Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame

文献类型： 外文期刊

第一作者： Cui, Chengqi

作者： Cui, Chengqi;Mei, Hongxian;Liu, Yanyang;Zhang, Haiyang;Zheng, Yongzhan;Mei, Hongxian;Liu, Yanyang;Zhang, Haiyang;Zheng, Yongzhan;Mei, Hongxian;Liu, Yanyang;Zhang, Haiyang;Zheng, Yongzhan

作者机构：

关键词： Sesamum indicum L.;SNPs;genetic diversity;population structure;linkage disequilibrium

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： 2017 年 8 卷

页码：

收录情况： SCI

摘要： The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 x 10(-3), with averages of 1.0 x 10(-4), 2.7 x 10(-4), and 3.6 x 10(-4) obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to similar to 99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel.

分类号：

  • 相关文献

[1]Association Analysis in Rice: From Application to Utilization. Zhang, Peng,Zhong, Kaizhen,Tong, Hanhua,Shahid, Muhammad Qasim. 2016

[2]Association Analysis of the Amino Acid Contents in Rice. Zhao, Weiguo,Chung, Jong-Wook,Park, Yong-Jin,Zhao, Weiguo,Park, Eun-Jin,Chung, Ill-Min,Ahn, Joung-Kuk,Kim, Gwang-Ho,Zhao, Weiguo. 2009

[3]An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines (Retracted article. See vol. 28, pg. 135, 2011). Xie, Chuanxiao,Li, Mingshun,Li, Xinhai,Xiao, Muji,Hao, Zhuanfang,Zhang, Shihuang,Warburton, Marilyn,Zhao, Qi. 2008

[4]Genetic Diversity and Population Structure of Chinese Foxtail Millet [Setaria italica (L.) Beauv.] Landraces. Wang, Chunfang,Jia, Guanqing,Zhi, Hui,Niu, Zhengang,Chai, Yang,Lu, Ping,Diao, Xianmin,Wang, Chunfang,Zhao, Baohua,Wang, Chunfang. 2012

[5]Association mapping of agronomic traits on chromosome 2A of wheat. Yao, Ji,Liu, Lihua,Zheng, Yonglian,Yao, Ji,Wang, Lixin,Liu, Lihua,Zhao, Changping.

[6]Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population. Chen, Guangfeng,Zhang, Han,Deng, Zhiying,Tian, Jichun,Chen, Guangfeng,Li, Dongmei,Wang, Mingyou,Zhang, Han,Wu, Rugang.

[7]Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: Implications for domestication history and genome wide association studies. Xu, P.,Wu, X.,Wang, B.,Liu, Y.,Lu, Z.,Wang, S.,Li, G.,Luo, J.,Ehlers, J. D.,Close, T. J.,Roberts, P. A..

[8]Evaluation of the genetic diversity and genome-wide linkage disequilibrium of Chinese maize inbred lines. Wang, Ming,Zhang, Xiaobo,Zheng, Yonglian,Zhao, Jiuran,Song, Wei. 2011

[9]The dopamine D2 receptor gene polymorphisms associated with chicken broodiness. Xu, H. P.,Shen, X.,Zhou, M.,Luo, C. L.,Kang, L.,Liang, Y.,Zeng, H.,Nie, Q. H.,Zhang, D. X.,Zhang, X. Q.,Zhou, M.,Kang, L.. 2010

[10]Genetic diversity, linkage disequilibrium, and association mapping analyses of peach (Prunus persica) landraces in China. Cao, Ke,Wang, Lirong,Zhu, Gengrui,Fang, Weichao,Chen, Changwen,Luo, Jing. 2012

[11]Analysis of Genetic Diversity in Synthetic Wheat Assemblage (T. turgidumxAegilops tauschii; 2n=6x=42; AABBDD) for Winter Wheat Breeding. Hanif, Uzma,Kazi, Alvina Gul,Afzal, Fakiha,Khalid, Maria,Rasheed, Awais,Munir, Muhammad,Mujeeb-Kazi, Abdul.

[12]Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program. Yu, SB,Xu, WJ,Vijayakumar, CHM,Ali, J,Fu, BY,Xu, JL,Jiang, YZ,Marghirang, R,Domingo, J,Aquino, C,Virmani, SS,Li, ZK. 2003

[13]Characterization of SNPs in strawberry cultivars in China. Ge, A. J.,Dong, Q. H.,Han, J.,Liu, H.,Fang, J. G.,Li, X. D.,Zhao, M. Z.. 2013

[14]Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs. Yang, Xingping,Ren, Runsheng,Xu, Jinhua,Li, Pingfang,Zhang, Man,Liu, Guang,Yao, Xiefeng,Yang, Xingping,Ren, Runsheng,Xu, Jinhua,Li, Pingfang,Zhang, Man,Liu, Guang,Yao, Xiefeng,Ren, Runsheng,Ray, Rumiana,Kilian, Andrzej.

[15]Characterization of 40 single nucleotide polymorphism (SNP) via T (m)-shift assay in the mud crab (Scylla paramamosain). Feng, Nana,Ma, Hongyu,Ma, Chunyan,Xu, Zhen,Li, Shujuan,Jiang, Wei,Liu, Yuexing,Ma, Lingbo,Feng, Nana,Xu, Zhen,Li, Shujuan,Jiang, Wei,Liu, Yuexing.

[16]Association mapping of yield-related traits and SSR markers in wild soybean (Glycine sofa Sieb. and Zucc.). Hu, Zhenbin,Zhang, Dan,Zhang, Guozheng,Kan, Guizhen,Hong, Delin,Yu, Deyue,Hu, Zhenbin,Zhang, Dan. 2014

[17]Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers. Wang, T.,Wang, T.,Zou, Q. D.,Qi, S. Y.,Wang, X. F.,Wu, Y. Y.,Zhang, Y. M.,Zhang, Z. J.,Li, H. T.,Liu, N.. 2016

[18]Mitochondrial DNA reveals low population differentiation in elongate loach, Leptobotia elongata (Bleeker): implications for conservation. Zhou, Dinggang,Liu, Guangxun,Zhou, Jian. 2012

[19]Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers. Cai, Hongwei,Guan, Xuanli,Cai, Hongwei,Guan, Xuanli,Cai, Hongwei,Yuyama, Nana,Cai, Hongwei,Stewart, Alan,Ding, Chenglong,Xu, Nengxiang,Kiyoshi, Takako. 2017

[20]Genetic variation and population structure of the oriental fruit moth Grapholita molesta in Shanxi, a major pome fruits growing region in North China. Yang, Jing,Liu, Zhong-Fang,Fan, Ji-Qiao,Fan, Ren-Jun,Yang, Jing,Liu, Zhong-Fang,Fan, Ji-Qiao,Fan, Ren-Jun,Wu, Yu-Peng,Ma, Rui-Yan. 2016

作者其他论文 更多>>

微信小程序