Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.
Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.
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批量分类RNA-Seq揭示了针对cat鱼肠败血症的抗病性抗病性的表达和位置候选基因和等位基因特异性表达。
DOI：
10.1186/1471-2164-14-929
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发表时间：
2013-12-30
期刊：
影响因子：
4.4
通讯作者：
Liu Z
中科院分区：
文献类型：
--
作者：
Wang R;Sun L;Bao L;Zhang J;Jiang Y;Yao J;Song L;Feng J;Liu S;Liu Z
RNA-seq的应用加速了许多物种基因表达谱和基因相关SNPs的鉴定。然而，对基因表达和SNP定位的综合研究一直缺乏。RNA-seq与散装分离分析（BSA）的耦合应该允许表达模式和相关snp与表型的相关性。在这项研究中，我们展示了使用散装分离RNA-seq （BSR-Seq）来分析与鲶鱼肠败血症（ESC）疾病抗性相关的差异表达基因和相关snp。在抗性和易感鱼之间共发现1255个差异表达基因。此外，4304个独特基因上的56419个snp被鉴定为易感鱼和抗性鱼之间的显著snp。通过对这些显著snp的详细分析，可以区分由遗传分离引起的显著snp和由等位基因特异性表达引起的显著snp。对显著snp的定位，以及对差异表达基因的分析，可以鉴定出对ESC疾病具有抗病能力的候选基因。本研究证明了BSR-Seq通过表达谱和显著相关snp的定位来鉴定参与ESC疾病抗性的基因。BSR-Seq适用于各种性能和生产性状的基因分析，无需大量投资开发大型基因分型平台，如SNP阵列。
The application of RNA-seq has accelerated gene expression profiling and identification of gene-associated SNPs in many species. However, the integrated studies of gene expression along with SNP mapping have been lacking. Coupling of RNA-seq with bulked segregant analysis (BSA) should allow correlation of expression patterns and associated SNPs with the phenotypes. In this study, we demonstrated the use of bulked segregant RNA-seq (BSR-Seq) for the analysis of differentially expressed genes and associated SNPs with disease resistance against enteric septicemia of catfish (ESC). A total of 1,255 differentially expressed genes were found between resistant and susceptible fish. In addition, 56,419 SNPs residing on 4,304 unique genes were identified as significant SNPs between susceptible and resistant fish. Detailed analysis of these significant SNPs allowed differentiation of significant SNPs caused by genetic segregation and those caused by allele-specific expression. Mapping of the significant SNPs, along with analysis of differentially expressed genes, allowed identification of candidate genes underlining disease resistance against ESC disease. This study demonstrated the use of BSR-Seq for the identification of genes involved in disease resistance against ESC through expression profiling and mapping of significantly associated SNPs. BSR-Seq is applicable to analysis of genes underlining various performance and production traits without significant investment in the development of large genotyping platforms such as SNP arrays.
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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：
--
作者：
Fisher, RA
通讯作者：
Fisher, RA
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
1.5
作者：
Cheema, Kuljit K.;Grewal, Navjit K.;Singh, Kuldeep
通讯作者：
Singh, Kuldeep
RNA测序揭示了鸡在性腺分化之前的性二态基因表达，并允许对W-染色体的全面注释。
影响因子：
12.3
作者：
Ayers KL;Davidson NM;Demiyah D;Roeszler KN;Grützner F;Sinclair AH;Oshlack A;Smith CA
通讯作者：
Smith CA