Skip to main content

Research Repository

Advanced Search

Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing

Ho, Wai Kuan; Muchugi, Alice; Muthemba, Samuel; Kariba, Robert; Mavenkeni, Busiso Olga; Hendre, Prasad; Song, Bo; Van Deynze, Allen; Massawe, Festo; Mayes, Sean

Authors

Wai Kuan Ho

Alice Muchugi

Samuel Muthemba

Robert Kariba

Busiso Olga Mavenkeni

Prasad Hendre

Bo Song

Allen Van Deynze

Festo Massawe

SEAN MAYES SEAN.MAYES@NOTTINGHAM.AC.UK
Associate Professor



Abstract

Maximizing the research output from a limited investment is often the major challenge for minor and underutilized crops. However, such crops may be tolerant to biotic and abiotic stresses and are adapted to local, marginal, and low-input environments. Their development through breeding will provide an important resource for future agricultural system resilience and diversification in the context of changing climates and the need to achieve food security. The African Orphan Crops Consortium recognizes the values of genomic resources in facilitating the improvement of such crops. Prior to beginning genome sequencing there is a need for an assessment of line varietal purity and to estimate any residual heterozygosity. Here we present an example from bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilized drought tolerant African legume. Two released varieties from Zimbabwe, identified as potential genotypes for whole genome sequencing (WGS), were genotyped with 20 species-specific SSR markers. The results indicate that the cultivars are actually a mix of related inbred genotypes, and the analysis allowed a strategy of single plant selection to be used to generate non-heterogeneous DNA for WGS. The markers also confirmed very low levels of heterozygosity within individual plants. The application of a pre-screen using co-dominant microsatellite markers is expected to substantially improve the genome assembly, compared to a cultivar bulking approach that could have been adopted.

Journal Article Type Article
Acceptance Date Mar 14, 2016
Online Publication Date May 12, 2016
Publication Date Jun 30, 2016
Deposit Date Apr 18, 2018
Print ISSN 0831-2796
Electronic ISSN 1480-3321
Publisher NRC Research Press
Peer Reviewed Peer Reviewed
Volume 59
Issue 6
Pages 427-431
DOI https://doi.org/10.1139/gen-2016-0029
Public URL http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2016-0029
Publisher URL http://www.nrcresearchpress.com/doi/10.1139/gen-2016-0029#.XDyir2ngrb0