Comparative genomic characterization of indigenous fat-tailed Akkaraman sheep with local and transboundary sheep breeds

The domestic sheep with over 1200 breeds descended from those early domesticated animals that are bred for a variety of resources such as meat, milk and wool. Akkaraman, a fat-tailed indigenous sheep breed of Turkiye, is widespread throughout Central Anatolia, with the largest indigenous sheep population. Assessing the genetic diversity and genomic structure of animal breeds is among the key contributors to deciphering adaptation to environmental extremes and constructing efficient genetic improvement strategies. Therefore, this study aimed to characterize the genome of Akkaraman breed against various world-renowned transboundary sheep and indigenous sheep with fat and thin tails. Genetic similarities and differences between those breeds have been displayed by estimating and comparing various genetic diversity indices, linkage disequilibrium (LD) estimates and fixation index (FST), runs of homozygosity (ROH) as well as PCA and neighbour-joining tree analysis. Akkaraman sheep were observed to form a cluster alongside Moghani, Karakas, Tibetan and Cyprus Fat Tail sheep, which are primarily the sole representatives of fat-tailed sheep in the study. This clustering was evident in both the PCA and neighbour-joining tree analysis. The Akkaraman sheep was also observed to have the lowest genomic inbreeding and one of the lowest numbers of ROHs, which might also indicate that the breed has not been exposed to historical intensive selection pressure, inbred mating or a massive population bottleneck that might leave strong marks of genomic homozygosity. The results improve our understanding of the genetic diversity in Akkaraman sheep in comparison with certain mainstream sheep breeds as well as those indigenous breeds from around the world. Additionally, findings will also provide valuable insights to perform further GWAS effectively by considering population structure, diversity and LD patterns observed among the breeds while providing practical knowledge that will contribute to designing efficient and successful genome-based selection programmes for worldwide sheep production systems

Genome-Wide Scan of Wool Production Traits in Akkaraman Sheep

The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes

Association of TMEM8B with Mature Weight in Sheep

Multiple signature-of-selection studies have identified single nucleotide polymorphism (SNP)&nbsp;rs426272889&nbsp;as having been under extreme selection pressure in the recent evolutionary history of domestic sheep. However, no study had provided and explored phenotypic data suggesting a functional reason associated with this extreme selection. We tested&nbsp;rs426272889&nbsp;for association with a panel of production traits in 779 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. We identified association with mature weight at ages 3 and 4 years (P&lt;0.05). This confirmed that sheep body size may be a primary reason for the extreme historical selection in this genomic region. The region surrounding SNP&nbsp;rs426272889&nbsp;has had updated genomic annotation, and it is now identified in&nbsp;TMEM8B.&nbsp;Transmembrane protein 8B&nbsp;has little functional annotation in any mammalian species beyond a role inhibition of cancer cell proliferation. To our knowledge, this is the first study to link&nbsp;TMEM8B&nbsp;to body size under normal extensive production conditions. Additional work is required to identify the underlying functional variant or variants affecting body size. Once functional variants are identified, they may be used for selective breeding to improve sheep production.</div