SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

Odireleng Molosiwa, Siise Aliyu, Florian Stadler, Katie Mayes, Festo Massawe, Sean Mayes

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.
Original languageEnglish
Pages (from-to)1225-1243
Number of pages19
JournalGenetic Resources and Crop Evolution
Volume62
Issue number8
DOIs
Publication statusPublished - 2015
Externally publishedYes

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Vigna subterranea
groundnut
landraces
population structure
Genotype
genetic variation
Seeds
Botswana
Population
genotype
Inbreeding
Ecology
agroecology
seed
inbreeding coefficient
inbreeding
seeds
agronomic traits
heterozygosity
yield components

Cite this

Molosiwa, Odireleng ; Aliyu, Siise ; Stadler, Florian ; Mayes, Katie ; Massawe, Festo ; Mayes, Sean. / SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces. In: Genetic Resources and Crop Evolution. 2015 ; Vol. 62, No. 8. pp. 1225-1243.
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SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces. / Molosiwa, Odireleng; Aliyu, Siise; Stadler, Florian; Mayes, Katie; Massawe, Festo; Mayes, Sean.

In: Genetic Resources and Crop Evolution, Vol. 62, No. 8, 2015, p. 1225-1243.

Research output: Contribution to journalArticle

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AU - Molosiwa, Odireleng

AU - Aliyu, Siise

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AU - Mayes, Katie

AU - Massawe, Festo

AU - Mayes, Sean

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N2 - We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.

AB - We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.

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