Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes.
Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes.
复制标题
DOI：
10.1186/s12870-014-0371-7
复制
发表时间：
2014-12-19
影响因子：
5.3
通讯作者：
Courtois B
中科院分区：
文献类型：
--
作者：
Phung NT;Mai CD;Mournet P;Frouin J;Droc G;Ta NK;Jouannic S;Lê LT;Do VN;Gantet P;Courtois B
作物全基因组关联研究（GWAS）的发展使得挖掘隐藏在基因库资源中的有趣等位基因成为可能。然而，迄今为止，在世界范围内进行的抽样研究中，只有一小部分特定国家的水稻遗传多样性得到了利用。本研究提出了一个小组的水稻品种从越南GWAS的目的的发展。该小组，最初由270加入，其特征在于简单的农艺性状（成熟度类，粒形和胚乳类型）通常用于分类水稻品种。我们首先使用多样性阵列技术（DArT）标记对面板进行基因分型。我们分析了面板结构，确定了两个亚面板对应的籼稻和粳稻亚种，并选择了182个非冗余的材料。然而，可用的DArT标记的数量（对于6444个克隆的初始文库为241个）对于GWAS目的来说太少。因此，我们通过测序使用基因分型来表征具有25，971个标记的182个加入物的组。鉴定了相同的籼稻和粳稻亚组。采用基于模型的方法，将籼稻亚组进一步分为6个群体（I1至I6）。粳稻亚组分化程度较高，可分为4个居群（J1-J 4），其中包括一个温带型（J2）。护照数据和表型性状被用来描述这些人群。有些群体完全由粘性类型（I3和J2）组成。一些高地品种似乎属于籼稻群体，这在世界上这一地区是罕见的。连锁不平衡衰减快，在籼稻子面板（R2低于0.2在101 kb）比在粳稻子面板（R2低于0.2在425 kb），可能是因为最强的分化的粳稻子面板。通过消除具有低于5%的次要等位基因频率的标记并插补缺失数据来构建适用于GWAS的矩阵。该矩阵包含21，814个标记。在开花时间进行GWAS以证明该面板的实用性。这一公开可用的小组构成了获得原始等位基因多样性的重要资源。它将用于根和穗性状的GWAS。本文的在线版本（doi：10.1186/s12870-014-0371-7）包含补充材料，可供授权用户使用。
The development of genome-wide association studies (GWAS) in crops has made it possible to mine interesting alleles hidden in gene bank resources. However, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. This study presents the development of a panel of rice varieties from Vietnam for GWAS purposes. The panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. We first genotyped the panel using Diversity Array Technology (DArT) markers. We analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. However, the number of usable DArT markers (241 for an initial library of 6444 clones) was too small for GWAS purposes. Therefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. The same indica and japonica subpanels were identified. The indica subpanel was further divided into six populations (I1 to I6) using a model-based approach. The japonica subpanel, which was more highly differentiated, was divided into 4 populations (J1 to J4), including a temperate type (J2). Passport data and phenotypic traits were used to characterize these populations. Some populations were exclusively composed of glutinous types (I3 and J2). Some of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. Linkage disequilibrium decayed faster in the indica subpanel (r2 below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. A matrix adapted for GWAS was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. This matrix contained 21,814 markers. A GWAS was conducted on time to flowering to prove the utility of this panel. This publicly available panel constitutes an important resource giving access to original allelic diversity. It will be used for GWAS on root and panicle traits. The online version of this article (doi:10.1186/s12870-014-0371-7) contains supplementary material, which is available to authorized users.
登录
查看更多内容
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：
3.7
作者：
Elshire RJ;Glaubitz JC;Sun Q;Poland JA;Kawamoto K;Buckler ES;Mitchell SE
通讯作者：
Mitchell SE
影响因子：
64.8
作者：
Huang X;Kurata N;Wei X;Wang ZX;Wang A;Zhao Q;Zhao Y;Liu K;Lu H;Li W;Guo Y;Lu Y;Zhou C;Fan D;Weng Q;Zhu C;Huang T;Zhang L;Wang Y;Feng L;Furuumi H;Kubo T;Miyabayashi T;Yuan X;Xu Q;Dong G;Zhan Q;Li C;Fujiyama A;Toyoda A;Lu T;Feng Q;Qian Q;Li J;Han B
通讯作者：
Han B
影响因子：
2
作者：
Fukuoka, S;Alpatyeva, NV;Nagamine, T
通讯作者：
Nagamine, T
影响因子：
7
作者：
Feltus, FA;Wan, J;Paterson, AH
通讯作者：
Paterson, AH