Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species.

Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species ssp. . Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, () and . To understand the conserveness of and in wild rice relatives, we analyzed and sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional and , whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of and were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of and were selected after the speciation of . , and that two-step loss of function in and contributed to awnlessness in Asian cultivated rice.