Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin

Abstract

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes.Key MessageWe identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.

Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)

“…The imputation of the missing data was performed by mean allelic frequency. To obtain the genetic position of the significant SNPs we used the information and protocols provided by Skovbjerg et al., 2022 . Thus, 17,403 out of the 21,915 SNPs markers could be assigned to genomic positions.…”

Identifying physiological and genetic determinants of faba bean transpiration response to evaporative demand

“… Yan et al ., 2010 ; Chongtham et al ., 2022 ), simple documentation, co-dominance, a common occurrence amongst elite germplasm (e.g. Cottage et al ., 2012 ; Skovbjerg et al ., 2022 ), and potential for high-throughput analysis ( Wang et al ., 2021 ). Recently, a high-density faba bean genotyping array (‘Vfaba_v2’) containing 24 929 polymorphic high-resolution SNP markers located in 15 846 different genes has been developed ( O’Sullivan et al ., 2019 ; Donal M. O’Sullivan, pers.…”