Genetic diversity within economically important loci in European, Middle Eastern, and African sheep breeds: An insight into their development

Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

Single and combined effects of CSN1S1 and CSN2-casein genes on Awassi sheep milk quantity and quality

Background and Aim: Milk produced from Awassi sheep is of high nutritive value; its production is relatively low in Awassi sheep, so the genetic improvement programs targeted milk production and its components are of high importance, especially when using genes that have an important signal to milk traits. This study was aimed at assessing the influence of alpha S1 (CSN1S1) and beta-casein (CSN2) genes genotypes interaction on Awassi ewes milk productivity. Materials and Methods: A total number of 391 milk yield and its composition records (taken through five consecutive years, 2007-2011) of 167 ewes were utilized for this study. DNA samples were extracted from the ewe's blood samples, then the polymerase chain reaction products of alpha S1 (CSN1S1) and beta-casein (CSN2) genes were sequenced. The obtained sequences were analyzed; thereafter, the detected variants were tested for their possible association with milk traits. Results: The CSN1S1 and CSN2 variants allelic frequencies were 0.85 and 0.15, and 0.95 and 0.05, respectively. Lactose and solid not fat (SNF) % were associated with TC CSN1S1 genotypes. No association was found among CSN1S1 polymorphic genotypes with milk production, lactose, and SNF % were associated with TC CSN1S1 genotypes. Ewes of CSN2 AC genotype showed higher milk production traits, while no association was found between milk composition traits and CNS2 genotypes. Nevertheless, CSN1S1∗CSN2 interaction showed the highest SNF, fat percentages, and milk production. Conclusion: The substantial interaction effects between CSN1S1×CSN2 genes were significantly affected the amount of milk, fat, and SNF% produced. The detected variants should be included in the breeding programs of Awassi sheep that are designed for improving their milk quantity and quality.

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

We aimed to determine whether casein variants that are currently segregating in ovine populations existed before the domestication of sheep or, to 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 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 α_S1 (CSN1S1, 248 SNPs), casein α_S2 (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.

Association between the GHR, GHRHR, and IGF1 gene polymorphisms and milk yield and quality traits in Sarda sheep

The growth hormone receptor (GHR), the growth hormone releasing hormone receptor (GHRHR), and the insulin-like growth factor 1 (IGF1) genes are known to modulate growth, reproduction, and lactation traits in livestock. The aim of the current work was to investigate if the variation of the sheep GHR, GHRHR, and IGF1 genes is associated with milk yield and quality traits. Three hundred eighty dairy Sarda sheep were genotyped for 36 single nucleotide polymorphisms (SNP) mapping to these 3 loci, and records for milk yield and daily fat and protein yield, as well as for fat, protein, casein, lactose, and milk urea contents, pH, somatic cell score, logarithmic bacterial count, and milk energy were obtained. The linkage disequilibrium analysis was performed only for GHR, as both GHRHR and IGF1 had only 1 polymorphic SNP. Haplotype analysis revealed the existence of 7 haplotype blocks in GHR. Two haplotype blocks, including part of the intron 1 and the upstream region, were clearly separated from the remaining 5 blocks by SNP rs412986330, which may be a recombination hotspot. The latter 5 blocks were contiguous, spanning from intron 2 to exon 10. Statistical analysis revealed that the GHR polymorphism is significantly associated with milk traits for daily fat and protein yield and fat, milk urea, and lactose content. Moreover, variation in IGF1 was associated with milk protein and casein content. Data generated in this research provide new insights into the allelic effects of the ovine GHRHR, GHR, and IGF1 genes on milk production and quality traits, information that may be useful in gene-assisted selection programs.