Wai Kuan Ho
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
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 |
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