High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds

Abstract

BackgroundWith the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.ResultsBased on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.ConclusionsHere, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0354-x) contains supplementary material, which is available to authorized users.

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

“…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]. A previous genome-wide association study (GWAS) demonstrated that this region was associated with body weight in Australian Merino [35].…”

Analysis of Whole Genome Resequencing Datasets from a Worldwide Sample of Sheep Breeds to Identify Potential Causal Mutations Influencing Milk Composition Traits

“…One important issue regarding the variant calling analyses reported here is that all the WGR datasets, those obtained from the public SRA repository and those generated by our research group, were processed following the same bioinformatic analysis workflow and were considered jointly for the variant calling analysis. This procedure has been used in previous studies analyzing WGR datasets [ 35 , 43 , 44 ] and has been proven to prevent biased results regarding the variant calling detection process.…”

“…We analyzed WGR datasets of 43 The variant calling analyses performed across the whole genome revealed, after quality filters, a total of 81,053,638 variants across the entire genome, 59.98% of which had been previously described in the database provided by Ensembl (dbSNP release 91). After filtering the regions corresponding to the 24 functional candidate genes considered here, the total number of variants to be further assessed was 20,100, most of which were SNPs (17,037 and 16,960, for SnpEff and VEP, respectively), with lower numbers of insertions (1489 and 1245, for SnpEff and VEP, respectively) and deletions (1574 and 1396, SnpEff and VEP, respectively) (see details in Table 1).…”

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

“…We propose that this phenotypic differentiation reflects the opposing and varying effects of human selection for fine wool production and environmental adaptation favoring the more natural coarse wool. As for the tail traits, wool quality is controlled by a restricted number of genes [59,73,74].…”