A genomic map of climate adaptation in Mediterranean cattle breeds

Laurence Flori, Katayoun Moazami‐Goudarzi, Veronique Alary, Abdelillah Araba, Ismail Boujenane, Nadjet Boushaba, Francois Casabianca, Sara Casu, Roberta Ciampolini, Armelle D’Acier, Corinne Coquelle, Juan‐Vicente Delgado, Ahmed R. Elbeltagy, Georgia Hadjipavlou, Emmanuelle Jousselin, Vincenzo Landi, Anne Lauvie, Philippe Lecomte, Christina Ligda, Caroline Marinthe, Amparo Martinez, Salvatore Mastrangelo, Dalal Menni, Charles-Henri Moulin, Mona Abd El-Zaher Osman, Olivier Pineau, Baldassare Portolano, Clementina Rodellar, Nadhira Saidi‐Mehtar, Tiziana Sechi, Guilhem Sempere, Sophie Thevenon, Dimitrios Tsiokos, Denis Laloe, Mathieu Gautier. (1/3/2019). A genomic map of climate adaptation in Mediterranean cattle breeds. Molecular Ecology, 28 (5), pp. 1009-1029.

Abstract

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attrac‐ tive biological models to characterize the genetic basis of short‐term evolutionary response to climate pressure induced by their post‐domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome‐wide association analyses with covariables discriminating the dif‐ ferent Mediterranean climate subtypes. This provided insights into both the demo‐ graphic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate varia‐ tions highlighted several biological functions involved in Mediterranean climate adap‐ tation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV expo‐ sure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different popula‐ tions suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support con‐ servation of these populations.