SNP-Based KASP Markers Reveal Genetic Diversity and Population Structure Among African Sorghum Breeding Lines and Hybrids

Abstract

Sorghum is a strategic food-security and livestock-feed crop in Africa, and molecular characterization of its germplasm underpins genetic diversity assessment and hybrid parent selection. This study evaluated 106 sorghum accessions (23 A-lines, 28 B-lines, 32 R-lines, and 23 hybrids) from ICRISAT and Seed Co gene banks using 79 single nucleotide polymorphism (SNP)-based Kompetitive Allele-Specific PCR (KASP) markers. Genetic diversity, population structure, cluster analysis, and analysis of molecular variance (AMOVA) were assessed to support heterotic grouping. Gene diversity ranged from 0.23 in R-lines to 0.32 in hybrids, and polymorphic information content from 0.19 to 0.26, indicating moderate marker discriminatory power. Population structure analysis identified an optimum of K = 3: Cluster 1 comprised paired A- and B-lines forming a putative maintainer pool, Cluster 2 was dominated by R-lines forming a divergent restorer pool, and Cluster 3 formed a second seed-parent subgroup. AMOVA confirmed highly significant differentiation (ΦST = 0.55; p < 0.001), with molecular variance partitioned among the three clusters (44.0%), among individuals within clusters (45.2%), and among breeding-line types (10.8%). These findings provide a genomic framework for assigning sorghum accessions to putative heterotic groups and accelerating hybrid parent selection for climate-resilient sorghum production.