Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map

Abstract

faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based Snps, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 genebased Snp markers polymorphic in three recombinant line populations was selected to enable the construction of a high-density consensus genetic map encompassing 1,728 markers well distributed in six linkage groups and spanning 1,547.71 cM with an average inter-marker distance of 0.89 cM. orthology-based comparison of the faba bean consensus map with legume genome assemblies highlighted synteny patterns that partly reflected the phylogenetic relationships among species. Solid blocks of macrosynteny were observed between faba bean and the most closely-related sequenced legume species such as pea, barrel medic or chickpea. Numerous blocks could also be identified in more divergent species such as common bean or cowpea. the genetic tools developed in this work can be used in association mapping, genetic diversity, linkage disequilibrium or comparative genomics and provide a backbone for map-based cloning. This will make the identification of candidate genes of interest more efficient and will accelerate marker-assisted selection (MAS) and genomic-assisted breeding (GAB) in faba bean.Legume crops serve as a source of food and feed. They also play an important role in sustainable agriculture because of their ability to improve soil fertility by fixing atmospheric nitrogen and increasing crop yield when used in crop rotation with cereals or intercropping 1 . In particular, faba bean (Vicia faba L.; Vf) is a primary ingredient of daily meals in both developing and industrialized countries due to its high content in proteins, carbohydrates, dietary fibers and micronutrients 2,3 . It is the most yielding pulse crop after field pea. However, its yield is still about half that of wheat, indicating that great breeding efforts are still needed 4 . Faba bean yield is greatly affected by environmental conditions, especially extreme temperatures, drought and acidity 5,6 . In addition, diseases such as chocolate spot (Botrytis fabae S. or B. cinerea P.) or ascochyta blight (Ascochyta fabae S.), viruses such as faba bean necrotic viruses, parasitic weeds of Orobanche genus and pests such as leaf weevil (Sitona lineatus L.), aphids (Aphis fabae S., A. craccivora K., Acyrthosiphon pisum H., Myzus persicae S.) or seed weevils (Bruchus rufimanus B.) considerably reduce its yield and affect the commercialization of the grains 5,7 . Other factors limiting the production of faba bean include the overproduction of flowers resulting in a variable fertilization

PeaMUST (Pea MultiStress Tolerance), a multidisciplinary French project uniting researchers, plant breeders, and the food industry

“…Using exome capture, which combines single nucleotide polymorphism (SNP) discovery and genotyping, 1.9‐M SNPs were detected for the pea architecture and multistress (AMS) collection and 1.7 M for the faba bean collection. By sequencing of the faba bean transcriptomes of four parental lines of the RIL populations, 104,000 SNPs were detected, and 2,000 of those have been used for genotyping of segregating populations using genotyping by capture technique (Carrillo‐Perdomo et al, 2020).…”

Recent Advances in Faba Bean Genetic and Genomic Tools for Crop Improvement

“…It contained 687 SNP markers on six linkage groups, each presumed to correspond to one of the faba bean chromosomes. Carrillo-Perdomo et al (2020) recently reported the most saturated consensus genetic map to date: it was constructed using three mapping populations and encompassed 1,728 SNP markers distributed in six linkage groups. Solid proof of macro-synteny was also observed between this map and the most closely-related legume species that have been sequenced.…”

“…However, from these reported transcriptome datasets, only limited DNA sequence data are available in public databases (Mokhtar et al, 2020). Additionally, the development of high-density genetic maps derived from multiple populations and gene-based molecular markers, particularly those developed by Webb et al (2016) and Carrillo-Perdomo et al (2020), have paved the road to marker-assisted selection (MAS) and gene discovery. For example, the elucidation of the biosynthetic pathway for the pyrimidine glycosides vicine and convicine (v-c) (Björnsdotter et al, 2020), which have been the main factors limiting faba bean cultivation and usage in many warm regions, was not possible without the combination of transcriptome data (Ray et al, 2015) and gene-based comparative mapping approaches (Khazaei et al, 2015;.…”

“…Two recent review papers on this topic cover the coming of age of faba bean genetics and genomics in some detail (see O'Sullivan & Angra, 2016;Maalouf et al, 2019) but, since then, major progress on the key seed anti-nutrients v-c (Björnsdotter et al, 2020), seed coat tannins (e.g., Gutierrez & Torres, 2019;Gutierrez et al, 2020), as well as improved mapping approaches (Carrillo-Perdomo et al, 2020) and transcriptome data, has been made. We provide here a comprehensive review on the mapping population and genomic resources in this species.…”

Genetic study of the resistance of faba bean (Vicia faba) against the fungus Ascochyta fabae through a genome‐wide association analysis

“…Meanwhile further such consensus maps have become known (e.g. Carrillo‐Perdomo et al., 2020; Ocaña‐Moral et al., 2017; Sudheesh et al., 2019). Although previously various types of markers were employed to detect and map QTL for Ascochyta resistance in faba beans (Avila et al., 2004; Cruz‐Izquierdo et al., 2012; Díaz‐Ruiz et al., 2009; Ellwood et al., 2008; El‐Rodeny et al., 2014; Kaur et al., 2014; Roman et al., 2003), today, mainly SNPs are used for such analyses.…”