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

Publication Overview
TitleA SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)
AuthorsWebb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard FL, Maalouf F, Ogbonnaya FC, Link W, Thomas J, O'Sullivan DM
TypeJournal Article
Journal NamePlant biotechnology journal
Year2015
CitationWebb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard FL, Maalouf F, Ogbonnaya FC, Link W, Thomas J, O'Sullivan DM. A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). Plant biotechnology journal. 2015 Apr 10.

Abstract

Faba 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.

Features
This publication contains information about 651 features:
Feature NameUniquenameType
GLIP133SNPGLIP133SNPgenetic_marker
GLIP245SNPGLIP245SNPgenetic_marker
GLIP253SNPGLIP253SNPgenetic_marker
GLIP265SNPGLIP265SNPgenetic_marker
GLIP337SNPGLIP337SNPgenetic_marker
LG031SNPLG031SNPgenetic_marker
LG068SNPLG068SNPgenetic_marker
LG085SNPLG085SNPgenetic_marker
LUP108SNPLUP108SNPgenetic_marker
RNARSNPRNARSNPgenetic_marker
Vf_Mt1g007160_001Vf_Mt1g007160_001genetic_marker
Vf_Mt1g007160_002Vf_Mt1g007160_002genetic_marker
Vf_Mt1g007480_001Vf_Mt1g007480_001genetic_marker
Vf_Mt1g008140_001Vf_Mt1g008140_001genetic_marker
Vf_Mt1g009200_001Vf_Mt1g009200_001genetic_marker
Vf_Mt1g012440_001Vf_Mt1g012440_001genetic_marker
Vf_Mt1g015770_001Vf_Mt1g015770_001genetic_marker
Vf_Mt1g015820_001Vf_Mt1g015820_001genetic_marker
Vf_Mt1g016100_001Vf_Mt1g016100_001genetic_marker
Vf_Mt1g016390_001Vf_Mt1g016390_001genetic_marker
Vf_Mt1g017950_001Vf_Mt1g017950_001genetic_marker
Vf_Mt1g018320_001Vf_Mt1g018320_001genetic_marker
Vf_Mt1g018790_001Vf_Mt1g018790_001genetic_marker
Vf_Mt1g019770_001Vf_Mt1g019770_001genetic_marker
Vf_Mt1g019810_001Vf_Mt1g019810_001genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
faba-compositeMap-2015
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1467-7652
eISSN1467-7652
Publication Date2015 Apr 10
Journal AbbreviationPlant Biotechnol. J.
Elocation10.1111/pbi.12371
Copyright© 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article
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DatabaseAccession
PMID: PubMedPMID:25865502