Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes

Publication Overview
TitleIntegrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes
AuthorsHo WK, Chai HH, Kendabie P, Ahmad NS, Jani J, Massawe F, Kilian A, Mayes S
TypeJournal Article
Journal NameBMC Genomics
Volume18
Year2017
CitationHo WK, Chai HH, Kendabie P, Ahmad NS, Jani J, Massawe F, Kilian A, Mayes S. Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes. BMC Genomics. 2017; 18:192.

Abstract

Background: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata). From these comparisons we identify conserved synteny blocks corresponding to the Linkage Groups (LGs) in bambara groundnut genetic maps and evaluate the potential to identify genes in conserved syntenic locations in a sequenced genome that underlie a QTL position in the underutilised crop genome. Results: Two individual intraspecific linkage maps consisting of DArTseq markers were constructed in two bambara groundnut (2n = 2x = 22) segregating populations: 1) The genetic map of Population IA was derived from F2 lines (n = 263; IITA686 x Ankpa4) and covered 1,395.2 cM across 11 linkage groups; 2) The genetic map of Population TD was derived from F3 lines (n = 71; Tiga Nicuru x DipC) and covered 1,376.7 cM across 11 linkage groups. A total of 96 DArTseq markers from an initial pool of 142 pre-selected common markers were used. These were not only polymorphic in both populations but also each marker could be located using the unique sequence tag (at selected stringency) onto the common bean, adzuki bean and mung bean genomes, thus allowing the sequenced genomes to be used as an initial ‘pseudo’ physical map for bambara groundnut. A good correspondence was observed at the macro synteny level, particularly to the common bean genome. A test using the QTL location of an agronomic trait in one of the bambara groundnut maps allowed the corresponding flanking positions to be identified in common bean, mung bean and adzuki bean, demonstrating the possibility of identifying potential candidate genes underlying traits of interest through the conserved syntenic physical location of QTL in the well annotated genomes of closely related species. Conclusions: The approach of adding pre-selected common markers in both populations before genetic map construction has provided a translational framework for potential identification of candidate genes underlying a QTL of trait of interest in bambara groundnut by linking the positions of known genetic effects within the underutilised species to the physical maps of other well-annotated legume species, without the need for an existing whole genome sequence of the study species. Identifying the conserved synteny between underutilised species without complete genome sequences and the genomes of major crops and model species with genetic and trait data is an important step in the translation of resources and information from major crop and model species into the minor crop species. Such minor crops will be required to play an important role in future agriculture under the effects of climate change. Keywords: Conserved synteny markers, Mapping, Genotyping-by-sequencing, Genomic comparative analysis
Stocks
This publication contains information about 4 stocks:
Stock NameUniquenameType
IITA686IITA686cultivar
Ankpa4Ankpa4cultivar
IITA686/Ankpa4-F2IITA686/Ankpa4-F2population
Tiga_Nicuru/DipC-F3.2Tiga_Nicuru/DipC-F3.2population
Features
This publication contains information about 419 features:
Feature NameUniquenameType
UN21_DQ100019007UN21_DQ100019007genetic_marker
UN21_DQ100042088UN21_DQ100042088genetic_marker
UN21_nSNP100002086|F|0-22UN21_nSNP100002086|F|0-22genetic_marker
UN21_nSNP100003313|F|0-59UN21_nSNP100003313|F|0-59genetic_marker
UN21_nSNP100003742|F|0-18UN21_nSNP100003742|F|0-18genetic_marker
UN21_nSNP100004200|F|0-31UN21_nSNP100004200|F|0-31genetic_marker
UN21_nSNP100004872|F|0-7UN21_nSNP100004872|F|0-7genetic_marker
UN21_nSNP100005345|F|0-46UN21_nSNP100005345|F|0-46genetic_marker
UN21_nSNP100005403|F|0-56UN21_nSNP100005403|F|0-56genetic_marker
UN21_nSNP100005669|F|0-17UN21_nSNP100005669|F|0-17genetic_marker
UN21_nSNP100005876|F|0-39UN21_nSNP100005876|F|0-39genetic_marker
UN21_nSNP100006357|F|0-56UN21_nSNP100006357|F|0-56genetic_marker
UN21_nSNP100006454|F|0-24UN21_nSNP100006454|F|0-24genetic_marker
UN21_nSNP100006501|F|0-51UN21_nSNP100006501|F|0-51genetic_marker
UN21_nSNP100006735|F|0-19UN21_nSNP100006735|F|0-19genetic_marker
UN21_nSNP100006907|F|0-47UN21_nSNP100006907|F|0-47genetic_marker
UN21_nSNP100007090|F|0-34UN21_nSNP100007090|F|0-34genetic_marker
UN21_nSNP100007101|F|0-53UN21_nSNP100007101|F|0-53genetic_marker
UN21_nSNP100007131|F|0-27UN21_nSNP100007131|F|0-27genetic_marker
UN21_nSNP100007315|F|0-51UN21_nSNP100007315|F|0-51genetic_marker
UN21_nSNP100007737|F|0-35UN21_nSNP100007737|F|0-35genetic_marker
UN21_nSNP100008057|F|0-66UN21_nSNP100008057|F|0-66genetic_marker
UN21_nSNP100008099|F|0-14UN21_nSNP100008099|F|0-14genetic_marker
UN21_nSNP100009182|F|0-58UN21_nSNP100009182|F|0-58genetic_marker
UN21_nSNP100009586|F|0-19UN21_nSNP100009586|F|0-19genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Bambara-Internode_length-Ho-2017
Featuremaps
This publication contains information about 2 maps:
Map Name
Bambara-IITA686/Ankpa4-F2
Bambara-Tiga_Nicuru/DipC-F3.2
Properties
Additional details for this publication include:
Property NameValue
URLhttps://link.springer.com/article/10.1186/s12864-016-3393-8