Multi-locus genome-wide association mapping reveals loci underlying malt quality traits in heterogeneous Ethiopian barley (Hordeum vulgare L.) germplasm

Barley (<i>Hordeum vulgare</i> L.) is widely cultivated for animal feed, human consumption, and most notably, for malting. Malt quality is determined by both genetic and environmental factors, and its improvement requires a clear understanding of the genomic regions controlling related traits. This study aimed to investigate the genetic basis of malt quality traits in Ethiopian barley genotypes using multi-locus genome-wide association studies (ML-GWAS). A barley panel of 260 were evaluated for malt quality traits across four sites in Ethiopia. ML- GWAS were performed on five traits related to malt quality using the information on Illumina 50 K iSelect single nucleotide polymorphisms (SNPs). Six different models were used for the ML-GWAS analysis. Significant variation in malt quality traits was observed across the studied genotypes. Extract Content (EC) ranged from 81.66% to 60.00%, while Protein Content (PC) varied between 17.63% and 9.03%. These traits exhibited moderate to high narrow-sense heritability, ranging from 72% for EC to 69% for GS, indicating strong genetic control and promising potential for selection in breeding programs. The coefficient of variation (CV) for all traits ranged from 5.37% to 32.63%. K-means clustering grouped the association panel into 5 distinct clusters. The principal component analysis (PCA) covers 76.1% variation. The genotypes B115.1, B248, B248 and B31.2 are the best overall performance across malt quality traits. The relative importance of the trait is BGC > EC > PC > GS. ML-GWAS identified 19 significant QTNs associated with malt quality traits. The Significant QTNs exhibited LOD scores ranging from 3.06 to 5.36 and r² values between 6.98% and 25.35%, and minor allele frequencies (MAF) from 0.054 to 0.465. The highest number of significant associations was detected on chromosomes 4 H, 6 H, and 7 H. The identified QTNs represent promising molecular markers for improving malt quality through marker-assisted selection, providing valuable tools for developing superior malting barley cultivars in Ethiopia. Further functional validation of these loci will contribute to a deeper understanding of the genetic architecture underlying malt quality traits in Ethiopian barley.