrates, and wood density at age 4 and tree volume at age 6. By capturing hidden relatedness and correcting pedigree errors, SNP data disentangled non-additive from additive variance providing more realistic estimates of narrow-sense heritability than pedigrees, and more accurate predictions of trait values. Predictive abilities (PAs) ranged from 0.12 for volume (pedigree-based model) to 0.44 for wood density (models H, GA, and GAD). Considerable dominance variance was seen for all traits, growth was the trait most influenced by it, resulting in PAs 48.9% higher when this effect is considered, a result with important consequences both for clonal propagation and overall selection efficiency (Seff). Using a HBLUP model, phenotypes of non-genotyped trees increased PAs by increasing sample size and provided realized relationships with reduced genotyping cost. In a recurrent selection program, the preclusion of progeny testing provides an increase in Seff between 232% and 299%. In a clonal selection program, the elimination of both progeny and initial clonal trial may increase Seff between 134% and 277%. Increasing selection intensity by genomic prediction resulted in an additional impact on Seff. This study provides groundwork to implement genomic selection in E. benthamii breeding.