Selection of Striga Resistant Sorghum Accessions in East Africa and Identification of Associated Genes Using Genome Wide Association Studies
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Date
2022
Authors
Chelangat, Irine Sugut
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Abstract
Sorghum is a salient staple food crop under cultivation in semi-arid regions of the world depended upon by millions of the poor population. Its production is hampered by both abiotic and biotic constraints resulting in low grain yields. Among the biotic constraints, Striga hermonthica is a major impediment to production of cereal crops in Sub-Saharan Africa with heaviest infestation being found in Eastern and Central Africa. Implemented control strategies for Striga infections are expensive and do not offer a complete solution. Screening of sorghum accessions for Striga resistance and locating the responsible genes through Genome Wide Association Studies (GWAS) is useful in marker aided selection in breeding programs. Sorghum genotypes harboring resistance genes may register improved yields due to limitation of Striga infections, hence is a cost-effective method for controlling Striga infestation. This study‘s main objective was to determine S. hermonthica resistance in East African sorghum landraces and to perform genome wide association mapping using Genotyping-by-Sequencing (GBS)-based Single Nucleotide Polymorphism (SNP) markers. Thirty two East African sorghum accessions were screened for post-attachment Striga resistance against one Striga ecotype using a soil free assay. N13, a cultivated race was used as a resistant control while Ochuti, a landrace preferred by farmers was used as a susceptible control. Determination of post-germination resistance was done at twenty one days after infection through scoring and analysis of Striga number, length and biomass of attached to the sorghum roots. Genome-Wide Association Mapping was carried out with the aid of Genomic Association and Prediction Integrated Tool (GAPIT) so as to determine the statistical association between phenotypic data of Striga resistance and the molecular marker data. This study revealed resistant accessions IS 8283, IS 8685, IS 3443 and IS 19016, which had the lowest number, length and biomass of the attached Striga when compared to the resistant control. The highly susceptible accessions namely IS 2263, IS 14446 and IS 22506 had the highest number, length and biomass of the attached Striga when compared to the susceptible control. GWAS revealed associations on five 5 genetic loci on chromosomes 2, 6, 7 and 8 for defense-related genes including; Serine/threonine protein kinase, Serine/arginine repetitive matrix, F-box protein, Proton-pump interactor and Zinc finger protein, all of which encode proteins that regulate signal transduction pathways leading to plant defense responses. These genes, if integrated in breeding programs may enhance development of Striga-resistant sorghum that will limit Striga infestations increasing yields leading to a better livelihood for the population.
Description
A Thesis Submitted in Partial Fulfillment of the Requirements for the Award of the Degree of Master of Science (Biotechnology) in the School of Pure and Applied Sciences of Kenyatta University, July, 2022
Keywords
Striga, Sorghum, East Africa, Genes, Genome, Wide Association Studies