Contribution à l'étude génomique des histoires démographique et adaptative des bovins et ovins de l'Océan Indien

The Indian Ocean represents a central migration zone for bovine (Bos taurus) and ovine (Ovis aries) populations accompanying human populations between East Africa, the Middle East and Southeast Asia, but their genetic diversity as well as their demographic and adaptive histories remain poorly known. The main objective of the thesis was to study the demographic and adaptive histories of cattle and sheep in the Indian Ocean, based on medium and high density genotyping data, with particular attention to the breeds of the western part of the zone located on the island of Mayotte, in the Comoros (never before phenotypically and genetically characterized) and on the island of Madagascar. For this purpose, a first phenotypic characterization was conducted on the sheep and cattle populations of Mayotte, allowing to highlight their phenotypic heterogeneity and to contribute to the recognition of the Zebu breed of Mayotte as a local French breed. This phenotypic characterization revealed a malformation of the external ear in 20% of the studied sheep, which present reduced or totally atrophied ears (microtia). The study of SNP-HD data of current cattle from Mayotte and Madagascar by comparing them to those of a larger panel of breeds representative of the bovine genetic diversity of the world has allowed to highlight a great genetic proximity (predominantly indicine ancestry and weak African taurine ancestry) between these two breeds, having diverged in the 16th century, at the time of the arrival of the Europeans. Their common ancestral population is the result of a crossbreeding event involving an African zebu population (African taurine x zebu) and an Indian index population dating back to the 12th century. A sharp increase in the size of the estimated populations is observed between the 16th and 17th centuries and coincides with the expansion of the livestock trade to supply European ships in particular. The origin of the cattle populations of the western Indian Ocean islands reflects the complex history of human migration and trade in this area. The Mayotte sheep population, which is close to the African fat-tailed sheep, is genetically homogeneous and would have undergone two peaks of inbreeding in the first half of the 20th century and another later one about ten years ago. An association analysis allowed us to locate a candidate mutation responsible for the microtia phenotype in the vicinity of the HMX1 gene, which is associated with the same type of malformation in Awassi and Altay sheep, and Highland cattle. For each population, the search for selection signatures and functional annotation on candidate genes allowed us to determine the main biological functions impacted by natural and artificial selection. At the Indian Ocean scale, we completed the search for selection signatures in the genome of 17 cattle breeds and 9 sheep breeds of the coast (SNP50K data), by GEA analyses, which facilitate the identification of genetic variants associated with population environmental covariates. Functional annotation of candidate genes associated with 6 climatic covariates in both species identified key biological functions associated with the climate of the area. Of the regions under selection identified in both species, only two regions contain genes associated with a climate variable (mean annual precipitation). Taken together, these results highlight the genetic originality of the Indian Ocean cattle and sheep breeds and specify the chromosomal regions, genes and biological functions/pathways involved in the adaptation of these breeds to the specific environmental conditions of this geographical area.