Variations in () contribute to the diversity of the panicle trait in high-yielding rice varieties in northern China.

Rice is one of mankind's major food staples, and the erect panicle architecture in rice is an important morphological improvement. The () locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of remains narrow. In order to improve the genetic diversity of , we used a rice germplasm collection of 72 high yielding rice varieties to analyze the contribution of to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of . We further detected 7 haplotypes and found that the replacement of 637 bp by a 12 bp fragment could explain the erect panicle architecture in all 72 germplasms. An SNP (G/C) at the -1253 bp of the promoter region caused a core sequence shift (TGGGCC) of a site II transcriptional regulatory element. The association analysis showed that the SNP(G/C) largely affects the number of primary and secondary branches, and grain number per panicle. Our results provide novel insights into the function and genetic diversity of . The SNP (G/C) at the promoter region will contribute to the flexible application of in rice breeding.