Genome-wide association study of pre-indicative agronomic traits affecting malt quality in Ethiopian barley (Hordeum vulgare L.) germplasm

Background: Barley (<i>Hordeum vulgare</i> L.) is a diploid cereal crop and one of the major crops grown in Ethiopia, with a long history of domestication. It serves two primary purposes: as a staple food and as a raw material to produce alcohol. Barley germplasm resources can serve as sources of new alleles in breeding programs. This study aimed to evaluate the performance of diverse germplasm for primary malt quality indicators, agro-morphological and nutritional traits across diverse environments and to identify marker-trait associations with these traits using genome-wide studies (GWAS) among 260 barley germplasm. The experiment was conducted at four experimental sites, Holeta, Debre Markos, Bekoji, and Welkite Agricultural Research Centers using an Alpha Lattice Design. Nine agronomic and nutritional data were collected on Heading Date (HD), Flowering Date (FD), Maturity Date (MD), Plant Height (PH), Pedicle Length (PL), Grain Size (GS), Free Amino Nitrogen (FAN), Soluble Nitrogen (SN) and Moisture Content (MC).

Results: Among the 260 genotypes, 43% had straw-colored glumes, 33.4% had black, 15.7% had purple, and 7.6% had light-colored glumes. Additionally, 72.2% had two rows, 19.6% had six rows, and 6.1% had irregular rows. The narrow-sense heritability estimates are based on quantitative data, ranging from 0.52 to 0.97. Correlation analysis revealed that FAN have a strong positive correlation with SN (r = 0.91), HD has a negative correlation with MD (r² = -0.03), MC has a weak positive correlation with all traits (r² = 0.06–0.14), and FD has a moderate correlation with PL (r² = 0.43). Principal Component Analysis (PCA) identified three major components: PCA1 (39.13%), PCA2 (22.01%), and PCA3 (19.28%). The population were clustered into three k-means Cluster 1 (31 accessions s), Cluster 2 (107 accessions), and Cluster 3 (122 accessions). A total of > 50 Mb SNP density was generated across seven barley chromosomes. Linkage disequilibrium decay is 177.76 kb, with an r² value of 0.2. In total, 65 SNP markers were significantly associated with HD, FD, MD, PH, PL, GC, FAN, and SN. These include 2 SNPs for HD (5 H), 7 SNPs for FD (2 H, 5 H, 6 H, 7 H), 13 SNPs for MD (2 H, 3 H, 7 H), 3 SNPs for PH (2 H, 5 H), 3 SNPs for PL (5 H, 6 H),23 SNPs for GC(1 H, 2 H, 4 H, 5 H, 6 H and 7 H), 5 SNPs for FAN(1 H) and 7 SNPs for SN(1 H, 2 H, 4 H, 5 H and 7 H), with a P-value range of 3.0–5.8. The minor allele frequencies range from 0.24 to 0.52.

Conclusion: The identification of malt quality pre-indicative agronomic traits under natural conditions lays a foundation for malt barley improvement. To ensure industrial relevance, these traits and associated SNP markers must be validated under real-world processing conditions for their application in molecular breeding. This will drive precision breeding strategies, enhancing malt quality, market competitiveness, and industrial sustainability in Ethiopia.