Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep

Abstract

Herewith, we aimed to determine whether casein variants that are currently segregating in ovine populations existed before the domestication of sheep or, on the contrary, if their emergence is much more recent. To this end, we have retrieved whole genome sequences from Iranian and domestic sheep from Africa, Europe, South and East Asia and West Asia. Population structure analysis based on 55,352,935 single nucleotide polymorphisms (SNPs) revealed a clear separation between Iranian mouflons and domestic sheep. Moreover, we also observed a strong genetic differentiation between Iranian mouflons sampled in geographic areas close to Tehran and Tabriz. Based on sequence data, hundreds of SNPs mapping to the casein αS1 (CSN1S1, 248 SNPs), casein αS2 (CSN1S2, 268 SNPs), casein ß (CSN2, 146 SNPs) and casein κ (CSN3, 112 SNPs) genes were identified. Approximately 25 -63.02% of the casein variation was shared between Iranian mouflons and domestic sheep, and the four domestic sheep populations also shared 44.2 -57.4 % of the casein polymorphic sites.These findings suggest that an important fraction of the casein variation present in domestic sheep was already segregating in the mouflon prior to its domestication.Genomic studies performed in horses and dogs are consistent with this view, suggesting that much of the diversity that we currently detect in domestic animals comes from standing variation already segregating in their wild ancestors.

Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits

“…The individuals that showed the closest relationship in the phylogenetic classification belonged to the same species (Ovis dalli). The higher nucleotide diversity observed here in wild vs. domestic sheep has been previously described and can be explained as the consequence of bottlenecks experienced during the domestication of sheep [35,44]. The wild sheep were classified independently from the domestic sheep, considering both the variants identified across the whole genome and the variants included within the studied candidate genes, which is in agreement with the diversity study on the casein genes presented by Luigi-Sierra et al [44].…”

“…The higher nucleotide diversity observed here in wild vs. domestic sheep has been previously described and can be explained as the consequence of bottlenecks experienced during the domestication of sheep [35,44]. The wild sheep were classified independently from the domestic sheep, considering both the variants identified across the whole genome and the variants included within the studied candidate genes, which is in agreement with the diversity study on the casein genes presented by Luigi-Sierra et al [44]. However, when the phylogenetic tree was built only considering the variants found in the milk composition candidate genes analyzed here, the domestic sheep samples could not be classified within breeds.…”

“…Despite that, Naval-Sanchez et al [35] described a selective sweep located in the coding region of the DGAT1 gene that could play a role in adaptive changes during domestication or selection. On the other hand, considering that the domestic and the wild sheep samples analyzed here were clearly classified in different nodes based on the genetic variability detected in the considered candidate genes for milk composition, it could be suggested that variants in these genes could have played a role in adaptive changes during the domestication process, as previously suggested by Luigi-Sierra et al [44] in relation to the casein coding genes. Furthermore, the differences of nucleotide diversity between wild and domestic sheep detailed in this paper agreed with the higher nucleotide diversity previously reported for wild sheep compared with that of domestic sheep by other studies [35,44].…”

“…The frequency of these variants in each breed (Table S6) could be useful to select functional variants to include in the design of SNP-chips aiming for the increase in genomic selection efficiency when applied to dairy breeding programs (e.g., PAEP:c.500T>C, only found in Assaf and Churra domestic breeds). One of these novel variants (CSN3:c.410A>G) was only present in wild sheep, as previously detailed by Luigi-Sierra et al [44]. Additionally, a total of 26 QTLs related to milk compositional/functional traits (casein, fat, lactose, and protein percentage) and coagulation properties (curd firmness, curd firming time, and rennet coagulation time) have been identified in a 250 Kb region of these candidate genes in both Churra and Sarda sheep [8,16] (Table S7).…”

“…One important issue regarding the variant calling analyses reported here is that all the WGR datasets, those obtained from the public SRA repository and those generated by our research group, were processed following the same bioinformatic analysis workflow and were considered jointly for the variant calling analysis. This procedure has been used in previous studies analyzing WGR datasets [ 35 , 43 , 44 ] and has been proven to prevent biased results regarding the variant calling detection process.…”