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The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population wa...
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... localized within gene sequences whereas 2560 markers were found in loci lacking any annotation. There were 4185 MACE markers retained after application of total missing data threshold (counting heterozygotes and no data scores), followed by inference of consensus segregation for genes represented by several single nucleotide polymorphism, SNPs . There were 3532 genes represented by single markers, four genes were represented by pairs of markers with heterogeneous segregation patterns, and 645 markers were localized in unannotated loci. The annotation of markers is provided in the Table ...Context 2
... BAC-end based marker allele sequences were deposited in NCBI Genbank under accession numbers (MN518055-MN518073). Information on primer pair sequences, PCR primer annealing temperature, PCR product lengths, enzyme used for polymorphism detection, and restriction product lengths for both alleles is provided in Table S2. For the past 15 years, the use of BAC-derived PCR markers has been a method of choice in studies involving L. angustifolius genome physical and linkage mapping. ...Context 3
... of the MACE-based L. angustifolius linkage map. Length (cM) Number of Scaffolds NLL-01 289 120 251 156.38 11 NLL-02 207 73 185 132.78 21 NLL-03 204 77 169 115.02 22 NLL-04 193 95 157 126.93 8 NLL-05 144 70 130 101.29 10 NLL-06 304 119 267 144.66 10 NLL-07 191 85 155 The segregation pattern of 59.7% of the markers was redundant, and therefore the map contains 1735 loci, namely from 60 to 120 loci per linkage group. The lengths of linkage groups vary from 78.5 to 156.38 cM, reaching 2163.63 cM in total. ...Context 4
... interval mapping revealed the presence of numerous eQTL peaks close to domestication trait loci. Within a genetic linkage distance of 2 cM from a particular domestication trait locus, from one (mollis) to 61 (iucundus) genes had eQTL peaks localized ( Table 2). The LOD values for eQTL permutation test are provided in Table S9, whereas data on eQTL localization on the linkage map are provided in Table S10. ...Citations
... Классификация используется при апробации посевов, способствует поддержанию аутентичности образцов коллекций в ходе их репродуцирования и необходима генетикам для установления сцепления генов (Vishnyakova et al., 2021). Она дает представление о фенотипическом разнообразии вида, знание которого необходимо для решения проблемы сокращения генетического полиморфизма среди возделываемых сортов (Cow ling, 2020;Vishnyakova et al., 2020) и проведения молекулярно-генетических исследований (Plewiński et al., 2019). Однако спектр рекомбинационной изменчивости L. angustifolius динамически расширяется под влиянием гибридизации и мутагенеза (Kuptsov, Popov, 2019). ...
Background. The phenotypic structure of Lupinus angustifolius L. is dynamically expanding due to genetic recombinations and mutagenesis. Therefore, the existing concepts of the inflorescence color diversity in narrowleaf lupine need regular updating.
Materials and methods . Research materials consisted of 887 narrowleaf lupine accessions from the VIR collection. Their morphological descriptions were made in 2009–2023 during field trials under the conditions of Moscow Province, Russia. Longterm observations made it possible to evaluate probable color modifications in inflorescences under varying weather conditions.
Results. The lupine gene pool was divided into 15 biotypes differing in the anthocyanin pigmentation of separate inflorescence parts, such as the vexillum, wings, and keel, as well as the inflorescence axis. Individual color features of cotyledons, leaves, stem, and seeds also characterized the biotypes. Phenotypic characteristics of lupine biotypes were compared with diagnostic traits of intraspecific taxa and known genes for flower color.
Conclusion. Three new varieties and six new subvarieties were marked out for narrowleaf lupine. Probable carriers of genes responsible for the flower’s basic color: roseus (fco 1), violaceus (fco 3), albus (fco 4), and leucospermus (fco 21, fco 22), and its modifications: Supercoeruleus, dispersus, discolor, and albiflorus, were identified. Descriptions of some biotypes failed to agree with the data on any known gene’s phenotypic expression, which attested to the presence of new mutations, recombinations, or unstudied gene associations.
... We considered a gene network structure common to many plant species including legumes, in which FT-like genes regulate AP1-like genes ( Figure 1) [8,35,36]. However, in this case, AGL8 expression was considered in leaves, where it showed strong association with vernalization independence of the Ku locus [37]. The expression and function of AP1 orthologs in leaves have been described in a number of plant species [38,39]. ...
... In the study [21], the authors examined the expression of two homologs of A. thaliana genes involved in the FLC vernalization pathway, CRLK1 and UGT85A2. These two genes were selected based on transcriptomic data on their contribution to the vernalization response via FTc1 in L. angustifolius [37]. CRLK1 functions in the C-repeat binding factor (CBF) cold sensitivity pathway, while UGT85A2 is involved in the UDP-glycosyltransferase pathway. ...
Flowering is initiated in response to environmental cues, with the photoperiod and ambient temperature being the main ones. The regulatory pathways underlying floral transition are well studied in Arabidopsis thaliana but remain largely unknown in legumes. Here, we first applied an in silico approach to infer the regulatory inputs of four FT-like genes of the narrow-leafed lupin Lupinus angustifolius. We studied the roles of FTc1, FTc2, FTa1, and FTa2 in the activation of meristem identity gene AGL8 in response to 8 h and 16 h photoperiods, vernalization, and the circadian rhythm. We developed a set of regression models of AGL8 regulation by the FT-like genes and fitted these models to the recently published gene expression data. The importance of the input from each FT-like gene or their combinations was estimated by comparing the performance of models with one or few FT-like genes turned off, thereby simulating loss-of-function mutations that were yet unavailable in L. angustifolius. Our results suggested that in the early flowering Ku line and intermediate Pal line, the FTc1 gene played a major role in floral transition; however, it acted through different mechanisms under short and long days. Turning off the regulatory input of FTc1 resulted in substantial changes in AGL8 expression associated with vernalization sensitivity and the circadian rhythm. In the wild ku line, we found that both FTc1 and FTa1 genes had an essential role under long days, which was associated with the vernalization response. These results could be applied both for setting up new experiments and for data analysis using the proposed modeling approach.
... Figure S12). It has been reported that purine permease transporter 1 (PUP1) encoding genes are associated with the biosynthesis, transport, and regulation of alkaloids in Nicotiana tabacum (Hildreth et al. 2011)d angustifolius (Plewiński et al. 2019). An ortholog gene of LanPUP1 was identi ed in the L. luteus genome. ...
Lupinus luteus is a grain legume crop of agricultural importance due to its high seed protein content. In this study, the first chromosome-scale genome assembly of L. luteus (962.97 Mb) is presented, integrating data from Illumina, PacBio, and Hi-C platforms. The assembly exhibits exceptional completeness (98.9% BUSCO score) and a high repetition rate (76.15%). Genomic annotation identifies 36,884 protein-coding genes, including 2,492 transcription factors and 23 microRNA families.
Synteny analysis with lupin species reveals important chromosomal rearrangements, indicating complex interactions between conserved regions and structural variations. Our analyses suggest that chromosome 8 may have originated from a translocation event involving two chromosomes during the speciation of L. luteus. Orthologous group characterization between L. luteus and related species indicates an enrichment in gene families associated with biotic and abiotic stress responses, secondary metabolism, and nutrient reservoir activity. Moreover, 911 resistance (R) genes are identified, highlighting their importance in pathogen defence. Exploration of alkaloid biosynthesis and regulation reveals 16 genes associated with quinolizidine alkaloids (QAs) with expression analysis revealing tissue-specific expression patterns for key enzymes in QA biosynthesis. Furthermore, secondary metabolite transporters are explored, including a Lupinus angustifolius PUP1 ortholog, providing insights into QA translocation mechanisms. This comprehensive genome analysis provides valuable resources for further understanding the genetic basis of important traits in Lupinus luteus, facilitating advancements in crop adaptation, improvement, and sustainability.
... Five molecular markers, including two flanking the Lanr1 gene at 0.9 cM, were implemented into breeding programs [68]. Subsequent refinements to the map, utilizing improved marker systems [69][70][71], narrowed down the position of the Lanr1 locus to a 388 Kb fragment containing 41 predicted genes, including an NBS-LRR resistance gene [70]. Another locus, designated AnMan, was identified from a cross between 'Mandalup' (resistant) and 'Quilinock' (susceptible) cultivars [62]. ...
Anthracnose stands as the primary obstacle to lupin cultivation, impeding development despite the considerable agronomic, ecological, and economic potential of such legume crops. This review explores recent efforts to unravel the complexities of anthracnose in domesticated lupins, focusing on both the plant perspective and the causative pathogenic agent, Colletotrichum lupini. Leveraging cutting-edge technologies has yielded crucial insights into various facets of this devastating disease, encompassing plant and pathogen biology, genetic and molecular regulations of the interaction, fungal diversity and population dynamics, and screening of plant genetic resources for anthracnose resistance. The lack of effective disease control measures, relying primarily on the use of disease-free seeds, highlights the need to develop anthracnose-resistant varieties. However, challenges arise from the intricacy of lupin's response to the disease, influenced by polygenic inheritance, in spite of loci with major effects, and environmental factors. The slow pace of genetic improvement underscores the need for more efficient breeding processes, including biotechnological approaches. This review offers a comprehensive overview of current progress and knowledge gaps, stressing the urgent need to further enhance understanding of C. lupini pathogenic mechanisms and lupin‘s resistance. Integrating advanced technologies and accelerated research efforts is paramount for achieving efficient disease management and sustainable lupin cultivation in the face of anthracnose challenges.
... Maknickienė and Ražukas (2007), in Lithuania researched low-alkaloid hybrid lines in narrow-leaved lupin. Plewiński et al. (2019) revealed candidate genes for the expression of desirable traits, including alkaloid content, in narrow-leaved lupin adding to the core collection of molecular markers for desirable traits for the crop. Chen et al. (2016), developed methods to unlock rapid breeding techniques to better utilise narrow-leafed lupin as a protein source and within diversified cropping systems. ...
Background
Growing interest in agrobiodiversity and sustainable agricultural practices has stimulated debates on diversifying cropping systems, furthering the potential for the reintroduction of underutilised crops. These crops may support multiple ecosystem services and enhance food security and agricultural value chains. This study used a systematic mapping approach to collate and summarise the state of research literature addresses the research question: What is the evidence for ecosystem service provision and economic value of underutilised crops? We focused on oats, triticale, hull-less barley, narrow-leaved lupin, buckwheat and faba beans due to their limited use in Europe, their broad gene pool, ecological benefits, and nutritional value.
Method
Three academic databases were used to identify research articles investigating the impacts of using the six underutilised crops of interest on outcomes including breeding, agronomic traits, nutrition and health, and economic values. In addition, current and recently completed European projects were searched to identify ongoing relevant research. After screening for relevance, data was extracted from all included articles and projects and imported into a spreadsheet for cross-tabulation and to produce descriptive statistics.
Results
From an initial 34,522 articles identified by the searches, 1346 relevant primary research articles containing 2229 studies were included. A total of 38 relevant European projects were identified, with 112 research results or goals relating to the six underutilised crops. Faba bean was the most common crop in both European projects and published literature. No current projects had a focus on hull-less barley. Agronomic traits were the most common primary research topic across the crops (56.39%), with oats and faba bean being well researched. Hull-less barley was the least studied crop across all topics. Within sub-topics related to specific ecosystem services, desirable traits, disease, weed and pest control all ranked highly, whilst invertebrate diversity and nitrogen fixation ranked lowest.
Conclusion
Primary research varies between crops and topics, with hull-less barley receiving the least interest. Key knowledge gaps were identified in all crops across all topics relating to breeding tools, breeding for desirable traits, agronomic traits of buckwheat, narrow-leaved lupin and hull-less barley, inclusion of the crops in human nutrition and health, and the socioeconomics of these crops. Evidence presented in this map could inform further research areas with these crops and aid future policy making for the inclusion of these crops in rotations and practices that could benefit all stakeholders along the food systems value chain.
... These two lists were combined, and after removing redundancy, the final (Lorenz et al., 1988). It is a candidate gene in alkaloid biosynthesis in Lupinus angustifolius (Plewiński et al., 2019). PAL1 ...
Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated trans-criptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled trans-criptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. har-mala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.
... Besides LanFTc1, recent studies have shown the involvement of a number of novel candidate genes in the vernalization response [47,114]. The expression profiles of these genes were examined for vernalization responsiveness in three accessions, carrying domesticated allele Ku, intermediate allele Pal, and wild allele ku [47]. ...
... A recent study provided transcriptomic evidence on the role of LanCRLK1 and LanUGT85A2 genes, acting in C-repeat binding factor (CBF) cold responsiveness and UDP-glycosyltransferase pathways, in the LanFTc1-mediated vernalization response [114]. Nevertheless, the analysis of LanCRLK1 and LanUGT85A2 expression profiles did not provide convincing evidence for the role of these genes in the vernalization response of L. angustifolius [47]. ...
Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes.
... Keeping in view the economic importance of underutilized crops, these crops need to be enriched with genomic resources for further improvement. However, few molecular studies have been conducted for the identification of candidate gene(s)/QTLs linked with the traits, such as plant height, flower initiation, maturity, and yield traits in narrow-leafed lupin [203]. In a GWAS, four candidate genes associated with flower initiation (Lup019134, Lup015264, Lup021911, and Lup021909), two genes with maturity (Lup015264 and Lup004734), one gene with plant height (Medtr1g030750), and two genes with yield traits (Lup021835 and Lup022535) were identified in lupin [203]. ...
... However, few molecular studies have been conducted for the identification of candidate gene(s)/QTLs linked with the traits, such as plant height, flower initiation, maturity, and yield traits in narrow-leafed lupin [203]. In a GWAS, four candidate genes associated with flower initiation (Lup019134, Lup015264, Lup021911, and Lup021909), two genes with maturity (Lup015264 and Lup004734), one gene with plant height (Medtr1g030750), and two genes with yield traits (Lup021835 and Lup022535) were identified in lupin [203]. Similarly, SNPs linked with phosphorus utilization and phosphorus uptake efficiency traits were identified in 120 mungbean genotypes by using the GBS technique in a GWAS approach [204]. ...
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
... Применение метода массового анализа концов кДНК (MACE) для исследования картирующих популяций, полученных от контрастных по содержанию алкалоидов родителей, позволило выявить большое количество цис-и транс-регулируемых генов биосинтеза алкалоидов в образце с низким их содержанием. Было показано, что экспрессия генов биосинтеза алкалоидов регулируется геном, локализованным в локусе iuc, что в очередной раз подтверждает гипотезу о том, что транскрипционный фактор RAP2-7 может определять низкоалкалоидный фенотип узколистного люпина и иметь практическое значение в маркер-опосредованной селекции (Plewiński et al., 2019;Czepiel et al., 2021). ...
The narrow-leafed lupinе ( Lupinus angustifolius L.) is considered as a crop of untapped opportunities. The food and forage potential of the species is not fully exploited due to the presence of quinolizidine alkaloids (QA) in plants, which are secondary metabolites that make the seeds bitter and toxic to humans and animals. Varieties with a low content of QA (“sweet” varieties) created over the last 50-60 years turned out to be more susceptible to damage by sucking insects and insect-transmitted viruses than high alkaloid ones (“bitter” varieties). Based on the rapidly developing genomic, transcriptomic and metabolomic profiling of the species, some molecular determinants and features of alkaloid biosynthesis in narrow-leafed lupinе plants have been identified: alkaloids are formed in the vegetative organs of the plant and then transported to the seeds. This information substantiated the creation of “bitter-sweet” forms with a high content of alkaloids in the vegetative parts of the plant, which would make it possible to reduce the attack of pathogens, and a minimal content of alkaloids in the seeds. This review summarizes the existing prerequisites for obtaining such forms of narrow-leafed lupinе on the basis of the available scientific developments. Information on the creation of saturated genetic maps of the species, in which the iucundus (iuc) locus determining the overall low alkaloid content in seeds is integrated and is used in breeding programs. The use of the new generation sequencing allowed the identification of the RAP2-7 gene, encoding the transcription factor APETALA2/ETHYLENE RESPONSE FACTOR, which is coupled to the iuc locus and located in the area with the main QTLs that affect the composition of the QA. It is a likely candidate gene for regulating alkaloid content in narrow-leafed lupinе seeds. The initial stages of QA biosynthesis and its regulatory factors have been revealed. Two reference assemblies of the genome of narrow-leafed lupinе have been carried out. All these achievements constitute a valuable resource for the creation of forms of narrow-leafed lupinе with a high content of alkaloids in the vegetative mass and low in the seeds, which are absent in nature.
... Cytocromes-P450 have a role in hydroxylation reactions, as well as other reactions in MIA and BIA biosynthesis (Pauli and Kutchan, 1998;Thamm et al., 2016). Recently, the existence of a high number of QA biosynthesis genes controlled by a regulatory agent localized at iucundus locus in NLL was reported, which supports the idea that ethylene responsive transcription factor RAP2-7 gene may control low-alkaloid phenotype in NLL, acting as a promoter of the expression of biosynthesis genes (Plewiński et al., 2019;Czepiel et al., 2021). ...
Alkaloids are part of a structurally diverse group of over 21,000 cyclic nitrogen-containing secondary metabolites that are found in over 20% of plant species. Lupinus albus are naturally containing quinolizidine alkaloid (QA) legumes, with wild accessions containing up to 11% of QA in seeds. Notwithstanding their clear advantages as a natural protecting system, lupin-breeding programs have selected against QA content without proper understanding of quinolizidine alkaloid biosynthetic pathway. This review summarizes the current status in this field, with focus on the utilization of natural mutations such as the one contained in pauper locus, and more recently the development of molecular markers, which along with the advent of sequencing technology, have facilitated the identification of candidate genes located in the pauper region. New insights for future research are provided, including the utilization of differentially expressed genes located on the pauper locus, as candidates for genome editing. Identification of the main genes involved in the biosynthesis of QA will enable precision breeding of low-alkaloid, high nutrition white lupin. This is important as plant based high quality protein for food and feed is an essential for sustainable agricultural productivity.
