RESUMO
KEY MESSAGE: We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.
Assuntos
Fabaceae , Vicia faba , Vicia faba/genética , Estudo de Associação Genômica Ampla , Melhoramento Vegetal , Fenótipo , Fabaceae/genéticaRESUMO
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
Assuntos
Produtos Agrícolas , Diploide , Variação Genética , Genoma de Planta , Genômica , Melhoramento Vegetal , Proteínas de Plantas , Vicia faba , Cromossomos de Plantas/genética , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Variações do Número de Cópias de DNA/genética , DNA Satélite/genética , Amplificação de Genes/genética , Genes de Plantas/genética , Variação Genética/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Geografia , Melhoramento Vegetal/métodos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Recombinação Genética , Retroelementos/genética , Sementes/anatomia & histologia , Sementes/genética , Vicia faba/anatomia & histologia , Vicia faba/genética , Vicia faba/metabolismoRESUMO
Soil-borne barley yellow mosaic virus disease--caused by a complex of at least three viruses, i.e. Barley mild mosaic virus (BaMMV), Barley yellow mosaic virus (BaYMV) and BaYMV-2--is one of the most important diseases of winter barley in Europe. The two genes rym4, effective against BaMMV and BaYMV, and rym5, additionally effective against BaYMV-2, comprise a complex locus on chromosome 3HL, which is of special importance to European barley breeding. To provide the genetic basis for positional cloning of the Rym4/Rym5 locus, two high-resolution maps were constructed based on co-dominant flanking markers (MWG838/Y57c10 - MWG010/Bmac29). Mapping at a resolution of about 0.05% rec., rym4 has been located 1.07% recombination distal of marker MWG838 and 1.21% recombination proximal to marker MWG010. Based on a population size of 3,884 F2 plants (0.013% recombination) the interval harbouring rym5 was delimited to 1.49+/-0.14% recombination. By testing segmental recombinant inbred lines (RILs) for reaction to the different viruses at a resolution of 0.05% rec. (rym4) and 0.019% rec. (rym5), no segregation concerning the reaction to the different viruses could be observed. AFLP-based marker saturation for rym4, using 932 PstI+2/MseI+3 primer combinations only resulted in three markers with the closest one linked at 0.9% recombination to the gene. Two of these markers detected epialleles arising from the differential cytosine methylation of PstI sites. Regarding rym5, profiling of 1,200 RAPD primers (about 18,000 loci) and 2,048 EcoRI+3/MseI+3 AFLP primer combinations (about 205,000 loci) resulted in one RAPD marker and seven AFLP markers tightly linked to the resistance gene. Flanking markers with the closest linkage to rym5 (0.05% and 0.88% recombination) were converted into STS markers. These markers provide a starting point for chromosomal walking and may be exploited in marker-assisted selection for virus resistance based on rym5.
