A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.
复制标题
DOI：
10.1186/1471-2164-14-137
复制
发表时间：
2013-02-28
期刊：
影响因子：
4.4
通讯作者：
Dean JF
中科院分区：
文献类型：
--
作者：
Howe GT;Yu J;Knaus B;Cronn R;Kolpak S;Dolan P;Lorenz WW;Dean JF
花旗松是世界上经济和生态上最重要的树种之一，也是最大的树木育种计划之一。虽然沿海和内陆品种的道格拉斯冷杉（vars。menziesii和glauca）原产于北美，沿海品种也广泛种植，用于欧洲，新西兰，澳大利亚和智利的木材生产。我们的主要目标是开发一个足够大的SNP资源，以促进道格拉斯冷杉育种计划的基因组选择。为了实现这一目标，我们开发了一个基于454的沿海花旗松参考转录组，注释和评估了参考的质量，确定了推定的SNP，然后使用Illumina Infinium基因分型平台验证了这些SNP的样本。我们从沿海花旗松的276万个454和桑格cDNA序列中组装了一个由25，002个同源群（独特的基因模型）和102，623个单基因组成的参考转录组。我们通过将454和桑格序列映射到参考序列，并通过映射来自多个种子来源、基因型和组织的Illumina cDNA序列的四个数据集，鉴定了278，979个独特的SNP。Illumina数据集代表沿海道格拉斯冷杉（6400和1341万读取），内部道格拉斯冷杉（8045万读取）和与内部道格拉斯冷杉（899万读取）相似的亚基马种群。我们使用Illumina Infinium SNP基因分型阵列在260棵树上测定了8067个SNP。在这些SNPs中，5847个（72.5%）被成功调用，并且是多态性的。基于我们的验证效率，我们的SNP数据库可能包含多达~ 200，000个真正的SNP，以及多达~ 69，000个SNP，这些SNP可以使用Infinium II阵列在~ 20，000个基因位点进行基因分型-比在树木育种计划中使用基因组选择所需的SNP更多。最终，这些基因组资源将增强花旗松的育种，并使我们能够更好地了解花旗松规模的遗传变异模式和对气候变化的潜在反应。
Douglas-fir (Pseudotsuga menziesii), one of the most economically and ecologically important tree species in the world, also has one of the largest tree breeding programs. Although the coastal and interior varieties of Douglas-fir (vars. menziesii and glauca) are native to North America, the coastal variety is also widely planted for timber production in Europe, New Zealand, Australia, and Chile. Our main goal was to develop a SNP resource large enough to facilitate genomic selection in Douglas-fir breeding programs. To accomplish this, we developed a 454-based reference transcriptome for coastal Douglas-fir, annotated and evaluated the quality of the reference, identified putative SNPs, and then validated a sample of those SNPs using the Illumina Infinium genotyping platform. We assembled a reference transcriptome consisting of 25,002 isogroups (unique gene models) and 102,623 singletons from 2.76 million 454 and Sanger cDNA sequences from coastal Douglas-fir. We identified 278,979 unique SNPs by mapping the 454 and Sanger sequences to the reference, and by mapping four datasets of Illumina cDNA sequences from multiple seed sources, genotypes, and tissues. The Illumina datasets represented coastal Douglas-fir (64.00 and 13.41 million reads), interior Douglas-fir (80.45 million reads), and a Yakima population similar to interior Douglas-fir (8.99 million reads). We assayed 8067 SNPs on 260 trees using an Illumina Infinium SNP genotyping array. Of these SNPs, 5847 (72.5%) were called successfully and were polymorphic. Based on our validation efficiency, our SNP database may contain as many as ~200,000 true SNPs, and as many as ~69,000 SNPs that could be genotyped at ~20,000 gene loci using an Infinium II array—more SNPs than are needed to use genomic selection in tree breeding programs. Ultimately, these genomic resources will enhance Douglas-fir breeding and allow us to better understand landscape-scale patterns of genetic variation and potential responses to climate change.
登录
查看更多内容
影响因子：
3.1
作者：
Hayes, Ben;Goddard, Mike
通讯作者：
Goddard, Mike
影响因子：
4.4
作者：
Fernández-Pozo N;Canales J;Guerrero-Fernández D;Villalobos DP;Díaz-Moreno SM;Bautista R;Flores-Monterroso A;Guevara MÁ;Perdiguero P;Collada C;Cervera MT;Soto A;Ordás R;Cantón FR;Avila C;Cánovas FM;Claros MG
通讯作者：
Claros MG
影响因子：
3.7
作者：
El-Kassaby YA;Cappa EP;Liewlaksaneeyanawin C;Klápště J;Lstibůrek M
通讯作者：
Lstibůrek M
影响因子：
3.3
作者：
Eckert, Andrew J.;van Heerwaarden, Joost;Neale, David. B.
通讯作者：
Neale, David. B.
影响因子：
5.3
作者：
Barakat A;DiLoreto DS;Zhang Y;Smith C;Baier K;Powell WA;Wheeler N;Sederoff R;Carlson JE
通讯作者：
Carlson JE