The causal deletions in the second exon of <Emphasis Type="Italic">An-3</Emphasis> closely associated with awn development and rice yield

Awn is one of important traits during rice domestication. To understand the development of rice awn and the roles it played in rice domestication, we preliminary mapped a major QTL An-3 for awn development using chromosome segment substitution line CSSL138 developed by introgressed genomic fragments of long-awned Guangxi common wild rice (GXCWR, Oryza rufipogon Griff.) into genetic background of short-awned indica cultivar 93–11. An-3 was then fine mapped to a 7-kb region of chromosome 8. An epidermal patterning factor-like protein gene was identified as the single candidate gene corresponding to this QTL. An-3 was showed to be an allele of RAE2 and GAD1, and negatively regulated 1000-grains weight, grain length, and length–width ratio. Comparing with the coding sequences of An-3 from CSSL138, a 2- and 4-bp frame-shift deletions in the second exon were identified in 93–11 and Nipponbare, respectively. Taken together, our results provide valuable natural variation in the alleles of An-3 between common wild rice and cultivated rice, which will be helpful in clarifying the mechanism of awn development and promoting the application of an-3 in genetic improvement of rice yield traits.