Abstract
Simple SummaryMost of the production of sheep’s milk is used in the manufacture of mature cheeses. The milk composition has a strong influence on the technological and organoleptic properties of dairy products. Several genetic polymorphisms have been related to variations of milk protein and milk fatty acid content. The use of whole genome resequencing (WGR) has encouraged the discovery of polymorphisms in the sheep genome. Exploiting information derived from a large number of sheep WGR datasets, this study aimed to evaluate the variability of 24 candidate genes involved in physiological pathways related to milk production. The genetic variants highlighted by this work have a potential influence on the function of the protein encoded by the candidate genes. The relevance of sheep milk composition on the cheese-making industry enhances the potential interest of the present study as the variants highlighted herein could be considered to increase the efficiency of breeding programs currently applied to dairy sheep populations. Further studies would be needed to understand the role of these genetic variants on milk production traits.Different studies have shown that polymorphisms in the sequence of genes coding for the milk proteins and milk fatty acids are associated with milk composition traits as well as with cheese-making traits. However, the lack of coincident results across sheep populations has prevented the use of this information in sheep breeding programs. The main objective of this study was to exploit the information derived from a total of 175 whole genome resequencing (WGR) datasets from 43 domestic sheep breeds and three wild sheep to evaluate the genetic diversity of 24 candidate genes for milk composition and identify genetic variants with a potential phenotypic effect. The functional annotation of the identified variants highlighted five single nucleotide polymorphisms (SNPs) predicted to have a high impact on the protein function and 42 missense SNPs with a putative deleterious effect. When comparing the allelic frequencies at these 47 polymorphisms with relevant functional effects between the genomes of Assaf and Churra sheep breeds, two missense deleterious variants were identified as potential markers associated to the milk composition differences found between the Churra and Assaf: XDH:92215727C>T and LALBA:137390760T>C. Future research is required to confirm the effect of the potential functionally relevant variants identified in the present study on milk composition and cheese-making traits.
Highlights
Selection for specialized production traits and adaptation to a wide range of environments has involved changes within the genome of modern sheep breeds
We analyzed whole genome resequencing (WGR) datasets of 43 phenotypically diverse domestic sheep breeds for comparison with 19 Asiatic Mouflon samples (O. orientalis) representing their wild ancestor and five wild sheep samples including three Ovis canadiensis and two Ovis dalli to assess the genetic diversity of the sheep genome regions harboring the list of selected candidate genes under study
This study exploited the large amount of information provided by WGR datasets from a worldwide sample of sheep breeds to present a deep evaluation on the genetic variability of a list of genes that, due to their known biological function, are considered candidates to explain phenotypic differences for milk composition traits in dairy sheep
Summary
Selection for specialized production traits and adaptation to a wide range of environments has involved changes within the genome of modern sheep breeds. Sheep specialization for milk production began 4000–5000 years ago [1]. In the last few hundred years, the development of the different sheep breeds and the use of quantitative genetics methodology have resulted in the establishment of dairy sheep breeds, some of which show a high level of specialization for milk production [2]. Due to the higher total solid content of sheep milk compared to that of other dairy species, the main purpose of dairy sheep production is the manufacturing of high-quality cheese. Milk protein and fat content as well as the total solids content are directly correlated with the cheese yield trait [5,6]. Genetic selection programs in dairy sheep take into account milk yield, and milk composition traits
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