Genetic Diversity and Relationship Study among Ethiopian, East African accessions and lIT A Inbred Lines of Cowpea (Vigl/a III/glliclilata (L.) Walp) as revealed by SSR and SNP markers
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Date
2015-07
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Addis Ababa University
Abstract
Cowpea (Vigna unguiculata L. Walp) is an important grain legume in East Africa and is
mainly grown by small-scale farmers. Drought tolerance, early maturity, nitrogen jixation,
and loll' fertility requirement are important characteristics for adaptation to the (by regions
of Sub-Saharan Aji-ica. COll1Jea is a multijunctional crop providingfood to both humans and
animals. Because it is rich in protein, cowpea is a cheap source of protein for resourcelimited
families in Sub-Saharan AjiĀ·ica. Understanding the genetic diversity in cowpea is a
crucial initial step towards planning a comprehensive conservation and cowpea improvement
strategy. Little or no study has been conducted to understand the diversity and relatedness of
COllpea germplasm in East Aji'ica, particularly in Ethiopia. This PhD research jirst
investigated patterns of molecular diversity among 210 accessions of Ethiopian local COllpea
of cowpea using 23 microsatellite markers (SSR). Additionally, the levels of genetic diversity
of 95 COllpea accessions from East Aji'ica and inbred lines ji-OI1l llTA were assessed using a
set of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNP~). The average
genetic diversity (D), as quantified by the expected heterozygosity, was 0.47. A total of 75
alleles with the average number of 3 alleles pel' locus were recorded and two rare alleles
were registered when screened with SSRI marker. The mean polymol1Jhic information
content was 0.4. The accessions were not grouped according to their geographical origins.
Three main cluster groups were identifie(l, and the sub-groups identified by neighbor joining
were in accordance to the clusters revealed by the structure analysis. The AMOVA result
showed moderate differentiation among populations (Fst ~ 0.075) and high genejiow (Nm ~
3.176) between and among regions; indicating that there was significant germ plasm
exchange between the regions considered. The accessions in this study possess wide diversity
within both individuals and populations. The study also detected five promising Ethiopian
accessions ji'om 'Amhara', 'Gambella' and SNNP regions, tightly clustered and sharing a
common allele with the multi-race striga resistant accession B301ji'om Botswana, which
could help in identification of appropriate parental lines among Ethiopian accessions of
cOllpeafor Striga gesnerioides resistance. The rare alleles identified were linked to desirable
trait of striga resistance against Striga gesnerioides, SG3, RACE. The SSR markers tested in
this study can thus be used for analyzing cOllpea diversity reliably The polymorphic
information col1lent (PIC) value was IIlOre than that of some Aji'ican countries, Ghana,
Senegal and Kenya; however, considerably lower than that of the wild cOllpea types;
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therifore, the results obtained in the present study reinforce the need to protect alld conserve
valuable genetic resources and the finding also showed that the genetic base of Ethiopian
cowpea is narrow. Regarding the comparative study of accessions from some of East Aji-ican
countries and lITA inbred lines of cowpea, the result showed that the average genetic
diversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52)
than for SNPs (0.34). The average number of alleles per locus was higher for the SSR
markers (6) than for the SNP (2) markers. The PIC was 0.48 for SSRs and 0.28 for SNPs
while the fixation index was 0.095 for SSRs and 0.15 for SNPs showing moderate
differentiation and high gene fiow among East AjNcan countries; and thus the existence of
germ plasm exchange among the East AjNcan countries. The cluster analysis showed a
similar pattei'll for both SSR and SNP markers detecting a substantial degree of association
between origin and genotype. However, some accessions }i'om different regions clustered
together. The geographic distance and the genetic background of the accessions were not
clearly refiected in the accession clustering of genetic tree constriction and principal
component analysis. The results of fixation index, neighbor joining and genot)qJe clustering
agreed in both SNP and SSR markers. Thus for the assignment of genotypes to subgroups
both neighbor joining and PCoA clustering methods are equally appropriate. The
polymorphic information content (PIC) value of all of the east AjNcan countries were more
than some of west AjNcan countries, Ghana and Senegal but noticeably lower than the wild
cOlllJea types. Therefore, the results obtained in the present study showed that the cowpea
genetic base of Ethiopian and other East Aji'ican countries is narrow. It is recommended that
the narrow genetic base can be augmented through introduction of accessions with desirable
alleles. Since the study showed that /IIost of the accessions }i'om the gene bank are a mixture
of sub-accessions Ethiopian Biodiversity Institute (EBl) should consider reorganizing their
seed stock by taking the subtypes identified in this study into account.
Keywords: Cowpea, Genetic diversity, SSR, SNP, Ethiopia, Kenya, Somalia, Sudan, inbred
line, East Africa, germplasm
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Keywords
Cowpea, Genetic diversity, SSR, SNP, Ethiopia, Kenya;Somalia; Sudan; inbredline,, East Africa, germplasm