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A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits
BACKGROUND: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417139/ https://www.ncbi.nlm.nih.gov/pubmed/30866929 http://dx.doi.org/10.1186/s12915-019-0642-8 |
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author | Snoek, Basten L. Volkers, Rita J. M. Nijveen, Harm Petersen, Carola Dirksen, Philipp Sterken, Mark G. Nakad, Rania Riksen, Joost A. G. Rosenstiel, Philip Stastna, Jana J. Braeckman, Bart P. Harvey, Simon C. Schulenburg, Hinrich Kammenga, Jan E. |
author_facet | Snoek, Basten L. Volkers, Rita J. M. Nijveen, Harm Petersen, Carola Dirksen, Philipp Sterken, Mark G. Nakad, Rania Riksen, Joost A. G. Rosenstiel, Philip Stastna, Jana J. Braeckman, Bart P. Harvey, Simon C. Schulenburg, Hinrich Kammenga, Jan E. |
author_sort | Snoek, Basten L. |
collection | PubMed |
description | BACKGROUND: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. RESULTS: To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. CONCLUSION: Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12915-019-0642-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6417139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64171392019-03-25 A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits Snoek, Basten L. Volkers, Rita J. M. Nijveen, Harm Petersen, Carola Dirksen, Philipp Sterken, Mark G. Nakad, Rania Riksen, Joost A. G. Rosenstiel, Philip Stastna, Jana J. Braeckman, Bart P. Harvey, Simon C. Schulenburg, Hinrich Kammenga, Jan E. BMC Biol Research Article BACKGROUND: The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. RESULTS: To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. CONCLUSION: Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12915-019-0642-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-12 /pmc/articles/PMC6417139/ /pubmed/30866929 http://dx.doi.org/10.1186/s12915-019-0642-8 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Snoek, Basten L. Volkers, Rita J. M. Nijveen, Harm Petersen, Carola Dirksen, Philipp Sterken, Mark G. Nakad, Rania Riksen, Joost A. G. Rosenstiel, Philip Stastna, Jana J. Braeckman, Bart P. Harvey, Simon C. Schulenburg, Hinrich Kammenga, Jan E. A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title | A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title_full | A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title_fullStr | A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title_full_unstemmed | A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title_short | A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits |
title_sort | multi-parent recombinant inbred line population of c. elegans allows identification of novel qtls for complex life history traits |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417139/ https://www.ncbi.nlm.nih.gov/pubmed/30866929 http://dx.doi.org/10.1186/s12915-019-0642-8 |
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