Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.
Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.
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利用全基因组SNP标记表征中国西南地区玉米育种质的群体结构和遗传多样性
DOI：
10.1186/s12864-016-3041-3
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发表时间：
2016-08-31
期刊：
影响因子：
4.4
通讯作者：
Gao S
中科院分区：
文献类型：
--
作者：
Zhang X;Zhang H;Li L;Lan H;Ren Z;Liu D;Wu L;Liu H;Jaqueth J;Li B;Pan G;Gao S
西南地区生态特征多样，玉米育种种质资源具有高度的复杂性。本研究利用含有56，110个单核苷酸多态性（SNPs）的玉米SNP 50微珠芯片，对西南地区362个重要自交系的群体结构、遗传多样性和连锁不平衡衰减距离进行了分析。关于种群结构，鉴定了两个（热带和温带）、三个（热带、硬茎和非硬茎）、四个[热带、源自现代美国杂交种的A组种质（PA）、源自现代美国杂交种的B组种质（PB）和Reid]和六个亚组（热带、PB、Reid、爱荷华州硬茎合成、PA和North）。随着K值的增加，温带组表现出明显的层次结构与进一步的亚组划分。对各类群的遗传多样性进行了估计，热带类群的遗传多样性高于温带类群。7个低遗传多样性和一个高遗传多样性的区域被集体确定在温带，热带群体，和整个面板。还评估了热带和温带群体之间等位基因频率显著变化的SNP。其中，位于2号染色体130 Mb处的区域表现出最高的遗传多样性，包括显著变异的SNPs数量和显著SNPs占总SNPs的比例。温带群体的连锁不平衡衰减距离（2.5-3 Mb）大于整个群体（0.5-0.75 Mb）和热带群体（0.25-0.5 Mb）。通过对中国西南地区代表性的热带品系S37与其30个最相似的衍生系的比较，认为7号染色体30-120 Mb处的一个大区域是在育种过程中保守的区域。由于该群体涵盖了我国西南地区大部分常用自交系，不仅为玉米育种资源的基础和进化趋势提供了理论参考，而且为今后的全基因组关联研究和分子标记辅助选择等遗传研究提供了丰富的信息。本文的在线版本（doi：10.1186/s12864-016-3041-3）包含补充材料，可供授权用户使用。
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). 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. 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. The online version of this article (doi:10.1186/s12864-016-3041-3) contains supplementary material, which is available to authorized users.
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影响因子：
5.4
作者：
Wang, Ronghuan;Yu, Yongtao;Li, Yu
通讯作者：
Li, Yu
影响因子：
5.4
作者：
Van Inghelandt, Delphine;Melchinger, Albrecht E.;Lebreton, Claude;Stich, Benjamin
通讯作者：
Stich, Benjamin
影响因子：
5.8
作者：
Bradbury, Peter J.;Zhang, Zhiwu;Buckler, Edward S.
通讯作者：
Buckler, Edward S.
影响因子：
12.3
作者：
Romay MC;Millard MJ;Glaubitz JC;Peiffer JA;Swarts KL;Casstevens TM;Elshire RJ;Acharya CB;Mitchell SE;Flint-Garcia SA;McMullen MD;Holland JB;Buckler ES;Gardner CA
通讯作者：
Gardner CA
影响因子：
30.8
作者：
Jiao, Yinping;Zhao, Hainan;Lai, Jinsheng
通讯作者：
Lai, Jinsheng