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A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits

(2019) BMC BIOLOGY. 17.
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Abstract
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 11kb, 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.
Keywords
Multi-parent RILs, C, elegans, QTL, Life-history, Natural variation, Genetic map, CAENORHABDITIS-ELEGANS, NATURAL VARIATION, GENETIC-VARIATION, QUANTITATIVE GENETICS, LINKED SITES, GENOTYPE, POLYMORPHISM, ENVIRONMENT, EVOLUTION, SELECTION

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Citation

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MLA
Snoek, Basten L et al. “A Multi-parent Recombinant Inbred Line Population of C. Elegans Allows Identification of Novel QTLs for Complex Life History Traits.” BMC BIOLOGY 17 (2019): n. pag. Print.
APA
Snoek, B. L., Volkers, R. J., Nijveen, H., Petersen, C., Dirksen, P., Sterken, M. G., Nakad, R., et al. (2019). A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits. BMC BIOLOGY, 17.
Chicago author-date
Snoek, Basten L, Rita JM Volkers, Harm Nijveen, Carola Petersen, Philipp Dirksen, Mark G Sterken, Rania Nakad, et al. 2019. “A Multi-parent Recombinant Inbred Line Population of C. Elegans Allows Identification of Novel QTLs for Complex Life History Traits.” Bmc Biology 17.
Chicago author-date (all authors)
Snoek, Basten L, Rita JM Volkers, Harm Nijveen, Carola Petersen, Philipp Dirksen, Mark G Sterken, Rania Nakad, Joost AG Riksen, Philip Rosenstiel, Jana J Stastna, Bart Braeckman, Simon C Harvey, Hinrich Schulenburg, and Jan E Kammenga. 2019. “A Multi-parent Recombinant Inbred Line Population of C. Elegans Allows Identification of Novel QTLs for Complex Life History Traits.” Bmc Biology 17.
Vancouver
1.
Snoek BL, Volkers RJ, Nijveen H, Petersen C, Dirksen P, Sterken MG, et al. A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits. BMC BIOLOGY. 2019;17.
IEEE
[1]
B. L. Snoek et al., “A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits,” BMC BIOLOGY, vol. 17, 2019.
@article{8617958,
  abstract     = {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 11kb, 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.},
  articleno    = {24},
  author       = {Snoek, Basten L and Volkers, Rita JM and Nijveen, Harm and Petersen, Carola and Dirksen, Philipp and Sterken, Mark G and Nakad, Rania and Riksen, Joost AG and Rosenstiel, Philip and Stastna, Jana J and Braeckman, Bart and Harvey, Simon C and Schulenburg, Hinrich and Kammenga, Jan E},
  issn         = {1741-7007},
  journal      = {BMC BIOLOGY},
  keywords     = {Multi-parent RILs,C,elegans,QTL,Life-history,Natural variation,Genetic map,CAENORHABDITIS-ELEGANS,NATURAL VARIATION,GENETIC-VARIATION,QUANTITATIVE GENETICS,LINKED SITES,GENOTYPE,POLYMORPHISM,ENVIRONMENT,EVOLUTION,SELECTION},
  language     = {eng},
  pages        = {17},
  title        = {A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits},
  url          = {http://dx.doi.org/10.1186/s12915-019-0642-8},
  volume       = {17},
  year         = {2019},
}

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