Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats.

Laure Denoyelle,Badr Benjelloun,Florian Alberto,Meidhi Khelifi,Frédéric Boyer,François Pompanon,Clément Gaffet,Pierre De Villemereuil

doi:10.3389/fgene.2021.745284

Abstract

The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (FST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

Highlights

The evolution and distribution of species is driven by the variation of their environment
In relation with temperature annual range, we found candidate genes involved in production, including milk production for CP, MYAMD, PTPRE, SASH1 and SLC9A9 (Hussein and Staufenbiel, 2012; Dong et al, 2015; Laodim et al, 2017; Shin et al, 2017; Xiang et al, 2017), mammary gland development for PPFIA2 (Mota et al, 2020) and morphology for TMTC2
TMTC2 and EDIL3 are involved in adaptation to high altitude in sheep and cattle (Ji Yang et al, 2016; Pierce et al, 2020), this later variable being correlated with BIO7 in Morocco

Summary

Introduction

The evolution and distribution of species is driven by the variation of their environment. The ability of a genotype to produce, under different conditions, different phenotypes that are best fitted to the environment involves non-genetic mechanisms by which favorable variations can be acquired and even sometimes transmitted. They consist in epigenetic variations, parental effects, ecological and cultural variations (Danchin et al, 2011). Most of the studies pointing out the role of molecular epigenetic mechanisms were performed in stress-controlled conditions on plant or animal models In this case, the effect of one varying parameter on the physiological or epigenetic responses of the organisms is assessed. The glyphosate herbicide injury on Arabidopsis thaliana (Kim et al, 2017), or the maternal diet in mice (Cooney et al, 2002) were shown to affect the methylome

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