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

Abstract

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 FST-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 via 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 via the FST-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 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). 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 LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

“…The ROH hotspot with highest SNP occurrence was located on OAR6 , which consisted of the NCAPG/LCORL gene. Similar findings were also reported in Italian sheep breeds [22], Spanish sheep breeds [21], Swiss sheep breeds, and Merino [18,31]. Moreover, the selective signatures in NCAPG/LCORL region were found in many sheep breeds [18,32,33], including Merino [34].…”

“…GWAS results demonstrated that RXFP2 region was associated with horn phenotype in sheep [49]. The selective sweep region harbouring RXFP2 was also identified in Merino [31], and this region was successfully used to predict the horned and polled phenotypes in Merino [50,51]. Additionally, the recombination rate on this genome region was relatively high.…”

Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep

“…For instance, EXT1 located on OAR9 include the SNPs (75.5 Mb, p = 5.68E-07) was associated with FD near a known QTL (75.9 Mb) [ 10 ]. PAX9 located on OAR18, which include the SNPs (45.6 Mb, p = 8.13E-07), was identified to be related to hair defects [ 30 ]; this finding agrees with the genome-wide selection signatures for wool traits among Merino and Merino-derived sheep breeds [ 31 ]. KRT17 located on OAR11, which is near the SNPs (41.2 Mb, p = 1.34E-06), is required for the correct growth of hair follicles, especially for continuous growth [ 32 ].…”

Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color

“…In this study, we (i) pair-wise contrasted 15 "grey" cattle breeds each versus four "non-grey" cattle breeds; (ii) retained, for each pair-wise contrast, loci with q-value < 0.05 assumed to be putatively under selection; and (iii) applied an arbitrary and intentionally loose (to account for genetic heterogeneity of the considered breeds) across-scenario multi-occurrence threshold (25%). We previously demonstrated the robustness of a similar multi-cohort framework in a study for identification of selection signatures in Merino (and Merino-derived) sheep breeds contrasted with breeds that had no known Merino genetic background [40]. In this study, using the above-described approach, the highly supported selection signature at chromosome 14 mentioned above was identified.…”