Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers

文献类型： 外文期刊

第一作者： Zhang, Hua

作者： Zhang, Hua;Li, Lujiang;Lan, Hai;Ren, Zhiyong;Liu, Dan;Wu, Ling;Liu, Hailan;Pan, Guangtang;Gao, Shibin;Zhang, Xiao;Li, Lujiang;Lan, Hai;Ren, Zhiyong;Liu, Dan;Wu, Ling;Liu, Hailan;Pan, Guangtang;Gao, Shibin;Jaqueth, Jennifer;Li, Bailin;Zhang, Hua

作者机构：

关键词： Maize;Southwest China;SNP array;Population structure;Diversity;Tropical group;Temperate group;Breeding

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs). Results: With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [ Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5-3 Mb) than that in the entire panel (0.5-0.75 Mb) and the Tropical group (0.25-0.5 Mb). A large region at 30-120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines. Conclusions: For the panel covered most of widely used inbred lines in Southwest China, this work representatively not only illustrates the foundation and evolution trend of maize breeding resource as a theoretical reference for the improvement of heterosis, but also provides plenty of information for genetic researches such as genome-wide association study and marker-assisted selection in the future.

分类号：

  • 相关文献

[1]Diversity Research of Pleurotus Pulmonarius Based on Pheromone Receptor Gene from Yunnan Province China. Zhong, G. Y.,Zhou, D. Q.,Zhong, G. Y.,Chen, W. M.,Li, S. H.,Chai, H. M.,Zhao, Y. C.. 2015

[2]The characterization of goat genetic diversity: Towards a genomic approach. Ajmone-Marsan, P.,Colli, L.,Negrini, R.,Ajmone-Marsan, P.,Colli, L.,Han, J. L.,Han, J. L.,Achilli, A.,Lancioni, H.,Joost, S.,Crepaldi, P.,Pilla, F.,Stella, A.,Taberlet, P.,Boettcher, P.,Negrini, R.,Lenstra, J. A..

[3]Karyological diversity of wild Rosa in Yunnan, southwestern China. Jian, Hong Ying,Zhang, Ting,Wang, Qi Gang,Li, Shu Bin,Zhang, Hao,Tang, Kai Xue.

[4]Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers. Wang, Hui,Xie, Lianhui,Wang, Hui,Khera, Pawan,Culbreath, Albert K.,Wang, Hui,Guo, Baozhu,Wang, Hui,Yuan, Mei,Khera, Pawan,Varshney, Rajeev K.,Huang, Bingyan,Zhang, Xinyou,Katam, Ramesh,Zhuang, Weijian,Harris-Shultz, Karen,Moore, Kim M.. 2016

[5]Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation. Gao, LH.

[6]Molecular variation among Chinese and global germplasm in spring faba bean areas. Redden, R.,Zong, X.,Ren, J.,Guan, J.,Wang, S.,Zong, X.,Liu, Q.,Paull, J. G..

[7]DissectingthemaizedirectandindirectdefenseresponseagainstAsianCornBorer. 汪海,李圣彦,查象敏,朱莉,黄大昉,郎志宏. 2015

[8]Impact of recent breeding history on the competitiveness of Chinese maize hybrids. Zhai, Lichao,Xie, Ruizhi,Liu, Guangzhou,Fan, Panpan,Li, Shaokun,Zhai, Lichao,Wang, Pu.

[9]Analysis of Genetic Diversity and Population Structure of Maize Landraces from the South Maize Region of China. Liu Zhi-zhai,Guo Rong-hua,Wang Rong-huan,Shi Yun-su,Song Yan-chun,Wang Tian-yu,Li Yu,Liu Zhi-zhai,Cai Yi-lin,Guo Rong-hua,Cao Mo-ju,Zhao Jiu-ran,Wang Feng-ge,Wang Rong-huan. 2010

[10]Genetic diversity and structure of the core collection for maize inbred lines in China. Yu, Y.,Wang, R.,Shi, Y.,Song, Y.,Wang, T.,Li, Y.. 2007

[11]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

[12]POPULATION STRUCTURE AND GENETIC DIVERSITY OF MAIZE LANDRACES FROM THE SOUTHWEST MAIZE REGION OF CHINA. Liu, Z. Z.,Guo, R. H.,Wang, R. H.,Shi, Y. S.,Song, Y. C.,Wang, T. Y.,Li, Y.,Liu, Z. Z.,Cai, Y. L.,Guo, R. H.,Cao, M. J.,Zhao, J. R.,Wang, F. G.,Wang, R. H.. 2009

[13]Construction of Agropyron Gaertn. genetic linkage maps using a wheat 660K SNP array reveals a homoeologous relationship with the wheat genome. Zhou, Shenghui,Zhang, Jinpeng,Liu, Weihua,Lu, Yuqing,Yang, Xinming,Li, Xiuquan,Jia, Jizeng,Liu, Xu,Li, Lihui,Che, Yonghe. 2018

[14]Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio). Xu, Jian,Zhao, Zixia,Li, Jiongtang,Jiang, Yanliang,Zhang, Yan,Li, Qiang,Zhu, Yuanyuan,Liu, Yuanyuan,Xu, Peng,Sun, Xiaowen,Zhang, Xiaofeng,Zheng, Xianhu,Kuang, Youyi,Sun, Xiaowen,Feng, Jianxin,Li, Chuangju,Yu, Juhua,Xu, Peng. 2014

[15]Genetic variability assessed by microsatellites in the breeding populations of the shrimp Penaeus (Fenneropenaeus) chinensis in China. Zhang, Tianshi,Kong, Jie,Wang, Weiji,Wang, Qingyin,Zhang, Tianshi.

[16]Isolation, characterization and phylogenetic analysis of the resistance gene analogues (RGAs) in banana (Musa spp.). Pei, Xinwu,Li, Shengjun,Jiang, Ying,Zhang, Yongqiang,Wang, Zhixing,Jia, Shirong.

[17]Mushroom tumor: a new disease on Flammulina velutipes caused by Ochrobactrum pseudogrignonense. Zhang, Xiaoping,Wu, Zhipeng,Peng, Weihong,He, Xiaolan,Wang, Bo,Gan, Bingcheng,Wu, Zhipeng,Peng, Weihong,He, Xiaolan,Wang, Bo,Gan, Bingcheng. 2016

[18]Acaricide resistance of Tetranychus cinnabarinus (Acari: Tetraychidae) from mulberry plantations in southwest China. Luo, Yan-Jie,Ding, Wei,Luo, Yan-Jie,Ni, Jing,Liu, Yong-Guang,Jiang, Xiu-Jun,Chai, Jian-Ping,Xie, Dao-Yan,Da, Ai-si,Huang, Ping,Li, Shao-xiang. 2013

[19]Simulation of Morphological Development of Soil Cracks in Yuanmou Dry-hot Valley Region, Southwest China. Xiong Donghong,Yan Dongchun,Long Yi,Xiong Donghong,Yan Dongchun,Long Yi,Lu Xiaoning,Han Jianning,Han Xueqin,Shi Liangtao. 2010

[20]Surface morphology of soil cracks in Yuanmou Dry-hot Valley Region, Southwest China. Xiong Donghong,Long Yi,Yan Dongchun,Xiong Donghong,Long Yi,Yan Dongchun,Lu Xiaoning,Ji Zhonghua,Fang Haidong. 2009

作者其他论文 更多>>

微信小程序