Genomic insights into the divergence between hulled and hulless oats

Common oat, one of the most important crops worldwide, comprises hulled and hulless types with substantial agronomic differences. However, their evolutionary history and the genomic basis of phenotypic variations remain unclear. Herein, we report a 10.83 Gb high-quality genome (contig N50 of 104.56 Mb) for hulless oat Pinyan6 and construct the structural variation (SV) landscape between hulled and hulless oats. Population genetic analysis of 431 global oat accessions (21 wild, 246 hulled, and 164 hulless) reveals their evolutionary history and genetic divergence. Integrating the SV data, we demonstrate the potential impact of SVs on population divergence and phenotypic variation between hulled and hulless oats. An SV-based genome-wide association study further identifies a highly differentiated locus and the AsMC1 gene, a candidate linked to differences in lemma lignin content between hulled and hulless oats. Our Pinyan6 genome and rich genetic variations provide important resources for functional genomics and molecular breeding of oat.