Development and mapping of SNP assays in allotetraploid cotton.
Development and mapping of SNP assays in allotetraploid cotton.
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DOI：
10.1007/s00122-011-1780-8
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发表时间：
2012-05
影响因子：
5.4
通讯作者：
Udall, Joshua A.
中科院分区：
文献类型：
--
作者：
Byers, Robert L.;Harker, David B.;Yourstone, Scott M.;Maughan, Peter J.;Udall, Joshua A.
棉花种质基础狭窄，基因组复杂，单核苷酸多态性（SNP）标记的发现困难。为了产生用于SNP发现的序列，我们对两个G. hirsutum和G.巴巴多斯岛从基因组简化实验中，将总共204万个基因组序列读数组装成具有508 bp的N50的重叠群，并分析SNP。先前生成的表达序列标签（EST）组装为SNP发现提供了额外的来源。采用高度保守的参数（每个SNP的最小覆盖率为8×，次要等位基因频率为20%），在G.棉和barbadense在基因组缩减组件中的表达。另外，在G. EST组装中的多毛物。KBioscience KASPar检测针对一部分特异性G.多毛类SNPs。利用Fluidigm EP 1系统，从704个非基因标记和348个基因标记中筛选出367个标记（267个非基因标记，100个基因标记）定位在分离的F2群体（阿卡拉Maxxa × TX 2094）中。A G.完全基于这些新的SNP标记构建了1，688 cM的陆地棉遗传连锁图谱。在基于基因的SNP中，我们能够使用二倍体物种序列数据鉴定每个SNP位于哪个基因组（“A”或“D”）内。由这些新发现的标记生成的遗传图谱正被用于定位棉花基因组内的定量的、经济上重要的区域。本文的在线版本（doi：10.1007/s 00122 -011-1780-8）包含补充材料，可供授权用户使用。
A narrow germplasm base and a complex allotetraploid genome have made the discovery of single nucleotide polymorphism (SNP) markers difficult in cotton (Gossypium hirsutum). To generate sequence for SNP discovery, we conducted a genome reduction experiment (EcoRI, BafI double digest, followed by adapter ligation, biotin–streptavidin purification, and agarose gel separation) on two accessions of G. hirsutum and two accessions of G. barbadense. From the genome reduction experiment, a total of 2.04 million genomic sequence reads were assembled into contigs with an N50 of 508 bp and analyzed for SNPs. A previously generated assembly of expressed sequence tags (ESTs) provided an additional source for SNP discovery. Using highly conservative parameters (minimum coverage of 8× at each SNP and 20% minor allele frequency), a total of 11,834 and 1,679 non-genic SNPs were identified between accessions of G. hirsutum and G. barbadense in genome reduction assemblies, respectively. An additional 4,327 genic SNPs were also identified between accessions of G. hirsutum in the EST assembly. KBioscience KASPar assays were designed for a portion of the intra-specific G. hirsutum SNPs. From 704 non-genic and 348 genic markers developed, a total of 367 (267 non-genic, 100 genic) mapped in a segregating F2 population (Acala Maxxa × TX2094) using the Fluidigm EP1 system. A G. hirsutum genetic linkage map of 1,688 cM was constructed based entirely on these new SNP markers. Of the genic-based SNPs, we were able to identify within which genome (‘A’ or ‘D’) each SNP resided using diploid species sequence data. Genetic maps generated by these newly identified markers are being used to locate quantitative, economically important regions within the cotton genome. The online version of this article (doi:10.1007/s00122-011-1780-8) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
7
作者：
Udall, JA;Swanson, JM;Wendel, JF
通讯作者：
Wendel, JF
影响因子：
5.4
作者：
Lu, H;Romero-Severson, J;Bernardo, R
通讯作者：
Bernardo, R
影响因子：
5.4
作者：
PERCY, RG;WENDEL, JF
通讯作者：
WENDEL, JF
通过454转录组测序发现SNP。
影响因子：
7.2
作者：
Barbazuk, W Brad;Emrich, Scott J;Chen, Hsin D;Li, Li;Schnable, Patrick S
通讯作者：
Schnable, Patrick S