The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Abstract

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

“…In this work, we used the same Italian Goat Consortium2 (IGC2) dataset as described in Cortellari et al [ 5 ]. Among the 34 populations present in that dataset, we decided to exclude the Bezoar, which in the previous work was used as an outgroup, the Maltese × Sarda crosses and the two Montecristo populations due to their unique history of isolation (feral) or farming (mainland).…”

“…From this point of view, Italy provides a good model because it is characterized by a rich biodiversity in all domesticated species thanks to its varied history, environment, climate, and farming traditions [ 3 , 4 ]. Goats, in particular, represent one of the greatest expressions of Italian biodiversity with more than 30 autochthonous breeds and populations reared under very diverse climates and farming conditions, several of which are considered as low-input agricultural systems [ 5 ].…”

“…Central-southern Italy and the islands count the largest number of goat farms and heads [ 9 ]. In these regions, which are characterized by a hotter and dryer climate [ 5 ] than in Northern Italy, the traditional extensive or semi-extensive farms of autochthonous goat breeds prevail and are generally located in marginal mountainous areas [ 10 , 11 ]. The vertical transhumance was usually combined with a horizontal transhumance; for example, the shepherds transferred all their animals—cattle, sheep, goats, and shepherd dogs—in the mild Apulian plains during the winter and returned to the Abruzzo mountains in the summer [ 12 ].…”

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

“…In the analysis of a goat database of more than 1000 animals covering 33 Italian populations using landscape genomics methods and LFMM [213], identified many loci putatively associated with environmental variables, although there was no overlap in loci identified by each of the methods. Samβada identified 62 genes associated with temperature or precipitation; among these, RYR3 has been associated with mean temperature and ANK3 and BTRC with longitude [214]. The LFMM analysis identified four SNPs associated with Mean Diurnal Range and Mean Temperature.…”

Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping

“…Thus, the primary challenge today is to identify breeds that need to be conserved first. Decisions might be supported by the compilation of databases containing objective information about the genotypes of these breeds: their genetic risks, phylogenetic relationships, as well as knowledge of the socioeconomic processes that can affect the risks of these breeds [5,6]. SNP genotyping is widely recognized as the most appropriate tool due to the availability of commercial SNP arrays that give unified comparable data [7].…”