Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.
Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.
复制标题
DOI：
10.1111/pbi.12183
复制
发表时间：
2014-08
影响因子：
13.8
通讯作者：
Akhunov E
中科院分区：
文献类型：
--
作者：
Wang S;Wong D;Forrest K;Allen A;Chao S;Huang BE;Maccaferri M;Salvi S;Milner SG;Cattivelli L;Mastrangelo AM;Whan A;Stephen S;Barker G;Wieseke R;Plieske J;International Wheat Genome Sequencing Consortium;Lillemo M;Mather D;Appels R;Dolferus R;Brown-Guedira G;Korol A;Akhunova AR;Feuillet C;Salse J;Morgante M;Pozniak C;Luo MC;Dvorak J;Morell M;Dubcovsky J;Ganal M;Tuberosa R;Lawley C;Mikoulitch I;Cavanagh C;Edwards KJ;Hayden M;Akhunov E
高密度单核苷酸多态性（SNP）基因分型芯片是研究基因组多样性模式、推断群体中个体之间的祖先关系以及在作图实验中研究标记-性状关联的有力工具。我们开发了一个基因分型阵列，包括约90 000个基因相关的SNPs，并用它来表征异源六倍体和异源四倍体小麦群体的遗传变异。该阵列包括在不同地理来源的人群中代表的常见全基因组分布的SNP的显著部分。我们使用基于密度的空间聚类算法，使高通量基因型调用复杂的数据集获得的多倍体小麦。我们表明，这些无模型聚类算法提供了准确的基因型调用在存在多个集群，包括集群与低信号强度导致在目标SNP位点或基因缺失的显着序列分歧。检测低强度簇的测定可以提供对小麦群体中存在-不存在变异（PAV）分布的深入了解。共46 977个SNPs从小麦90 K阵列的遗传定位使用8个作图群体的组合。开发的阵列和聚类识别算法提供了一个机会，推断详细的单倍型结构的多倍体小麦，并将作为一个宝贵的资源，多样性研究和调查小麦性状变异的遗传基础。
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
登录
查看更多内容
影响因子：
13.8
作者：
Lai, Kaitao;Duran, Chris;Edwards, David
通讯作者：
Edwards, David
影响因子：
56.9
作者：
Periyannan, Sambasivam;Moore, John;Lagudah, Evans
通讯作者：
Lagudah, Evans
影响因子：
3
作者：
Berkman, Paul J.;Lai, Kaitao;Edwards, David
通讯作者：
Edwards, David
影响因子：
6.9
作者：
Maccaferri, Marco;Sanguineti, Maria Corinna;Tuberosa, Roberto
通讯作者：
Tuberosa, Roberto
影响因子：
30.8
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
通讯作者：
Ware, Doreen