Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation F_ST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the F_ST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.

Genetic and genomic analyses underpin the feasibility of concomitant genetic improvement of milk yield and mastitis resistance in dairy sheep

Milk yield is the most important dairy sheep trait and constitutes the key genetic improvement goal via selective breeding. Mastitis is one of the most prevalent diseases, significantly impacting on animal welfare, milk yield and quality, while incurring substantial costs. Our objectives were to determine the feasibility of a concomitant genetic improvement programme for enhanced milk production and resistance to mastitis. Individual records for milk yield, and four mastitis-related traits (milk somatic cell count, California Mastitis Test score, total viable bacterial count in milk and clinical mastitis presence) were collected monthly throughout lactation for 609 ewes of the Chios breed. All ewes were genotyped with a mastitis specific custom-made 960 single nucleotide polymorphism (SNP) array. We performed targeted genomic association studies, (co)variance component estimation and pathway enrichment analysis, and characterised gene expression levels and the extent of allelic expression imbalance. Presence of heritable variation for milk yield was confirmed. There was no significant genetic correlation between milk yield and mastitis traits. Environmental factors appeared to favour both milk production and udder health. There were no overlapping of SNPs associated with mastitis resistance and milk yield in Chios sheep. Furthermore, four distinct Quantitative Trait Loci (QTLs) affecting milk yield were detected on chromosomes 2, 12, 16 and 19, in locations other than those previously identified to affect mastitis resistance. Five genes (DNAJA1, GHR, LYPLA1, NUP35 and OXCT1) located within the QTL regions were highly expressed in both the mammary gland and milk transcriptome, suggesting involvement in milk synthesis and production. Furthermore, the expression of two of these genes (NUP35 and OXCT1) was enriched in immune tissues implying a potentially pleiotropic effect or likely role in milk production during udder infection, which needs to be further elucidated in future studies. In conclusion, the absence of genetic antagonism between milk yield and mastitis resistance suggests that simultaneous genetic improvement of both traits be achievable.

Genetic differentiation and phylogeny of 27 sheep populations based on structural gene loci

To explore the genetic divergence and phylogeny of Chinese indigenous sheep breeds, in the current study, we analyzed the polymorphisms of 5 structural loci in ten sheep populations, including Sishui Fur, Sunite, Wurank, Bayinbuluke, Altay, Small-Tailed Han, Wadi, Tan, Tong and Hu sheep. The data were then compared with those from an additional 13 Asian and 4 European sheep populations acquired by the same experimental method. Based on the genetic distance and the results of a cluster analysis, we constructed the phylogenetic relationship of 27 populations. The results showed that the sheep populations in this study could be classified into four genetic groups: "Mongolian", "Tibetan", "South-Southeast Asian" and "European" sheep groups. All 10 Chinese sheep breeds belonged to the "Mongolian sheep" lineage; however, Finnish Landrace sheep and Yunnan sheep could not be classified into any of the four groups. These results could provide a good reference for the protection and utilization of primary breed resources in China and phylogenic research on Asian sheep populations.

Genome-Wide Specific Selection in Three Domestic Sheep Breeds

BACKGROUND

Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed.

RESULTS

We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study.

CONCLUSIONS

Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep

In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E.

To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations.

Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).

Polymorphism of FecB gene in nine sheep breeds or strains and its effects on litter size, lamb growth and development

Nine sheep breeds or strains, including 615 individuals were screened with forced PCR RFLP method for the FecB gene to study the polymorphism and its effects on litter size, body weight and body size. Results showed that the polymorphism frequencies of FecB gene were significantly imbalanced in these breeds or strains. The Hu sheep were all homozygous carriers of FecB gene(BB). In the Chinese Merino prolific meat strain, the genotype frequencies of BB, B+ and ++ were 51%, 30% and 19%, respectively, whereas all the other flocks had only the wild-type (++) genotype. Results within the Chinese Merino prolific meat strain showed that the mean litter size of ewes with genotype BB and B+ were 2.8 (+/-0.74) and 2.3 (+/- 0.63) (P < 0.05), whereas ++ genotype ewes had a litter size of only 1.2 (+/-0.68) (P < 0.01). At day 90 after birth, the body weights of BB/B+ genotype lambs were higher than that of ++ genotype lambs (18.6 +/- 3.70 kg, 18.0 +/- 3.71 kg vs 15.6 +/- 2.22 kg, P < 0.05). In addition, the heart girth and chest width of BB/B+ genotype lambs were significantly longer than those of the ++ lambs (P < 0.05). No significant differences were observed in either body weight or body size at day 120. Litter size at first lambing from Hu at Natural Source Conservative Region was found to be significantly higher than that from the other two regions sampled (P < 0.05). In addition to the additive effect on litter size, these findings showed for the first time that the FecB gene had a positive effect on early postnatal body growth.

Mitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds

This survey represents the first characterization of mitochondrial DNA diversity within three breeds of Indian sheep (two strains of the Deccani breed, as well as the Bannur and Garole breeds) from different geographic regions and with divergent phenotypic characteristics. A 1061-bp fragment of the mitochondrial genome spanning the control region, a portion of the 12S rRNA gene and the complete phenyl tRNA gene, was sequenced from 73 animals and compared with the corresponding published sequence from European and Asian breeds and the European Mouflon (Ovis musimon). Analysis of all 156 sequences revealed 73 haplotypes, 52 of which belonged to the Indian breeds. The three Indian breeds had no haplotypes in common, but one Indian haplotype was shared with European and other Asian breeds. The highest nucleotide and haplotype diversity was observed in the Bannur breed (0.00355 and 0.981 respectively), while the minimum was in the Sangamneri strain of the Deccani breed (0.00167 and 0.882 respectively). All 52 Indian haplotypes belonged to mitochondrial lineage A. Therefore, these Indian sheep are distinct from other Asian and European breeds studied so far. The relationships among the haplotypes showed strong breed structure and almost no introgression among these Indian breeds, consistent with Indian sheep husbandry, which discourages genetic exchange between breeds. These results have implications for the conservation of India's ovine biodiversity and suggest a common origin for the breeds investigated.

Genetic structure of European sheep breeds

Large-scale evaluations of genetic diversity in domestic livestock populations are necessary so that region-specific conservation measures can be implemented. We performed the first such survey in European sheep by analysing 820 individuals from 29 geographically and phenotypically diverse breeds and a closely related wild species at 23 microsatellite loci. In contrast to most other domestic species, we found evidence of widespread heterozygote deficit within breeds, even after removing loci with potentially high frequency of null alleles. This is most likely due to subdivision among flocks (Wahlund effect) and use of a small number of rams for breeding. Levels of heterozygosity were slightly higher in southern than in northern breeds, consistent with declining diversity with distance from the Near Eastern centre of domestication. Our results highlight the importance of isolation in terms of both geography and management in augmenting genetic differentiation through genetic drift, with isolated northern European breeds showing the greatest divergence and hence being obvious targets for conservation. Finally, using a Bayesian cluster analysis, we uncovered evidence of admixture between breeds, which has important implications for breed management.

Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds

The population structure and genetic diversity of 57 European and Middle Eastern marginal and cosmopolitan sheep breeds from 15 countries were analysed by typing 31 microsatellite markers. Mean unbiased expected heterozygosities ranged from 0.63 in British Exmoor Horn to 0.77 in Albanian Ruda. South-eastern European and Middle-Eastern sheep breeds were significantly more variable than northwestern and western European breeds. An overall heterozygote deficiency (f) across all loci was observed (P < 0.001), while genetic differentiation (theta) was 5.7%. Principal component analysis and Bayesian model-based clustering indicate a south-east to north-west cline, but also revealed distinct groups of Middle-Eastern fat-tailed sheep, south-eastern European sheep and north-western/western European sheep. Within the last group, two less-distinct clusters comprised the Merino-type and Alpine breeds respectively. The incomplete demarcations of most clusters probably reflects cross-breeding and/or upgrading.

Mitochondrial diversity and the origin of Iberian sheep

Mitochondrial DNA diversity was analysed in 19 Iberian and six foreign sheep breeds. Three mtDNA lineages (B, A and C) were found in the Iberian sheep, with type B clearly predominating over the others. The results were analysed for each of the morphologically determined breed groups in Iberian sheep: Merino, Entrefino, Churro and Iberian trunks. MtDNA lineage C was found only in the Iberian trunk composed of Montesina and Ojalada. These two populations had high mtDNA variability, and in the Iberian sheep only Merino Branco had more variation. The other three Merino types studied showed moderate variability, including the most authentic Merino, the Spanish Merino. These three Merinos clustered closely in a multidimensional scaling representation of distances, while the fourth breed (Merino Branco) showed a clear separation. As for the other two trunks, breeds from the Churro group showed greater maternal uniformity while results for populations included in the so-called Entrefino trunk seemed to have a more heterogeneous maternal origin. The results obtained are discussed with available data from nuclear markers and with morphological classifications, and all this information is analysed in relation to the origin of the different Iberian sheep breeds.

Genetic relationships among Turkish sheep

Genetic relationships among Turkish sheep breeds were analysed on the basis of 30 microsatellite markers. Phylogenetic analyses based on the estimation of genetic distances revealed the closest relationships for the Akkaraman, Morkaraman and Tuj breeds, which were clearly differentiated from the others in the dendrogram. Our pattern was completely confirmed by results from the Factorial Correspondence Analysis. All the results described analysing either population parameters or individuals revealed a clear separation between the fat-tailed group and the others. These results, based on nuclear DNA, are discussed along with those already reported for these breeds through the investigation of mitochondrial DNA, which had revealed the invaluable significance of the genetic background of these Turkish sheep.

[Estrogen receptor as a candidate gene for prolificacy of small tail Han sheep]

Single nucleotide polymorphism in exon 1 of the estrogen receptor (ESR) gene was detected by PCR-SSCP in both high fecundity sheep breeds (Small Tail Han sheep, Hu sheep and German Mutton Merino sheep) and low fecundity sheep breeds (Dorset sheep,Suffolk sheep). Results indicated that there were three genotypes (AA, AB and BB) in all three high fecundity sheep breeds, but only two genotypes (AA, AB) in both low fecundity breeds. In Hu sheep,German Mutton Merino sheep, Small Tail Han sheep, Suffolk sheep and Dorset sheep,the frequency of allele A was 0.672, 0.786, 0.846, 0.857 and 0.867, respectively, and the frequency of allele B was 0.328, 0.214, 0.154, 0.143, and 0.133, respectively. Sequencing revealed a C-->G mutation at 363 bp of exon 1 of ESR gene in the BB genotype in comparison to the AA genotype. The genotype distribution was significantly different between Small Tail Han sheep and Hu sheep (P<0.01) and between Dorset sheep and Hu sheep (P <0.05). There was no difference in genotype distribution between other sheep breeds. The Small Tail Han sheep ewes with genotypes AB or BB had 0.51 (P < 0.05) and 0.7 (P < 0.05) more lambs than those with genotype AA, respectively. These results showed that the estrogen receptor locus is either a major gene that influences the prolificacy in Small Tail Han sheep or in close linkage with such a gene. In view of our results, marker-assisted selection using ESR is warranted to increase litter size in sheep and will be of considerable economic value to mutton producers.

The growth of sheep scab lesions in relation to sheep breed and time of the year

Numerically equal groups of between five and ten young Merino and Dorper sheep were artificially infested with sheep scab mites, Psoroptes ovis. Separate groups of sheep were infested during the early winter of two successive years as well as during the early summer of the second year. Lesion growth was measured at two-weekly intervals for a period of six weeks during the first winter and for eight weeks during the second winter and in the summer. The rate of lesion growth and mean lesion size on Merino sheep was significantly greater than that on Dorper sheep at each two-weekly recording during the winter of both years. The rate of growth of the lesions did not differ significantly between the two sheep breeds during summer, although, with the exception of eight weeks post-infestation, the mean lesion size on Merino sheep was significantly larger than that on Dorper sheep at each assessment.