Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing.
Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing.
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DOI：
10.1186/1471-2164-13-521
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发表时间：
2012-10-03
期刊：
影响因子：
4.4
通讯作者：
Seeb JE
中科院分区：
文献类型：
--
作者：
Everett MV;Miller MR;Seeb JE
减数分裂图谱是比较基因组学和关联作图研究的重要工具。下一代测序和通过测序进行基因分型正在加速SNP发现和新遗传工具的开发，包括许多物种的减数分裂图谱。目前，红鲑的遗传资源有限。我们开发的第一个密集的减数分裂图红鲑鱼使用的限制性位点相关的DNA（RAD标签）和SNP从现有的表达序列标签（EST）为基础的测定中发现的新的SNP的组合。我们在3，430个RAD标签中发现了推定的SNP并进行了基因分型。我们去除了旁系同源序列变体，留下1，672个SNP;将这些与53个基于EST的SNP基因型结合进行连锁图谱。该图谱包含29个雄性和雌性连锁群，与红鲑鱼预期的单倍体染色体数目一致。雌性图谱包含1，057个位点，跨度为4，896 cM，雄性图谱包含1，118个位点，跨度为4，220 cM。建立了基于RAD的虹鳟鱼地图和红鲑地图之间的虹鳟鱼和同线性保护区。使用RAD测序和基于EST的SNP分析，我们成功地产生了第一个高密度的红鲑鱼连锁图谱。
Meiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays. We discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established. Using RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.
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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：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
影响因子：
1.7
作者：
Alfaqih, M. A.;Phillips, R. B.;Thorgaard, G. H.
通讯作者：
Thorgaard, G. H.
影响因子：
7.7
作者：
Campbell, Nathan R.;Narum, Shawn R.
通讯作者：
Narum, Shawn R.