The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions

Abstract

The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed's main purpose is to produce milk and meat, but is peculiar for its involvement in the "Batailles de Chèvres," a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed.

Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

“…Moreover, the selection signatures found in our study do not display classic hard sweep characteristics, which is to be expected for complex traits. This is in contrast to the findings with Valdostana goats in Italy ( Talenti et al, 2017 ). This may arise due to the very diverse nature of the populations and absence of hard and long selection signature regions observed within the populations at the 50K SNP marker density.…”

“…This may arise due to the very diverse nature of the populations and absence of hard and long selection signature regions observed within the populations at the 50K SNP marker density. Second, our study pooled genotypes from six different breeds and lending to picking out differences between the breeds, unlike in the study of Talenti et al (2017) , whose focus was on only one breed.…”

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

“…The authors reported that this increase in homozygosity would be consistent with selection for mutations affecting fat-tail size several thousand years following domestication. Therefore, although the existence of ROH islands has been attributed to several factors (recombination events, demography) [42], our results corroborate the hypothesis that regions of high-homozygosity may indeed harbor targets of positive selection, as also observed in previous studies [20,22,43].…”

“…Another method for detecting signatures of positive selection based on intra-population analysis is the identification of high-homozygosity regions [6]. Since ROHs are normally abundant in regions under positive selection, their accumulation at specific loci, or islands, has been used to identify genomic regions that reflect directional selection in cattle [19], sheep [20], horse [21] and goat [22]. We therefore checked if such regions of high-homozygosity overlapped with putative selection signatures in the sheep breeds considered in this study.…”

Genome-wide analysis of goat genetic diversity and production systems in Uganda

“…Moreover, the selection signatures found in our study do not display classic hard sweep characteristics, which is to be expected for complex traits. This is in contrast to the findings with Valdostana goats in Italy (Talenti et al, 2017), This may arise due to the very diverse nature of the populations and absence of hard and long selection signature regions observed within the populations at the 50K SNP marker density. Secondly, our study pooled genotypes from six different breeds and lending to picking out differences between the breeds, unlike in the study of Talenti and colleagues (Talenti et al, 2017), whose focus was on only one breed.…”