AUTHOR=Megdiche Sami , Mastrangelo Salvatore , Ben Hamouda Mohamed , Lenstra Johannes A. , Ciani Elena 

TITLE=A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01025

DOI=10.3389/fgene.2019.01025

ISSN=1664-8021

ABSTRACT=<p>Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical F<sub>ST</sub>-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested <italic>via</italic> the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested <italic>via</italic> the F<sub>ST</sub>-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (<italic>MSRB3</italic> and <italic>LEMD3</italic>), OAR10 (<italic>FRY</italic> and <italic>RXFP2</italic>), OAR 13 (<italic>RALY</italic>), OAR17 (<italic>FAM101A</italic>), and OAR18 (<italic>NFKBIA, SEC23A</italic>, and <italic>PAX9</italic>). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably <italic>LOC101120019</italic> and <italic>TMEM132B</italic> (OAR17), <italic>LOC105609948</italic> (OAR3), <italic>LOC101110773</italic> (OAR10), and <italic>EIF2S2</italic> (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.</p>