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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

View ORCID ProfileYann Dorant, View ORCID ProfileHugo Cayuela, View ORCID ProfileKyle Wellband, View ORCID ProfileMartin Laporte, View ORCID ProfileQuentin Rougemont, View ORCID ProfileClaire Mérot, Eric Normandeau, Rémy Rochette, Louis Bernatchez
doi: https://doi.org/10.1101/2020.01.28.923490
Yann Dorant
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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  • ORCID record for Yann Dorant
  • For correspondence: yann.dorant.1@ulaval.ca
Hugo Cayuela
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Kyle Wellband
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Martin Laporte
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Quentin Rougemont
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Claire Mérot
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Eric Normandeau
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Rémy Rochette
Department of Biology, University of New Brunswick, P.O. Box 5050, Saint John, NB, Canada, E2L 4L5
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Louis Bernatchez
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada, G1V0A6
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Abstract

Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. Yet, our knowledge on genotypic variation and evolution is often limited to single nucleotide polymorphism (SNPs) and the role of CNVs has been overlooked in non-model species, partly due to their challenging identification until recently. Here, we document the usefulness of reduced-representation sequencing data (RAD-seq) to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs accounts for higher genetic differentiation than SNP markers. Contrary to SNPs for which no association was found, genetic-environment association revealed that 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal than SNPs. Our study provides the means to study CNVs in non-model species and underlines the importance to consider structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.

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Posted January 29, 2020.
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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
Yann Dorant, Hugo Cayuela, Kyle Wellband, Martin Laporte, Quentin Rougemont, Claire Mérot, Eric Normandeau, Rémy Rochette, Louis Bernatchez
bioRxiv 2020.01.28.923490; doi: https://doi.org/10.1101/2020.01.28.923490
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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
Yann Dorant, Hugo Cayuela, Kyle Wellband, Martin Laporte, Quentin Rougemont, Claire Mérot, Eric Normandeau, Rémy Rochette, Louis Bernatchez
bioRxiv 2020.01.28.923490; doi: https://doi.org/10.1101/2020.01.28.923490

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