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Title: Genetic Diversity and Relationship Study among Ethiopian, East African Accessions and IITA Inbred Lines of Cowpea (Vigna Unguiculata (L.) Walp) as Revealed by SSR and SNP Markers
???metadata.dc.contributor.*???: Dr. Kifle Dagne
Ayalew, Belayneh
Keywords: Cowpea;Genetic Diversity;SSR;SNP;Ethiopia;Kenya;Somalia;Sudan;Inbred Line;East Africa;Germplasm
Issue Date: Jul-2015
Publisher: Addis Ababa University
Abstract: Cowpea (Vigna imguiculata L. Walp) is an important grain legume in East Africa and is mainly grown by small-scale farmers. Drought tolerance, early maturity, nitrogen fixation, and low fertility requirement are important characteristics for adaptation to the dry regions of Sub-Saharan Africa. Cowpea is a multifunctional crop providing food to both humans and animals. Because it is rich in protein, cowpea is a cheap source of protein for resourcelimited families in Sub-Saharan Africa. Understanding the genetic diversity in cowpea is a crucial initial step towards planning a comprehensive conservation and cowpea improvement sfrategy. Little or no study has been conducted to understand the diversity and relatedness of cowpea germplasm in East Africa, particularly in Ethiopia. This PhD research first investigated patterns of molecular diversity among 210 accessions of Ethiopian local cowpea of cowpea using 23 microsatellite markers (SSR). Additionally, the levels of genetic diversity of 95 cowpea accessions from East Africa and inbred lines from IITA were assessed using a set of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNPs). 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 per locus were recorded and two rare alleles were registered when screened with SSR1 marker. The mean polymorphic information content was 0.4. The accessions were not grouped according to their geographical origins. Three main cluster gi'oups were identified, 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 amongpoptdations (Fst = 0.075) and high gene flow (Nm = 3.176) between and among regions; indicating that there was significant germplasm 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 from lAmhara ' 'Gambolled and SNNP regions, tightly clustered and sharing a common allele with the multi-race striga resistant accession B301from Botswana, which could help in identification of appropriate parental lines among Ethiopian accessions of cowpea for Striga gesnerioides resistance. The rare alleles identified were linked to desirable trait of stiiga resistance against Striga gesnerioides, SG3, RACE. The SSR markers tested in this study can thus be used for analyzing cowpea diversity reliably The polymorphic information content (PIC) value was more than that of some African countries, Ghana, Senegal and Kenya; however, considerably lower than that of the wild cowpea types;therefore, the results obtained hi the present study reinforce the need to protect and 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 African countries and JITA 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 flow among East African countries; and thus the existence of germplasm exchange among the East African countries. The cluster analysis showed a similar pattern for both SSR and SNP markers detecting a substantial degree of association between origin and genotype. However, some accessions from different regions clustered together. The geographic distance and the genetic background of the accessions were not clearly reflected in the accession clustering of genetic tree constriction and principal component analysis. The results of fixation index, neighbor joining and genotype 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 African countries were more than some of west African countries, Ghana and Senegal but noticeably lower than the wild cowpea types. Therefore, the results obtained in the present study showed that the cowpea genetic base of Ethiopian and other East African 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 most of the accessions from the gene bank are a mixture of sub-accessions Ethiopian Biodiversity Institute (EB1) should consider reorganizing their seed stock by taking the subtypes identified in this study into account.
Description: In Partial Fullfillment of the Requirenments for the Degree of Doctor of Philosophy in Biology (Applied Genetics).
Appears in Collections:Thesis - Biology

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