Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans

L.B. Snoek, R.J.M. Volkers, H. Nijveen, M.G. Sterken, J.A.G. Riksen, B. Braeckman, H.J.G. Schulenburg, J.E. Kammenga

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Abstract

The combination of recent advances in cost-effective RNA sequencing and a new freshly isolated C. elegans strains from the wild brings forth the next-generation of quantitative genetic approaches. We used RNA-sequencing to measure variation in gene expression and genotype in a panel of 200 recombinant inbred lines derived from a collaborative cross between four wild isolates: JU1511, JU1926, JU1931 and JU1941. The RNA-seq data provided information on two levels. Firstly, by extracting the SNP variation from the RNA-seq data we could create a genetic map. Secondly, by extracting the gene expression variation from the same RNA-seq data we could use expression QTL mapping to the find the regulatory loci causal for the variation in gene expression between the RILs. We found that the crossing design resulted in an increased number of recombination events in the RILs, compared to a standard two parental CB4856 and N2 cross. This increased number of recombination events, genetic markers and local association mapping due to four types of parental types of genetic variation resulted in an increased resolution of eQTLs. Moreover we obtained insights into the divergent regulatory loci and their targets between natural isolates of C. elegans. Here we present several features and promises of the new multi parental recombinant inbred line population.
Original languageEnglish
Title of host publicationProceedings of Evolutionary Biology of Caenorhabditis and other Nematodes
Pages77-77
Publication statusPublished - 2014
EventEvolutionary Biology of Caenorhabditis and other Nematodes, Cambridge, UK -
Duration: 14 Jun 201417 Jun 2014

Conference

ConferenceEvolutionary Biology of Caenorhabditis and other Nematodes, Cambridge, UK
Period14/06/1417/06/14

Fingerprint

Caenorhabditis elegans
inbred lines
sequence analysis
RNA
genomics
gene expression
loci
quantitative genetics
chromosome mapping
quantitative trait loci
genetic variation
genetic markers
genotype

Cite this

Snoek, L. B., Volkers, R. J. M., Nijveen, H., Sterken, M. G., Riksen, J. A. G., Braeckman, B., ... Kammenga, J. E. (2014). Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans. In Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes (pp. 77-77)
Snoek, L.B. ; Volkers, R.J.M. ; Nijveen, H. ; Sterken, M.G. ; Riksen, J.A.G. ; Braeckman, B. ; Schulenburg, H.J.G. ; Kammenga, J.E. / Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans. Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. 2014. pp. 77-77
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Snoek, LB, Volkers, RJM, Nijveen, H, Sterken, MG, Riksen, JAG, Braeckman, B, Schulenburg, HJG & Kammenga, JE 2014, Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans. in Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. pp. 77-77, Evolutionary Biology of Caenorhabditis and other Nematodes, Cambridge, UK, 14/06/14.

Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans. / Snoek, L.B.; Volkers, R.J.M.; Nijveen, H.; Sterken, M.G.; Riksen, J.A.G.; Braeckman, B.; Schulenburg, H.J.G.; Kammenga, J.E.

Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. 2014. p. 77-77.

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

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AB - The combination of recent advances in cost-effective RNA sequencing and a new freshly isolated C. elegans strains from the wild brings forth the next-generation of quantitative genetic approaches. We used RNA-sequencing to measure variation in gene expression and genotype in a panel of 200 recombinant inbred lines derived from a collaborative cross between four wild isolates: JU1511, JU1926, JU1931 and JU1941. The RNA-seq data provided information on two levels. Firstly, by extracting the SNP variation from the RNA-seq data we could create a genetic map. Secondly, by extracting the gene expression variation from the same RNA-seq data we could use expression QTL mapping to the find the regulatory loci causal for the variation in gene expression between the RILs. We found that the crossing design resulted in an increased number of recombination events in the RILs, compared to a standard two parental CB4856 and N2 cross. This increased number of recombination events, genetic markers and local association mapping due to four types of parental types of genetic variation resulted in an increased resolution of eQTLs. Moreover we obtained insights into the divergent regulatory loci and their targets between natural isolates of C. elegans. Here we present several features and promises of the new multi parental recombinant inbred line population.

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Snoek LB, Volkers RJM, Nijveen H, Sterken MG, Riksen JAG, Braeckman B et al. Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans. In Proceedings of Evolutionary Biology of Caenorhabditis and other Nematodes. 2014. p. 77-77