Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

Brito, Luiz F.; Jafarikia, Mohsen; Grossi, D. A.; Kijas, James W.; Porto-Neto, Laércio R.; Ventura, Ricardo Vieira; Salgorzaei, Mehdi; Schenkel, F.S.

doi:10.1186/s12863-015-0220-1

Cited by 83 publications

(102 citation statements)

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“…Consistent with our results, Al-Mamun et al (2015) reported that the maximum average LD was located between adjacent SNPs on OAR10 and a higher average LD was seen in meat sheep breeds. Values of r 2 for adjacent SNP pairs were also similar to the values observed in other livestock species such as cattle (r 2 = 0.20 for SNPs with an average distance of 68 Kb) (Bohmanova et al, 2010) and goats (r 2 = 0.11 to 0.29 for SNPs with physical distance ranging from 53 to 73 kb) (Brito et al, 2015), although these were lower than those observed in pigs, where one study reported an average r 2 of 0.41 to 0.46 for SNPs <50 kb apart (Veroneze et al, 2013), and in horses (Corbin et al, 2010), which showed r 2 values remaining >0.3 for distances up to 185 kb. The relatively small number of genotyped Barbaresca individuals may have resulted in an overestimation of r 2 , which could explain the differences in the LD values v. the other Sicilian sheep breeds (Mastrangelo et al, 2014).…”

Section: Discussionsupporting

confidence: 79%

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.

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Section: Discussionsupporting

confidence: 79%

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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“…The dataset used here has been previously described [19, 24]. In brief, there were between 48 (Cashmere) and 403 (Alpine) animals genotyped per breed.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, the heterogeneity of effective population size (N e ) among breeds can potentially contribute to large locus-specific F ST values among breed groups [18]. Using the same dataset, Brito et al [19] reported a variation in N e among the breeds included in this investigation. Therefore, the approach named hapFLK, proposed by Fariello et al [20] and based on haplotype differentiation between populations, seems like another reasonable alternative to confirm or identify signatures of selection in goat populations.…”

Section: Introductionmentioning

confidence: 91%

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

et al. 2017

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BackgroundThe detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation.ResultsThe proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis.ConclusionsIn general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.

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“…Following LD pruning, there should be no SNP pair within a given window, usually 50 kb, that are correlated, taken as r 2 >0.2 (Anderson et al, 2010). The SNP density obtained before LD-based filtering (1 SNP/~59 kb) was lower than the densities of 1 SNP/~53 SNP obtained for Alpine and Saanen goats, but higher than the densities of 1 SNP/~67kb and 1 SNP/~71kb for SA Boer and Toggenburg goats, respectively (Brito et al, 2014). SNP densities obtained after LD-based filtering (1 SNP/~226kb), however, were considerably lower than the original average inter-SNP distance range of 30 -90 kb, as stated by Tosser-Klopp et al (2014).…”

mentioning

confidence: 93%

Validation of the 50k Illumina goat SNP chip in the South African Angora goat

Lashmar¹,

Visser²,

Marle-Köster³

2015

SA J. An. Sci.

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Tools for the genomic evaluation of goats have generally lagged behind those for other species. However, the recent availability of the goat SNP50 consortium bead chip has marked a positive change for this small ruminant species. Polymorphic loci can differ greatly between breeds of the same species. Exclusion of fibre-producing breeds, such as the Angora goat, during the development of this genotyping array necessitates the validation of SNPs included on the chip to allow for genomic applications that would accelerate genetic progress in mohair yield and quality. Forty eight unrelated Angora goats, displaying phenotypic variation in two important price-determining traits, namely fibre diameter and fleece weight, were genotyped with the goat SNP50 consortium bead chip. Results revealed that 46 983 SNP (88.1%) of the 53 347 called SNPs were polymorphic (MAF>0.05). After quality control, 3 960 SNP were filtered from further analysis for violating Hardy-Weinberg and call-rate parameter thresholds, leaving 43 759 (82%) of the 53 347 SNPs to be validated for downstream analysis. Observed and expected heterozygosity values of 0.365 and 0.370, respectively, were obtained for polymorphic SNPs. A total of 30 357 SNPs in linkage disequilibrium (LD) were removed to obtain a set of independent markers, resulting in a final SNP density of 1 SNP/ ~226 kb. Results indicate that the goat SNP50 bead chip was informative in the Angora goats that were studied, and should be useful in examining the underlying genetic variation. ______________________________________________________________________________________

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Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats

Cited by 83 publications

References 36 publications

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers

Validation of the 50k Illumina goat SNP chip in the South African Angora goat

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