Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits

Koning, Dirk-Jan de; McIntyre, Lauren

doi:10.1534/g3.117.042846

Cited by 18 publications

(13 citation statements)

References 28 publications

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“…The advantage of mpRIL populations to the classical two parental RIL populations is that mpRILs capture a larger part of natural genetic variants in more combinations and hence covers these variants better. This is supported by similar multi-parent RIL studies in A. thaliana populations derived from 19 different parental accessions 34 and many more MAGIC populations were developed for different species, including mice 35. In our mpRIL population the polymorphisms show more patterns of segregations due to SNP distribution patterns between the parental strains, making candidate/causal gene selections more efficient.…”

Section: Discussionsupporting

confidence: 70%

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A multi-parent recombinant inbred line population ofCaenorhabditis elegansenhances mapping resolution and identification of novel QTLs for complex life-history traits

Nijveen

et al. 2018

Preprint

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25 Local populations of the bacterivorous nematode Caenorhabditis elegans can be genetically 26 almost as diverse as global populations. To investigate the effect of local genetic variation on 27 heritable traits, we developed a new recombinant inbred line (RIL) population derived from 28 four wild isolates. The wild isolates were collected from two closely located sites in France: 29 Orsay and Santeuil. By crossing these four genetically diverse parental isolates a population 30 of 200 RILs was constructed. RNA-seq was used to obtain sequence polymorphisms 31 identifying almost 9000 SNPs variable between the four genotypes with an average spacing 32 of 11 kb, possibly doubling the mapping resolution relative to currently available RIL panels. 33The SNPs were used to construct a genetic map to facilitate QTL analysis. Life history traits, 34 such as lifespan, stress resistance, developmental speed and population growth were 35 measured in different environments. For most traits substantial variation was found, and 36 multiple QTLs could be detected, including novel QTLs not found in previous QTL analysis, 37 for example for lifespan or pathogen responses. This shows that recombining genetic 38 variation across C. elegans populations that are in geographical close proximity provides 39 ample variation for QTL mapping. Taken together, we show that RNA-seq can be used for 40 genotyping, that using more parents than the classical two parental genotypes to construct a 41 RIL population facilitates the detection of QTLs and that the use of wild isolates permits 42 analysis of local adaptation and life history trade-offs.43 44Determining how genotype-phenotype relationships are controlled is at the heart of genetics. 45Understanding how the relationships between traits, genotypes and environments are controlled is 46 also crucial for traits relevant to the evolved context of the species [1, 2]. The identification and 47 characterization of allelic variants associated with complex traits has been a major challenge in 48 plant and animal breeding as well as disease genetics. Many complex traits vary in a continuous 49 way across different genotypes of a species. It is this phenotypic variation that can be mapped to 50 the genome using quantitative trait locus (QTL) analysis. Standard QTL mapping for many 51 different species is based on recombinant inbred lines (RILs) derived from a cross between two 52 genetically and phenotypically divergent parents. One of the many species that has extensively 53 been used for exploring the genetics of complex traits is the bacterivorous nematode 54 Caenorhabditis elegans [3, 4]. 55Genetic diversity between C. elegans populations on a local scale can be almost as diverse 56 as on a global scale, with genetically distinct populations occurring within a few kilometers 57 distance [5-9] and it is likely that both local adaptation and local competition between genotypes 58 are critical for the species [1, 2, 10]. Most inbred mapping populations of C. elegans were derived 59 from two glo...

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Section: Discussionsupporting

confidence: 70%

“…The first of such populations was developed for Arabidopsis thaliana consisting of 527 RILs developed from 19 different parental accessions 34. Since then many more MAGIC populations have been developed for a range of species 35. Recently, a C. elegans multi-parental RIL population originating from 16 wild-types 32 was characterized 36.…”

Section: Introductionmentioning

confidence: 99%

A multi-parent recombinant inbred line population ofCaenorhabditis elegansenhances mapping resolution and identification of novel QTLs for complex life-history traits

Nijveen

et al. 2018

Preprint

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“…THERE has been a resurgence of interest in the mapping of quantitative trait loci (QTL) in experimental organisms, spurred in part by the use of gene expression phenotypes [eQTL mapping; see Albert and Kruglyak (2015)] to more rapidly identify the underlying genes, and by the development of multiparent populations (de Koning and McIntyre 2017), including heterogeneous stocks (Mott et al 2000; Mott and Flint 2002), MAGIC lines (Cavanagh et al 2008; Kover et al 2009), the Collaborative Cross (Churchill et al 2004), and Diversity Outbred mice (Churchill et al 2012; Svenson et al 2012).…”

mentioning

confidence: 99%

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

et al. 2019

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“…Here, we use a genetically highly variable laboratory population of pharaoh ant (Monomorium pharaonis) colonies that we created by systematically intercrossing eight initial parental lineages for nine generations (Walsh et al 2019). Such a genetically heterogeneous mapping population has proven powerful to elucidate the genetic architecture of a range of traits in rats, mice, and fruit flies (e.g., Hansen & Spuhler 1984;Mott et al 2000;Valdar et al 2006;King et al 2012;de Koning & McIntyre 2017). We first extract hydrocarbons from three groups of 15 workers (45 workers total) from three replicate sub-colonies of 48 distinct colony genotypes of known pedigree.…”

Section: Introductionmentioning

confidence: 99%

Ant cuticular hydrocarbons are heritable and associated with variation in colony productivity

Walsh

Pontieri

d’Ettorre

et al. 2019

Preprint

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In social insects, cuticular hydrocarbons function in nestmate recognition and also provide a waxy barrier against desiccation, but basic evolutionary genetic features, including the heritability of hydrocarbon profiles and how they are shaped by natural selection are largely unknown. We used a new pharaoh ant (Monomorium pharaonis) laboratory mapping population to estimate the heritability of individual cuticular hydrocarbons, genetic correlations between hydrocarbons, and fitness consequences of phenotypic variation in the hydrocarbons. Individual hydrocarbons had low to moderate estimated heritability, indicating that some compounds provide more information about genetic relatedness and can also better respond to natural selection. Strong genetic correlations between compounds are likely to constrain independent evolutionary trajectories, which is expected given that many hydrocarbons share biosynthetic pathways. Variation in cuticular hydrocarbons was associated with variation in colony productivity, with some hydrocarbons experiencing strong directional selection. Altogether, our study builds on our knowledge of the genetic architecture of the social insect hydrocarbon profile and demonstrates that hydrocarbon variation is shaped by natural selection.

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Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits

Cited by 18 publications

References 28 publications

A multi-parent recombinant inbred line population ofCaenorhabditis elegansenhances mapping resolution and identification of novel QTLs for complex life-history traits

A multi-parent recombinant inbred line population ofCaenorhabditis elegansenhances mapping resolution and identification of novel QTLs for complex life-history traits

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

Ant cuticular hydrocarbons are heritable and associated with variation in colony productivity

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