title: Variations inDENSE AND ERECT PANICLE 1(DEP1) contribute to the diversity of the panicle trait in high-yieldingjaponicarice 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. Thedense and erect panicle 1(DEP1) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity ofDEP1remains narrow. In order to improve the genetic diversity ofDEP1, we used a rice germplasm collection of 72 high yieldingjaponicarice varieties to analyze the contribution ofDEP1to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment ofDEP1. 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 ofDEP1. The SNP (G/C) at the promoter region will contribute to the flexible application ofDEP1in rice breeding.
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Mingzhu
authors: M
authors: Zhao
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Jian
authors: J
authors: Sun
authors: Laboratory of Agricultural Resource and Environment, College of Land and Environmental Science of Shenyang Agricultural University , Shenyang, 110866 , China.
authors: Zhiqiu
authors: Z
authors: Xiao
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Fei
authors: F
authors: Cheng
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Hai
authors: H
authors: Xu
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Liang
authors: L
authors: Tang
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Wenfu
authors: W
authors: Chen
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture , Shenyang 110866 , China.
authors: Zhengjin
authors: Z
authors: Xu
authors: Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province/Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang 110866, China; College of Agronomy of Shenyang Agricultural University, Shenyang, 110866, China.
authors: Quan
authors: Q
authors: Xu
keywords: DEP1; genetic diversity; high-yield breeding; panicle architecture