Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)

文献类型： 外文期刊

第一作者： Lu, Qing

作者： Lu, Qing;Niu, Xiaojun;Zhang, Mengchen;Wang, Caihong;Xu, Qun;Feng, Yue;Yang, Yaolong;Wang, Shan;Yuan, Xiaoping;Yu, Hanyong;Wang, Yiping;Wei, Xinghua;Lu, Qing;Chen, Xiaoping;Liang, Xuanqiang;Lu, Qing;Chen, Xiaoping;Liang, Xuanqiang

作者机构：

关键词： genome-wide association study;seed dormancy;selective sweeps;improvement footprints;rice (Oryza sativa L.)

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2018 年 8 卷

页码：

收录情况： SCI

摘要： Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding.

分类号：

  • 相关文献

[1]Genetic dissection of the seed dormancy trait in cultivated rice (Oryza sativa L.). Wan, JM,Jiang, L,Tang, JY,Wang, CM,Hou, MY,Jing, W,Zhang, L.

[2]Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mapping. Lu, Qing,Zhang, Mengchen,Niu, Xiaojun,Wang, Caihong,Xu, Qun,Feng, Yue,Wang, Shan,Yuan, Xiaoping,Yu, Hanyong,Wang, Yiping,Wei, Xinghua.

[3]Genetic variation and association mapping for 12 agronomic traits in indica rice. Lu, Qing,Zhang, Mengchen,Niu, Xiaojun,Wang, Shan,Xu, Qun,Feng, Yue,Wang, Caihong,Deng, Hongzhong,Yuan, Xiaoping,Yu, Hanyong,Wang, Yiping,Wei, Xinghua,Niu, Xiaojun. 2015

[4]Domestication footprints anchor genomic regions of agronomic importance in soybeans. Han, Yingpeng,Zhao, Xue,Zhao, Lin,Wang, Zhikun,Li, Wenbin,Liu, Dongyuan,Yang, Zhijiang,Zhou, Gang,Huang, Long,Zheng, Hongkun,Li, Yinghui,Qiu, Lijuan,Lightfoot, David A.,Zhang, Zhiwu.

[5]Microarray-based gene expression analysis of strong seed dormancy in rice cv. N22 and less dormant mutant derivatives. Wu, Tao,Yang, Chunyan,Ding, Baoxu,Feng, Zhiming,Wang, Qian,He, Jun,Jiang, Ling,Wan, Jianmin,Wan, Jianmin,Tong, Jianhua,Xiao, Langtao. 2016

[6]Identification of QTLs for seed dormancy in rice (Oryza sativa L.). Xie, Kun,Jiang, Ling,Lu, BingYue,Yang, ChunYan,Li, LinFang,Liu, Xi,Zhang, Long,Zhao, ZhiGang,Wan, JianMin,Wan, JianMin.

[7]Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice. Fang, Jun,Chai, Chenglin,Li, Chunlai,Tang, Jiuyou,Huang, Zejun,Guo, Xiaoli,Sun, Changhui,Liu, Min,Wang, Yiqin,Cheng, Zhukuan,Chu, Chengcai,Fang, Jun,Chai, Chenglin,Li, Chunlai,Tang, Jiuyou,Huang, Zejun,Guo, Xiaoli,Sun, Changhui,Liu, Min,Wang, Yiqin,Cheng, Zhukuan,Chu, Chengcai,Fang, Jun,Chai, Chenglin,Li, Chunlai,Tang, Jiuyou,Huang, Zejun,Guo, Xiaoli,Qian, Qian,Sun, Lei,Zhang, Yan,Lu, Qingtao,Lu, Congming,Han, Bin,Chen, Fan.

[8]Transcriptomics Analysis Identified Candidate Genes Colocalized with Seed Dormancy QTLs in Rice (Oryza sativa L.). Qin, Huaide,Xie, Kun,Jiang, Ling,Wan, Jianmin,Wu, Fuqing,Cheng, Zhijun,Guo, Xiuping,Zhang, Xin,Wang, Jie,Lei, Cailin,Wang, Jiulin,Mao, Long,Wan, Jianmin.

[9]Exogenous auxin regulates multi-metabolic network and embryo development, controlling seed secondary dormancy and germination in Nicotiana tabacum L.. Li, Zhenhua,Wang, Jianhua,Li, Zhenhua,Zhang, Jie,Zhao, Jiehong,Ren, Xueliang,Liu, Yiling,Fu, Junjie,Wang, Guoying. 2016

[10]Haplotype analysis of Viviparous-1 gene in CIMMYT elite bread wheat germplasm. Sun, Y. W.,Li, S. M.,Chen, X. M.,Xia, L. Q.,Jones, H. D.,Shewry, P. R.,Yang, Y.,Dreisigacker, S..

[11]DELAY OF GERMINATION1 (DOG1) regulates both seed dormancy and flowering time through microRNA pathways. Bradford, Kent J.,Wei, Shouhui.

[12]Variation of the OsGI intron and its phenotypic associations in Oryza rufipogon Griff. and Oryza sativa L.. Chen, Z.,Pei, X.,Jia, S.,Wang, F.,Yuan, Q.,Wu, H.,Peng, Y.. 2013

[13]Seed losses at harvest and seed persistence of oilseed rape (Brassica napus) in different cultural conditions in Chinese farming systems. Zhu, Y. M.,Ma, K. P.,Wei, W.,Mi, X. C.,Li, Y. D.,Colbach, N.. 2012

[14]Proteome changes associated with dormancy release of Dongxiang wild rice seeds. Xu, Heng-Heng,Liu, Shu-Jun,Wang, Wei-Qing,Song, Song-Quan,Song, Shun-Hua,Moller, Ian Max.

[15]A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy. Zheng, Jian,Chen, Fengying,Wang, Zhi,Cao, Hong,Li, Xiaoying,Liu, Yongxiu,Zheng, Jian,Wang, Zhi,Deng, Xin,Soppe, Wim J. J.,Li, Yong.

[16]A single cytosine deletion in the OsPLS1 gene encoding vacuolar-type H+-ATPase subunit A1 leads to premature leaf senescence and seed dormancy in rice. Yang, Xi,Gong, Pan,Li, Kunyu,Cheng, Fangmin,Pan, Gang,Huang, Fudeng.

[17]A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken. Luo, Chenglong,Qu, Hao,Ma, Jie,Wang, Jie,Shu, Dingming,Hu, Xiaoxiang,Li, Ning,Luo, Chenglong,Qu, Hao,Ma, Jie,Wang, Jie,Shu, Dingming. 2014

[18]Genome-wide association study (GWAS) of resistance to head smut in maize. Wang, Ming,Yan, Jianbing,Zhang, Xiaobo,Xiao, Yannong,Zheng, Yonglian,Zhao, Jiuran,Song, Wei. 2012

[19]Genome-wide association study of antibody response to Newcastle disease virus in chicken. Luo, Chenglong,Qu, Hao,Ma, Jie,Wang, Jie,Li, Chunyu,Yang, Chunfen,Shu, Dingming,Hu, Xiaoxiang,Li, Ning,Luo, Chenglong,Qu, Hao,Ma, Jie,Wang, Jie,Li, Chunyu,Yang, Chunfen,Hu, Xiaoxiang,Shu, Dingming. 2013

[20]Genome-Wide Association and Transcriptome Analyses Reveal Candidate Genes Underlying Yield-determining Traits in Brassica napus. Lu, Kun,Peng, Liu,Zhang, Chao,Lu, Junhua,Yang, Bo,Xiao, Zhongchun,Liang, Ying,Xu, Xingfu,Qu, Cunmin,Zhang, Kai,Liu, Liezhao,Li, Jiana,Peng, Liu,Zhang, Chao,Zhu, Qinlong,Fu, Minglian,Yuan, Xiaoyan. 2017

作者其他论文 更多>>

微信小程序