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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1458179

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

Provisionally accepted
Faizo Kasule Faizo Kasule 1*Boris M. Alladassi Boris M. Alladassi 2Charles J. Aru Charles J. Aru 3Scovia Adikini Scovia Adikini 3Moses Biruma Moses Biruma 3Michael A. Ugen Michael A. Ugen 3Ronald Kakeeto Ronald Kakeeto 3Williams Esuma Williams Esuma 4
  • 1 Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA 50011, Iowa, United States
  • 2 Department of Agronomy, College of Agriculture and Life Sciences, Iowa State University, Ames, Iowa, United States
  • 3 National Agricultural Research Organization (NARO), National Semi-Arid Resources Research Institute, P.O. Box 56, Soroti, Uganda
  • 4 National Agricultural Research Organization (NARO), National Crops Resources Research Institute (NaCRRI), Namulonge, P.O. Box 7084, Kampala, Uganda

The final, formatted version of the article will be published soon.

    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. Here, we used a newly developed genomic resource of 7,156 single nucleotide polymorphism (SNP) markers to characterize the genetic diversity and population structure of a collection of 543 sorghum accessions actively used in breeding programs in Uganda. 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. For the first time, a 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 13 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, Genetic Variation, GWAS, Linkage Disequilibrium, snps, Sorghum

    Received: 02 Jul 2024; Accepted: 17 Sep 2024.

    Copyright: © 2024 Kasule, Alladassi, Aru, Adikini, Biruma, Ugen, Kakeeto and Esuma. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Faizo Kasule, Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA 50011, Iowa, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.