Local adaptations of Mediterranean sheep and goats through an integrative approach

Bruno Serranito,Pablo Vidal,Eric Rouvellac,Carole Moreno-Romieux,Marie Bal,Stephen J G Hall,Anne Da Silva,Marco Cavalazzi,François Pompanon,Dominique Taurisson-Mouret,Gwenola Tosser-Klopp,Bertrand Servin,Elena Ciani,Badr Benjelloun,Johannes A Lenstra

doi:10.1038/s41598-021-00682-z

Abstract

Small ruminants are suited to a wide variety of habitats and thus represent promising study models for identifying genes underlying adaptations. Here, we considered local Mediterranean breeds of goats (n = 17) and sheep (n = 25) from Italy, France and Spain. Based on historical archives, we selected the breeds potentially most linked to a territory and defined their original cradle (i.e., the geographical area in which the breed has emerged), including transhumant pastoral areas. We then used the programs PCAdapt and LFMM to identify signatures of artificial and environmental selection. Considering cradles instead of current GPS coordinates resulted in a greater number of signatures identified by the LFMM analysis. The results, combined with a systematic literature review, revealed a set of genes with potentially key adaptive roles in relation to the gradient of aridity and altitude. Some of these genes have been previously implicated in lipid metabolism (SUCLG2, BMP2), hypoxia stress/lung function (BMPR2), seasonal patterns (SOX2, DPH6) or neuronal function (TRPC4, TRPC6). Selection signatures involving the PCDH9 and KLH1 genes, as well as NBEA/NBEAL1, were identified in both species and thus could play an important adaptive role.

Highlights

Several genes involved in adaptation to thermal stress and hypoxia
We reasoned that (i) the inclusion of authentic local breeds in the analysis will limit the background noise caused by breeds for which the link to the environment is weak or has eroded, for instance by crossbreeding or migration; and (ii) targeting the geographical area in which populations have evolved rather than the present distribution will optimize the identification of adaptive genomic regions
Our study provides an approach for integrating ecological, historical and cultural approaches in the search for selection signatures in small ruminants, which as domestic animals are at the very interface of natural and anthropized environments

Summary

Introduction

Several genes involved in adaptation to thermal stress and hypoxia. Kim et al.[10], considering both local goats and sheep of hot and arid environment, have highlighted genes implicated in the adaptation to thermal stress. The area under consideration harbours contrasting environments, such as high altitude areas (Alps, Pyrenees, Corsica), coastal areas, wetlands and arid areas, with closely related sheep and goat breeds[11,12,13] All these features provide an ideal situation for the identification of adaptation signatures. The search for a selection signature may be optimized by considering the environmental conditions of the breed’s cradle, where the genomes have been shaped over time, rather than the current location of herds. The LFMM approach searches for significant associations with environmental factors while controlling for neutral population structure These approaches were coupled with a thorough analysis of the literature to identify the signatures including genes most likely related to environment adaptations. We attached particular importance to the selection signatures involving homologous genomic regions in sheep and goats

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Discussion

Conclusion