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Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica 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 dense 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 of...

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Autores principales: Zhao, Mingzhu, Sun, Jian, Xiao, Zhiqiu, Cheng, Fei, Xu, Hai, Tang, Liang, Chen, Wenfu, Xu, Zhengjin, Xu, Quan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Japanese Society of Breeding 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010314/
https://www.ncbi.nlm.nih.gov/pubmed/27795685
http://dx.doi.org/10.1270/jsbbs.16058
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author Zhao, Mingzhu
Sun, Jian
Xiao, Zhiqiu
Cheng, Fei
Xu, Hai
Tang, Liang
Chen, Wenfu
Xu, Zhengjin
Xu, Quan
author_facet Zhao, Mingzhu
Sun, Jian
Xiao, Zhiqiu
Cheng, Fei
Xu, Hai
Tang, Liang
Chen, Wenfu
Xu, Zhengjin
Xu, Quan
author_sort Zhao, Mingzhu
collection PubMed
description Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense 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 of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. 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 DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding.
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spelling pubmed-50103142016-10-28 Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China Zhao, Mingzhu Sun, Jian Xiao, Zhiqiu Cheng, Fei Xu, Hai Tang, Liang Chen, Wenfu Xu, Zhengjin Xu, Quan Breed Sci Research Paper Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense 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 of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. 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 DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding. Japanese Society of Breeding 2016-09 2016-07-27 /pmc/articles/PMC5010314/ /pubmed/27795685 http://dx.doi.org/10.1270/jsbbs.16058 Text en Copyright © 2016 by JAPANESE SOCIETY OF BREEDING http://creativecommons.org/licenses/by-nc-nd/3.0 This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Zhao, Mingzhu
Sun, Jian
Xiao, Zhiqiu
Cheng, Fei
Xu, Hai
Tang, Liang
Chen, Wenfu
Xu, Zhengjin
Xu, Quan
Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title_full Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title_fullStr Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title_full_unstemmed Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title_short Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China
title_sort variations in dense and erect panicle 1 (dep1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern china
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010314/
https://www.ncbi.nlm.nih.gov/pubmed/27795685
http://dx.doi.org/10.1270/jsbbs.16058
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