Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans

Abstract Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased...

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Main Authors: Basten L. Snoek, Mark G. Sterken, Roel P. J. Bevers, Rita J. M. Volkers, Arjen van’t Hof, Rachel Brenchley, Joost A. G. Riksen, Andrew Cossins, Jan E. Kammenga
Format: Article
Language:English
Published: BMC 2017-06-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-017-3899-8
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spelling doaj-7ad4cdfd663a4ccf8f86917d5c4bd3142020-11-24T21:42:10ZengBMCBMC Genomics1471-21642017-06-0118111510.1186/s12864-017-3899-8Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegansBasten L. Snoek0Mark G. Sterken1Roel P. J. Bevers2Rita J. M. Volkers3Arjen van’t Hof4Rachel Brenchley5Joost A. G. Riksen6Andrew Cossins7Jan E. Kammenga8Laboratory of Nematology, Wageningen University and ResearchLaboratory of Nematology, Wageningen University and ResearchLaboratory of Nematology, Wageningen University and ResearchLaboratory of Nematology, Wageningen University and ResearchCentre for Genome research, Institute of Integrative Biology, Biosciences Building, University of LiverpoolCentre for Genome research, Institute of Integrative Biology, Biosciences Building, University of LiverpoolLaboratory of Nematology, Wageningen University and ResearchCentre for Genome research, Institute of Integrative Biology, Biosciences Building, University of LiverpoolLaboratory of Nematology, Wageningen University and ResearchAbstract Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. Results We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. Conclusions These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.http://link.springer.com/article/10.1186/s12864-017-3899-8Caenorhabditis elegansGenetical genomicseQTLHeat stressCryptic genetic variationTrans-band
collection DOAJ
language English
format Article
sources DOAJ
author Basten L. Snoek
Mark G. Sterken
Roel P. J. Bevers
Rita J. M. Volkers
Arjen van’t Hof
Rachel Brenchley
Joost A. G. Riksen
Andrew Cossins
Jan E. Kammenga
spellingShingle Basten L. Snoek
Mark G. Sterken
Roel P. J. Bevers
Rita J. M. Volkers
Arjen van’t Hof
Rachel Brenchley
Joost A. G. Riksen
Andrew Cossins
Jan E. Kammenga
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
BMC Genomics
Caenorhabditis elegans
Genetical genomics
eQTL
Heat stress
Cryptic genetic variation
Trans-band
author_facet Basten L. Snoek
Mark G. Sterken
Roel P. J. Bevers
Rita J. M. Volkers
Arjen van’t Hof
Rachel Brenchley
Joost A. G. Riksen
Andrew Cossins
Jan E. Kammenga
author_sort Basten L. Snoek
title Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
title_short Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
title_full Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
title_fullStr Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
title_full_unstemmed Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans
title_sort contribution of trans regulatory eqtl to cryptic genetic variation in c. elegans
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2017-06-01
description Abstract Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. Results We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. Conclusions These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.
topic Caenorhabditis elegans
Genetical genomics
eQTL
Heat stress
Cryptic genetic variation
Trans-band
url http://link.springer.com/article/10.1186/s12864-017-3899-8
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