Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda

Faizo Kasule; Boris M E Alladassi; Charles John Aru; Scovia Adikini; Moses Biruma; Michael Adrogu Ugen; Ronald Kakeeto; Williams Esuma

doi:10.3389/fpls.2024.1458179

Genetic diversity, population structure, and a genome-wide association study of sorghum lines assembled for breeding in Uganda

Front Plant Sci. 2024 Oct 7:15:1458179. doi: 10.3389/fpls.2024.1458179. eCollection 2024.

Authors

Faizo Kasule^{1

2

3}, Boris M E Alladassi², Charles John Aru³, Scovia Adikini³, Moses Biruma³, Michael Adrogu Ugen³, Ronald Kakeeto³, Williams Esuma^{3

4}

Affiliations

¹ Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA, United States.
² Department of Agronomy, Iowa State University, Ames, IA, United States.
³ National Semi-Arid Resources Research Institute (NaSARRI), Soroti, Uganda.
⁴ National Crops Resources Research Institute (NaCRRI), Kampala, Uganda.

Abstract

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.

Keywords: DArT-seq; GWAS; SNPs; genetic variation; linkage disequilibrium; sorghum.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study is made possible by the generous support of the American people through the United States Agency of International Development (USAID). The contents are the responsibility of the authors and do not necessarily reflect the views of USAID or the United States Government. Program activities of the Centre of Innovation for Finger Millet and Sorghum (CIFMS) under the Innovation Lab for Crop Improvement (ILCI) are funded by the United States Agency for International Development (USAID) under Cooperative Agreement No. 7200AA-19LE-00005. Genotyping funds were sourced from the government of Uganda through the National Agricultural Research Organization (NARO), Uganda. NARO Competitive Grants Scheme (CGS) and CIFMS provided the phenotyping funds.