Identifying genes associated with genetic control of color polymorphism in the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus 1758) using a comparative whole genome pool‐sequencing approach

Type Article
Acceptance Date 2022-08-02 IN PRESS
Language English
Author(s) Stenger Pierre-Louis1, Ky Chin-Long1, 2, Vidal Dupiol JeremieORCID2, Planes Serge3, Reisser CelineORCID1, 4
Affiliation(s) 1 : Ifremer, IRD, Institut Louis‐Malardé, Univ Polynésie française, EIO Taravao, Tahiti ,Polynésie Française France
2 : IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia Montpellier, France
3 : PSL Research University EPHE‐UPVD‐CNRS, USR 3278 CRIOBE, Labex Corail, Université de Perpignan Perpignan Cedex, France
4 : MARBEC, Univ Montpellier, CNRS, IFREMER, IRD Montpellier ,France
Source Evolutionary Applications (1752-4571) (Wiley) In Press
DOI 10.1111/eva.13464
Keyword(s) Pinctada margaritifera, Pooled Whole Genome Sequencing, color, pearl farming, pigmentation evolution, population genomics
Abstract

For hundreds of years, the color diversity of Mollusca shells has been a topic of interest for humanity. However, the genetic control underlying color expression is still poorly understood in mollusks. The pearl oyster Pinctada margaritifera is increasingly becoming a biological model to study this process due to its ability to produce a large range of colors. Previous breeding experiments demonstrated that color phenotypes were partly under genetic control, and while a few genes were found in comparative transcriptomics and epigenetic experiments, genetic variants associated to the phenotypes have not yet been investigated. Here, we used a pooled-sequencing approach on 172 individuals to investigate color-associated variants on three color phenotypes of economic interest for pearl farming, in three wild and one hatchery populations. While our results uncovered SNPs targeting pigment-related genes already identified in previous studies, such as PBGD, tyrosinases, GST, or FECH, we also identified new color-related genes occurring in the same pathways, like CYP4F8, CYP3A4 and CYP2R1. Moreover, we identified new genes involved in novel pathways unknown to be involved in shell coloration for P. margaritifera, like the carotenoid pathway, BCO1. These findings are essential to possibly implement future breeding programs focused on individual selection for specific color production in pearl oysters and improve the footprint of perliculture on Polynesian lagoon by producing less, but with a better quality.

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Author's final draft IN PRESS 60 1 MB Open access
Supplementary file S1A 13 MB Open access
Supplementary file S1B 13 MB Open access
Supplementary file S1C 14 MB Open access
Supplementary file S2 7 855 KB Open access
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Stenger Pierre-Louis, Ky Chin-Long, Vidal Dupiol Jeremie, Planes Serge, Reisser Celine Identifying genes associated with genetic control of color polymorphism in the pearl oyster Pinctada margaritifera var. cumingii (Linnaeus 1758) using a comparative whole genome pool‐sequencing approach. Evolutionary Applications IN PRESS. Publisher's official version : https://doi.org/10.1111/eva.13464 , Open Access version : https://archimer.ifremer.fr/doc/00787/89885/