Genome‐wide association study identifies consistent genomic loci for yield and nutritional quality in Ethiopian sorghum landraces

Abstract

Identifying genomic regions linked to yield and quality is crucial for sorghum (Sorghum bicolor L.) improvement, but limited studies on its genome and diversity hinder breeding efforts. This study aimed to identify phenotypic variance and common quantitative trait nucleotides (QTNs) associated with genomic regions linked with grain yield and quality traits. The experiment was conducted during the 2020 and 2021 growing seasons across three Ethiopian agroecological zones-wet intermediate (Jimma), dry lowland irrigated (Melkassa), and natural drought-prone lowland (Miesso)-using a diverse panel of 358 Ethiopian sorghum landraces. Grain yield reflected both genetic and environmental effects, while the other traits were mainly under genetic control. A multi-locus genome-wide association study (ML-GWAS) was conducted using 209,572 high-quality single-nucleotide polymorphism markers. A total of 27 stable QTNs were identified across six environments using multiple ML-GWAS models. Five QTNs were associated with grain yield, nine with protein content, seven with 1000-seed weight, and six with amylopectin. Two QTNs, S01_65245223 and S09_50940522, were notable in grain yield, with candidate genes encoding a universal stress protein (Sobic.001G363100) and an E3 ubiquitin ligase (Sobic.009G153100), involved in stress response and protein turnover. For protein content, S01_1332500 and S05_53371984 localized with genes encoding EMC2 (Sobic.001G014800) and HVA22-like storage proteins (Sobic.005G121200 and Sobic.005G121300), key for protein folding and accumulation. Note that 1000-seed weight, QTNs S03_3571908 and S01_73998261 were linked to a phospholipase A1 (Sobic.003G038000) and a peptidyl-prolyl isomerase/E3 ligase (Sobic.001G466700), supporting seed filling and growth regulation. For amylopectin, S04_62662803 and S08_53120256 corresponded to GBSSI/SSIIa (Sobic.004G284400) and APS reductase (Sobic.008G118900), central to starch biosynthesis and redox regulation. Multi-locus GWAS revealed stable QTNs for yield and grain quality in sorghum, validating known and novel loci as targets for breeding resilient, biofortified cultivars.