A SNP‐based consensus genetic map for synteny‐based trait targeting in faba bean (Vicia faba L.)

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.

Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

“…The distribution of E-values based on BLASTN results of the comparator reference legume species to the generated faba bean assemblies is summarised in The results of the comparison of Doza (Table S5) and Farah (Table S6) transcriptome assemblies to the previously published faba bean transcriptome sets (from Webb et al [29] and Kaur et al [22]) revealed that the current assemblies captured approximately 96% of transcripts from the Webb et al [29] datasets and approximately 98% of contigs and 78% of singletons from the Kaur et al [22] study. A total of 25.7% and 35.4% transcripts were found to be specific to the Doza and Farah transcriptome assemblies, respectively, based on comparison to the previously-published faba bean datasets.…”

“…The reciprocal read mapping of Farah to Doza showed that 81.2% of Farah-derived transcripts exhibited matches to Doza-derived sequences. Furthermore, an overall comparison results of Farah versus Doza in addition to the datasets from Kaur et al [22] and Webb et al [29] studies are summarised in Figure 2. This identified a total of 8428 Doza-specific transcripts, 9437 Farah-specific transcripts and 9572 transcripts common to both the assemblies that was not previously characterised in Vicia faba L. datasets.…”

“…Venn diagram depicting the distribution of BLAST matches between Farah-specific and Doza-specific reference transcripts with sequences from Albus [29], BPL10 [29], and Kaur et al [22] transcriptome studies.…”

“…Several transcriptome datasets have been previously generated for faba bean, from the cultivars Windsor [53], Icarus and Ascot [22], CDC Fatima, SSNS-1, and A01155 [39], Fiord [40,54], INRA-29H and Vf136 [42], BPL10 and Albus [29], and Wizard [43]. These datasets were generated from a selection of tissues including root, shoots, seedling, embryo, seed coat, leaves, or mixed tissues.…”

“…These datasets were generated from a selection of tissues including root, shoots, seedling, embryo, seed coat, leaves, or mixed tissues. The reference transcriptome assemblies from the current study were compared to the datasets obtained from the transcriptome studies of Webb et al [29] and Kaur et al [22]. The former was chosen as it has been used to generate a genetic linkage map with the densest SNP coverage that is currently available, while the latter used Australian cultivars, and a mixture of tissue types providing a broad survey of gene expression diversity.…”