The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.
The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population.
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DOI：
10.1093/g3journal/jkab258
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发表时间：
2021-09-27
期刊：
影响因子：
--
通讯作者：
Kammenga JE
中科院分区：
文献类型：
--
作者：
Snoek BL;Sterken MG;Nijveen H;Volkers RJM;Riksen J;Rosenstiel PC;Schulenburg H;Kammenga JE
研究基因表达的遗传变异为揭示复杂性状背后的分子成分提供了一种强有力的方法。表达数量性状基因座（eQTL）研究已在几种不同的模型物种中进行，但大多数连锁研究都是基于两个亲本等位基因的遗传分离。最近，我们开发了一个由 200 个重组自交系 (mpRIL) 组成的多亲本分离群体，这些自交系源自线虫秀丽隐杆线虫的四种野生分离株（JU1511、JU1926、JU1931 和 JU1941）。我们使用 RNA-seq 来研究多个等位基因如何影响这些 mpRIL 中的基因表达。我们发现 1789 个基因在亲本系之间差异表达。在 mpRIL 中发现了 7896 个基因的越界，即超出任何亲本系的表达。对于表达 QTL 定位，几乎有 9000 个 SNP 可用。通过结合这些 SNP 和 mpRIL 的 RNA-seq 图谱，我们检测到了近 6800 个 eQTL。大多数反式 eQTL (63%) 共同位于六个新识别的反式带中。之前双亲等位基因 eQTL 实验中发现的反式 eQTL 与本研究显示出一定的重叠（17.5-46.8%），一方面凸显出一大群基因受到跨群体和条件的多态性调节因子的影响，另一方面表明 mpRIL 群体允许识别新的基因表达调控位点。总而言之，对我们的 mpRIL 群体的分析提供了对秀丽隐杆线虫复杂性状遗传学和 eQTL 的更深入的了解，并为进一步测试和开发用于检测多等位基因 eQTL 的先进统计模型和研究基因型-表型关系的系统遗传学提供了起点。
Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression quantitative trait locus (eQTL) studies have been performed in several different model species, yet most of these linkage studies have been based on the genetic segregation of two parental alleles. Recently, we developed a multiparental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931, and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7896 genes. For expression QTL mapping almost 9000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous two-parental allele eQTL experiments and this study showed some overlap (17.5–46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand, it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multiallelic eQTLs and systems genetics studying the genotype–phenotype relationship.
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影响因子：
4.5
作者：
Kammenga JE;Doroszuk A;Riksen JA;Hazendonk E;Spiridon L;Petrescu AJ;Tijsterman M;Plasterk RH;Bakker J
通讯作者：
Bakker J
影响因子：
11.6
作者：
Cubillos, Francisco A.;Stegle, Oliver;Loudet, Olivier
通讯作者：
Loudet, Olivier
影响因子：
7
作者：
Gao AW;Sterken MG;Uit de Bos J;van Creij J;Kamble R;Snoek BL;Kammenga JE;Houtkooper RH
通讯作者：
Houtkooper RH
影响因子：
64.8
作者：
Bendesky, Andres;Tsunozaki, Makoto;Rockman, Matthew V.;Kruglyak, Leonid;Bargmann, Cornelia I.
通讯作者：
Bargmann, Cornelia I.
影响因子：
14.9
作者：
Doroszuk A;Snoek LB;Fradin E;Riksen J;Kammenga J
通讯作者：
Kammenga J