Variations in <i>DENSE AND ERECT PANICLE 1</i> (<i>DEP1</i>) contribute to the diversity of the panicle trait in high-yielding <i>japonica</i> rice varieties in northern China

Abstract

Rice is one of mankind's major food staples, and the erect panicle architecture in rice is an important morphological improvement. The <i>dense and erect panicle 1</i> (<i>DEP1</i>) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of <i>DEP1</i> remains narrow. In order to improve the genetic diversity of <i>DEP1</i>, we used a rice germplasm collection of 72 high yielding <i>japonica</i> rice varieties to analyze the contribution of <i>DEP1</i> to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of <i>DEP1</i>. 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 <i>DEP1</i>. The SNP (G/C) at the promoter region will contribute to the flexible application of <i>DEP1</i> in rice breeding.