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

Autor: Harm Nijveen, Philipp Dirksen, Mark G. Sterken, Rita J. M. Volkers, L. Basten Snoek, Bart P. Braeckman, Joost A. G. Riksen, Jan E. Kammenga, Hinrich Schulenburg, Simon C. Harvey, Philip Rosenstiel, Carola Petersen, Stastna Jj, Rania Nakad
Přispěvatelé: Sub Bioinformatics, Theoretical Biology and Bioinformatics
Jazyk: angličtina
Rok vydání: 2019
Předmět:
SELECTION
Multi-parent RILs
Physiology
Genetic Linkage
QTL
NATURAL VARIATION
Plant Science
0302 clinical medicine
Genetic map
Inbred strain
Structural Biology
Life History Traits
lcsh:QH301-705.5
Genetics
0303 health sciences
education.field_of_study
GENETIC-VARIATION
Chromosome Mapping
food and beverages
PE&RC
C. Elegans
GENOTYPE
C. elegans
General Agricultural and Biological Sciences
Natural variation
Biotechnology
Research Article
Genotype
Bioinformatics
Population
Quantitative Trait Loci
Single-nucleotide polymorphism
Quantitative trait locus
Biology
General Biochemistry
Genetics and Molecular Biology
03 medical and health sciences
Genetic variation
Bioinformatica
Animals
Life-history
education
Caenorhabditis elegans
Laboratorium voor Nematologie
Ecology
Evolution
Behavior and Systematics
030304 developmental biology
Local adaptation
ENVIRONMENT
Genetic diversity
Organisms
Genetically Modified
elegans
Biology and Life Sciences
Cell Biology
Quantitative genetics
POLYMORPHISM
EVOLUTION
lcsh:Biology (General)
LINKED SITES
EPS
Laboratory of Nematology
CAENORHABDITIS-ELEGANS
QUANTITATIVE GENETICS
030217 neurology & neurosurgery
Developmental Biology
Zdroj: BMC Biology, Vol 17, Iss 1, Pp 1-17 (2019)
BMC Biology, 17(24). BioMed Central
BMC Biology
BMC Biology, 17
BMC BIOLOGY
BMC Biology 17 (2019)
ISSN: 1741-7007
Popis: 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.
Databáze: OpenAIRE
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