Dynamics of deleterious mutation and selection at seven nuclear genes during barley domestication and...

Understanding how barley domestication affects deleterious mutations is crucial for breeding and germplasm conservation. This study analyzed seven single-copy nuclear genes (Alcohol dehydrogenase 2 (ADH2), Alcohol dehydrogenase 3 (ADH3), Dehydrin9 (DHN9), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Phosphoenolpyruvate carboxylase (PEPC), Photoperiod response gene (PPD-H1), and Granule-bound starch synthase (WAXY)) in 179 wild, 185 domesticated, and 21 de-domesticated barley accessions. Results showed that wild barley has the highest genetic diversity and the most private haplotypes. Deleterious SNPs were identified, with fewer in domesticated and de-domesticated groups compared to wild. Deleterious mutation load decreased from wild to domesticated barley as nucleotide diversity decreased (R = 0.78; p < 0.05), suggesting that domestication bottlenecks may purge these mutations. In wild barley, Nonsynonymous-to-synonymous substitution rate (dN/dS) ratios were ∼ 1 or > 1, indicating neutral or weak positive selection. These findings highlight how domestication shapes deleterious mutation patterns and provide insights for breeding and germplasm management.