title: Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing.
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.
authors.affiliation: a Biotechnology and Crop Genetics Theme, Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.|b School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
authors.forename: Wai Kuan
authors.initials: WK
authors.lastname: Ho
authors.affiliation: c World Agroforestry Centre, United Nations Avenue, Gigiri, Nairobi, Kenya.
authors.forename: Alice
authors.initials: A
authors.lastname: Muchugi
authors.affiliation: c World Agroforestry Centre, United Nations Avenue, Gigiri, Nairobi, Kenya.
authors.forename: Samuel
authors.initials: S
authors.lastname: Muthemba
authors.affiliation: c World Agroforestry Centre, United Nations Avenue, Gigiri, Nairobi, Kenya.
authors.forename: Robert
authors.initials: R
authors.lastname: Kariba
authors.affiliation: d Crop Breeding Institute, Harare Agricultural Research Centre, Fifth Street Extension, P.O. Box CY550, Causeway, Harare, Zimbabwe.
authors.forename: Busiso Olga
authors.initials: BO
authors.lastname: Mavenkeni
authors.affiliation: c World Agroforestry Centre, United Nations Avenue, Gigiri, Nairobi, Kenya.
authors.forename: Prasad
authors.initials: P
authors.lastname: Hendre
authors.affiliation: f BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Song
authors.affiliation: e Seed Biotechnology Center, University of California, 1 Shields Ave., Davis, CA, USA.
authors.forename: Allen
authors.initials: A
authors.lastname: Van Deynze
authors.affiliation: b School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
authors.forename: Festo
authors.initials: F
authors.lastname: Massawe
authors.affiliation: a Biotechnology and Crop Genetics Theme, Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.|g School of Biosciences, Faculty of Science, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK.
authors.forename: Sean
authors.initials: S
authors.lastname: Mayes
mesh_terms: D000383:Agriculture; D002874:Chromosome Mapping; D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D007887:Fabaceae / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D006579:Heterozygote; D018895:Microsatellite Repeats; D000069600:Plant Breeding; D013045:Species Specificity; D015030:Zimbabwe
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
keywords: assemblage de génome végétal; heterozygosity; hétérozygotie; marqueurs microsatellites; microsatellite markers; plant genome assembly; pureté variétale; varietal purity