Highly Polygenic Variation in Environmental Perception Determines Dauer Larvae Formation in Growing Populations of Caenorhabditis elegans

Green, James W. M.; Šťastná, Jana; Orbidans, Helen E.; Harvey, Simon C.

doi:10.1371/journal.pone.0112830

Cited by 20 publications

(21 citation statements)

References 46 publications

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“…Moreover, results from different types of mapping populations can be included. In this way the advantages of IL populations (30,54–56,103,114,115), RIL populations (28,50,92), multi-parental mapping panels (34, 111) and sets of wild-isolates for GWAS (33) can be combined. With this in mind, the next steps for WormQTL2 will be linking eQTL data to polymorphisms from massive sequencing projects of many different ecotypes (32, 33) and including eQTLs and SNPs obtained from RNA-seq experiments.…”

Section: Discussionmentioning

confidence: 99%

WormQTL2: an interactive platform for systems genetics inCaenorhabditis elegans

Snoek

Sterken

Hartanto

et al. 2019

Preprint

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18Quantitative genetics provides the tools for linking polymorphic loci (QTLs) to trait 19 variation. Linkage analysis of gene expression is an established and widely applied 20 method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL 21 detection facilitates the identification and understanding of the underlying molecular 22 components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here 23 we present WormQTL2 (www.bioinformatics.nl/WormQTL2/), a database and platform 24 for comparative investigations and meta-analyses of published (e)QTL datasets in the 25 model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 26 conditions as-well-as over 1000 traits from 32 studies and allows experimental results to 27 be compared, reused, and extended upon to guide further experiments and conduct 28 systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs 29 that could be linked to variation in other traits, detect gene-by-environment interactions 30 by comparing eQTLs under different conditions, or find correlations between QTL 31 profiles of classical traits and gene expression.32 100 (2,3,13,23,30,34,41,47,49,(53)(54)(55)(56)(57)(58)(59)61,76,(80)(81)(82)(83)(84)(85)(86)(87)(88)(89)(90) (Table 2). In this paper, we present WormQTL2 101 and showcase its use by presenting short research scenarios. 102 Results 103 104 eQTL studies in WormQTL2 105WormQTL2 is a browser-based interactive platform and database for investigating expression 106 and other Quantitative Trait Locus (QTL) studies conducted in C. elegans (Figure 1). It enables 107 access to the mapping data of six previously published eQTL studies (Table 1) (28,50,(76)(77)(78)(79). 108Together, these studies cover over 700 samples, including expression measurements of 109 approximately 20,000 different genes across different life stages and environmental conditions. 110The effect of genetic variation on gene expression is presented in 11 genome-wide sets of 111 eQTLs from three different RIL populations. The three populations consist of two different 112 CB4856 x N2 populations, recombinant inbred lines (RILs) (28) and recombinant inbred 113 advanced intercross lines (RIAILs) (91,92) and a mutation introgressed RIL population 114 resulting from a cross between a let-60 gain-of-function mutant in an N2 background, MT2124, 115 with CB4856 (11,50). For the Li et al. 2006, Viñuela & Snoek et al. 2010 and Li et al. 2010 116 Figure 1: WormQTL2 Homepage. On the top of the page the navigation bar can be found. This includes the WormQTL2 logo, which functions as a home button. It also includes a fast link to the Correlation and Locus overviews as well as links for help, data download, and visual examples. The search box is located in the centre, in which genes, phenotypes and GO terms can be entered. Shown in the blue middle square are the buttons for the investigations of single traits, correlating QTL profiles, QTLs at a specific locus, all eQTLs of an expe...

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Section: Discussionmentioning

confidence: 99%

WormQTL2: an interactive platform for systems genetics inCaenorhabditis elegans

Snoek

Sterken

Hartanto

et al. 2019

Preprint

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“…The nath-10 locus has been associated with several traits, including age at maturity [36, 37], an expression QTL trans -band [61], and dauer formation [58, 63]. It is difficult to assess the effect of the locus in general, as only one study reports the contribution to heritable variation (52%) [37].…”

Section: The Effects Of Natural Allelic Variation Is Obscured By Propmentioning

confidence: 99%

The laboratory domestication of Caenorhabditis elegans

Sterken¹,

Snoek²,

Kammenga³

et al. 2015

Trends in Genetics

185

186

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Model organisms are of great importance to understanding basic biology and to making advances in biomedical research. However, the influence of laboratory cultivation on these organisms is underappreciated, especially how that environment can affect research outcomes. Recent experiments led to insights into how the widely used laboratory reference strain of the nematode Caenorhabditis elegans compares to natural strains. Here, we describe potential selective pressures that led to fixation of laboratory-derived alleles for the genes npr-1, glb-5, and nath-10. These alleles influence a large number of traits, resulting in behaviors that affect experimental interpretations. Furthermore, strong phenotypic effects caused by these laboratory-derived alleles hinder the discovery of natural alleles. We highlight strategies to reduce the influences of laboratory-derived alleles and to harness the full power of C. elegans.

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“…An independent subculture from the same wild Bristol isolate was maintained in liquid axenic culture, and by comparing both strains, we now know of several mutations that appeared and were fixed in the N2 lineage, some of which appear adaptive in the agar plate environment. These mutations pleiotropically affect many traits, such as behavior, reproduction, susceptibility to pathogens, body size and entry into the dauer stage (where C. elegans undergo developmental arrest at the third larval stage) ( McGrath et al, 2009 , 2011 ; Duveau and Félix, 2012 ; Andersen et al, 2014 ; Green et al, 2014 ). Like other model organisms, C. elegans N2 has thus been modified by domestication.…”

Section: Introductionmentioning

confidence: 99%

C. elegans outside the Petri dish

Frézal

Félix

2015

eLife

385

367

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The roundworm Caenorhabditis elegans has risen to the status of a top model organism for biological research in the last fifty years. Among laboratory animals, this tiny nematode is one of the simplest and easiest organisms to handle. And its life outside the laboratory is beginning to be unveiled. Like other model organisms, C. elegans has a boom-and-bust lifestyle. It feasts on ephemeral bacterial blooms in decomposing fruits and stems. After resource depletion, its young larvae enter a migratory diapause stage, called the dauer. Organisms known to be associated with C. elegans include migration vectors (such as snails, slugs and isopods) and pathogens (such as microsporidia, fungi, bacteria and viruses). By deepening our understanding of the natural history of C. elegans, we establish a broader context and improved tools for studying its biology.DOI: http://dx.doi.org/10.7554/eLife.05849.001

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Highly Polygenic Variation in Environmental Perception Determines Dauer Larvae Formation in Growing Populations of Caenorhabditis elegans

Cited by 20 publications

References 46 publications

WormQTL2: an interactive platform for systems genetics inCaenorhabditis elegans

WormQTL2: an interactive platform for systems genetics inCaenorhabditis elegans

The laboratory domestication of Caenorhabditis elegans

C. elegans outside the Petri dish

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