Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

BackgroundAdvances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.ResultsHaplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).ConclusionWe found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.

1H NMR Metabolic Profile to Discriminate Pasture Based Alpine Asiago PDO Cheeses

The study was carried out in an alpine area of North-Eastern Italy to assess the reliability of proton nuclear magnetic resonance 1H NMR to fingerprint and discriminate Asiago PDO cheeses processed in the same dairy plant from upland pasture-based milk or from upland hay-based milk. Six experimental types of Asiago cheese were made from raw milk considering 2 cows’ feeding systems (pasture- vs. hay-based milk) and 3 ripening times (2 months, Pressato vs. 4 months, Allevo_4 vs. 6 months, Allevo_6). Samples (n = 55) were submitted to chemical analysis and to 1H NMR coupled with multivariate canonical discriminant analysis. Choline, 2,3-butanediol, lysine, tyrosine, and some signals of sugar-like compounds were suggested as the main water-soluble metabolites useful to discriminate cheese according to cows’ feeding system. A wider pool of polar biomarkers explained the variation due to ripening time. The validation procedure based on a predictive set suggested that 1H NMR based metabolomics was an effective fingerprinting tool to identify pasture-based cheese samples with the shortest ripening period (Pressato). The classification to the actual feeding system of more aged cheese samples was less accurate likely due to their chemical and biochemical changes induced by a prolonged maturation process.

Gateway to the Yayla: The Varneti Archaeological Complex in the Southern Caucasus Highlands

Recent ground surveys in the Samtskhe-Javakheti region of southern Georgia have investigated a previously undocumented group of sites along a ridge overlooking the upper Kura river valley. Features and artefacts recorded at Varneti suggest long but episodic occupation from the Chalcolithic to the later medieval periods, with prominent phases in the Early to Middle Bronze Age and the Late Bronze Age to Early Iron Age. Varneti has the potential to contribute to understanding economic and strategic aspects of the long-term settlement pattern in the southern Caucasus, especially the interplay between lowland and highland zones. Its position in the landscape, at a transitional point between the river valley and the upland pasture (yayla), may explain its persistent use by agro-pastoral communities that operated in varied cultural situations. The survey results help us frame a series of questions regarding economic and social dynamics at a local and regional scale and the continuity and discontinuity of practice in highland environments through long timespans.