Abstract
SummaryFaba bean (Vicia faba L.) is a globally important nitrogen‐fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence‐based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2‐cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40‐1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5′ end of the gene.
Highlights
Faba bean is a globally significant grain legume, with 4–5 million tonnes annual production worldwide in recent years (FAO, 2014), providing the predominant affordable dietary source of protein to subsistence farmers and urban populations across North Africa, Horn of Africa and the Middle and Near East as well as parts of China
We previously demonstrated conversion of set of mapped cleaved amplified polymorphic sequence (CAPS) and SNAPshot assays to Kompetitive Allele Specific PCR (KASP) format in faba bean (Cottage et al, 2012)
Pyrosequencing and de novo transcript assembly of RNA from seedling tissues of two contrasting faba bean lines – NV643-4, a partly inbred line derived from the white flowered, white hilum Polish variety ‘Albus’ and NV648-1, a derivative of the ICARDA Bean Pure Line ‘BPL100, a coloured flower, black hilum inbred line – yielded 17 397 and 16 041 contigs >200 bp in length for NV643-4 and NV648-1, respectively
Summary
Faba bean is a globally significant grain legume, with 4–5 million tonnes annual production worldwide in recent years (FAO, 2014), providing the predominant affordable dietary source of protein to subsistence farmers and urban populations across North Africa, Horn of Africa (including Ethiopia) and the Middle and Near East as well as parts of China. The almost unchecked spread of parasitic weeds of the genus Orobanche has led to abandonment for faba bean growing of entire provinces in Egypt but across the entire Mediterranean basin (Maalouf et al, 2009). These as well as other production constraints such as drought and extreme temperature sensitivity could potentially be addressed by more effective genomicsenabled genetic analysis/breeding strategies
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