Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of tran...
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Frontiers Media S.A.
2020-11-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.501376/full |
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| author | Mark G. Sterken Roel P. J. Bevers Rita J. M. Volkers Joost A. G. Riksen Jan E. Kammenga Basten L. Snoek Basten L. Snoek |
| author_facet | Mark G. Sterken Roel P. J. Bevers Rita J. M. Volkers Joost A. G. Riksen Jan E. Kammenga Basten L. Snoek Basten L. Snoek |
| author_sort | Mark G. Sterken |
| collection | DOAJ |
| description | The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60–93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture. |
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| last_indexed | 2024-12-11T08:07:21Z |
| publishDate | 2020-11-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-dadcf3145dfa47cc827cf3a99c6276082022-12-22T01:14:58ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-11-011110.3389/fgene.2020.501376501376Dissecting the eQTL Micro-Architecture in Caenorhabditis elegansMark G. Sterken0Roel P. J. Bevers1Rita J. M. Volkers2Joost A. G. Riksen3Jan E. Kammenga4Basten L. Snoek5Basten L. Snoek6Laboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University & Research, Wageningen, NetherlandsTheoretical Biology & Bioinformatics, Utrecht University, Utrecht, NetherlandsThe study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60–93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.https://www.frontiersin.org/articles/10.3389/fgene.2020.501376/fullgenetic architectureeQTLCaenorhabditis elegansintrogression linerecombinant inbred line |
| spellingShingle | Mark G. Sterken Roel P. J. Bevers Rita J. M. Volkers Joost A. G. Riksen Jan E. Kammenga Basten L. Snoek Basten L. Snoek Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans Frontiers in Genetics genetic architecture eQTL Caenorhabditis elegans introgression line recombinant inbred line |
| title | Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans |
| title_full | Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans |
| title_fullStr | Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans |
| title_full_unstemmed | Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans |
| title_short | Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans |
| title_sort | dissecting the eqtl micro architecture in caenorhabditis elegans |
| topic | genetic architecture eQTL Caenorhabditis elegans introgression line recombinant inbred line |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.501376/full |
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