Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Abstract

Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. Results We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

Genomic regions associated with resistance to gastrointestinal parasites in Australian Merino sheep

“…On the other hand, 12 candidate genes significantly associated with the FEC1 or FEC2 traits were identified in OAR 6: DCAF16, FAM184B, GPRIN3, HERC3, HERC5, IBSP, LAP3, LCORL, MED28, NCAPG, PIGY and PYURF, all of them except LAP3 were detected by Al Kalaldeh et al [38] in significant genomic regions for GIP resistance in sheep. Particularly the FAM184B gene has also been reported to be strongly associated with body size and weight in livestock [49][50][51], milk production [52] and reproductive traits in sheep [53].…”

“…The MED28 gene is involved in milk production in ewes [43,52] and is also related to liveweight [54]. In addition, this gene has been linked to both pre and postnatal body weights in ewes [49,54].…”

Pan-Omics in Sheep: Unveiling Genetic Landscapes

“…The diversity and richness inherent in sheep breeds, characterized by economically valuable traits such as high-quality wool, multiribbed features, distinctive teat characteristics, and remarkable stress resistance, have garnered intense research interest [17]. Studying phenotypic transformations during sheep domestication assumes paramount importance in refining breeding practices.…”