A genomic map of climate adaptation in Mediterranean cattle breeds

Abstract

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive 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 different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation 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 exposure, 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 populations 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 conservation of these populations.

Adaptive introgression from indicine cattle into white cattle breeds from Central Italy

“…Indeed, mitochondrial data suggest genetic proximity between central Italian and Podolian cattle 22 , and the CW-7 signal could be the consequence of gene-flow between indicine cattle and the cattle populations on the Podolian plateau, which subsequently spread towards southern Europe 86 . While the CW-18 signal identified in the Central Italian cattle breeds might result from a separate migration route (e.g., via a sea migration from the eastern Mediterranean region ~3,000 YA as suggested by mitochondrial analysis, or following the silk road route 2,000 years later 87,88 ), single admixture scenarios coupled with founder effects could also explain the obtained results. Further investigations with more extensive sampling of local cattle populations will therefore be required to firmly assess these scenarios.…”

Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

“…Therefore, this study represents the most complete and up-to-date dataset available for the indigenous Greek cattle and integrated into the most complete Minor Asia and European sample collection. Improving our knowledge of the genetic diversity within and among local breeds is an issue of crucial importance for implementing further conservation programs that are necessary for sustainable development and future animal farming in changing environments [34]. This could be particularly important for traditional unselected breeds that cover a geographical area close to the domestication center [32].…”

“…Since the indigenous breeds exhibit adaptive ability to their local environment and remarkable longevity, the genetic pool of unselected local breeds can represent a valuable source of genes [32]. However, with a few exceptions [33,34], little research has been carried out on the genetic diversity and genetic relationships of indigenous cattle from South East Europe with regard to Greece and Cyprus.…”

Evolution and domestication of the Bovini species

“…2019a, 2019b), the Mediterranean area (Flori et al . 2019), the Balkans (Simčič et al . 2015; Ramljak et al .…”