Browsing by Author "Kasule, Faizo"

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    Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda
    (Frontiers in Plant Science,, 2024-10-07) Kasule, Faizo; Adikini, Scovia; Ugen, Michael Adrogu; Esuma,Williams
    Sorghum is an important source of food and feed worldwide. Developing sorghum core germplasm collections improves our understanding of the evolution and exploitation of genetic diversity in breeding programs. Despite its significance, the characterization of the genetic diversity of local germplasm pools and the identification of genomic loci underlying the variation of critical agronomic traits in sorghum remains limited in most African countries, including Uganda. In this study, we evaluated a collection of 543 sorghum accessions actively used in Ugandan breeding program across two cropping seasons at NaSARRI, Uganda, under natural field conditions. Phenotypic data analysis revealed significant (p<0.01) variation among accessions for days to 50% flowering, plant height, panicle exsertion, and grain yield, with broad-sense heritability (H²) estimates of 0.54, 0.9, 0.81, and 0.48, respectively, indicating a high genetic variability for these traits. We used a newly developed genomic resource of 7,156 single nucleotide polymorphism (SNP) markers to characterize the genetic diversity and population structure of this collection. On average, the SNP markers exhibited moderately high polymorphic information content (PIC = 0.3) and gene diversity (He = 0.3), while observed heterozygosity (Ho = 0.07) was low, typical for self-pollinating crops like sorghum. Admixture-based models, PCA, and cluster analysis all grouped the accessions into two subpopulations with relatively low genetic differentiation. Genome-wide association study (GWAS) identified candidate genes linked to key agronomic traits using a breeding diversity panel from Uganda. GWAS analysis using three different mixed models identified 12 genomic regions associated with days to flowering, plant height, panicle exsertion, grain yield, and glume coverage. Five core candidate genes were co-localized with these significant SNPs. The SNP markers and candidate genes discovered provide valuable insights into the genetic regulation of key agronomic traits and, upon validation, hold promise for genomics-driven breeding strategies in Uganda.
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    Genome-wide Association Mapping of Bruchid Resistance Loci in Soybean
    (PloS one, 2025-01-10) Mukuze, Clever; Obua, Tonny; Kweyu, Sharon V.; Kasule, Faizo; Tukamuhabwa, Phinehas
    Soybean is a globally important industrial, food, and cash crop. Despite its importance in present and future economies, its production is severely hampered by bruchids (Callosobruchus chinensis), a destructive storage insect pest, causing considerable yield losses. Therefore, the identification of genomic regions and candidate genes associated with bruchid resistance in soybean is crucial as it helps breeders to develop new soybean varieties with improved resistance and quality. In this study, 6 multi-locus methods of the mrMLM model for genome-wide association study were used to dissect the genetic architecture of bruchid resistance on 4traits: percentage adult bruchid emergence (PBE), percentage weight loss (PWL), median development period (MDP), and Dobie susceptibility index (DSI) on 100 diverse soybean genotypes, genotyped with 14,469 single-nucleotide polymorphism (SNP) markers. Using the best linear unbiased predictors (BLUPs), 13 quantitative trait nucleotides (QTNs) were identified by the mrMLM model, of which rs16_14976250 was associated with more than 1 bruchid resistance traits. As a result, the identified QTNs linked with resistance traits can be employed in marker-assisted breeding for the accurate and rapid screening of soybean genotypes for resistance to bruchids. Moreover, a gene search on the Phytozome soybean reference genome identified 27 potential candidate genes located within a window of 478.45 kb upstream and downstream of the most reliable QTNs. These candidate genes exhibit molecular and biological functionalities associated with various soybean resistance mechanisms and, therefore, could be incorporated into the farmers’ preferred soybean varieties that are susceptible to bruchids.