Linkage disequilibrium over short physical distances measured in sheep using a high‐density <scp>SNP</scp> chip

Kijas, James W.; Porto-Neto, Laércio R.; Dominik, Sonja; Reverter, Antônio; Bunch, R. J.; McCulloch, Russell; Hayes, Ben J.; Bräuning, Rüdiger; McEwan, John C.

doi:10.1111/age.12197

Cited by 104 publications

(116 citation statements)

References 25 publications

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“…These studies of LD in dairy sheep breeds showed lower values than those seen for Barbaresca, indicating that LD decay was breed-specific. Recently, Kijas et al (2014), in a study of five sheep breeds that used a high-density SNP chip, found an average r 2 ranging from 0.080 to 0.224 for SNPs up to 70 kb apart and reported that LD decayed faster and at a much shorter genomic distance. 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.…”

Section: Discussionmentioning

confidence: 99%

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: Discussionmentioning

confidence: 99%

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

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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“…The moderate MAF levels demonstrate the great genetic diversity of this population. However, these values can even be underestimated, because in the development of the HD SNP chip, a proportion of SNP with low MAF were included [6]. From the 517,902 SNPs that passed quality control, 82,859 (16%) of the SNPs had MAF less than or equal to 0.10.…”

Section: Discussionmentioning

confidence: 99%

“…In a LD study including a collection of 74 sheep breeds and 49,034 SNP, Kijas et al [23] observed a high variation in LD levels among breeds, with a Scottish breed (Soay) presenting the highest levels of LD and Qezel sheep (sampled in Iran) the lowest levels of LD. Using the HD SNP chip, Kijas et al [6] reported LD levels at 10 kb of 0.186, 0.191, 0.279, 0.221 and 0.339 for Merino ewes, Merino sires, Poll Dorset, Suffolk and Border Leicester, respectively. For the population investigated in this study the LD levels at 10 kb were 0.179, smaller than estimates by Kijas et al [6].…”

Section: Discussionmentioning

confidence: 99%

“…Some of these composite breeds are Primera and Lamb Supreme. Therefore, to enable GS and characterise the genetic diversity in the New Zealand Terminal Sire composite breeds, a high density SNP array (606,006 SNPs) was commissioned by FarmIQ™ (joint New Zealand government and industry Primary Growth Partnership) and developed in conjunction with the International Sheep Genomics Consortium (ISGC) and Illumina [5, 6]. …”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity of a New Zealand multi-breed sheep population and composite breeds’ history revealed by a high-density SNP chip

et al. 2017

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BackgroundKnowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.ResultsOverall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r2 between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial.ConclusionsThis study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Ne highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0492-8) contains supplementary material, which is available to authorized users.

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“…Although highly informative, the current panels of microsatellites used for analyses are not capable of elucidating all the information required regarding breed variation in livestock (Toro et al, 2009). Recently, it is becoming more evident that SNP analysis is more suited for the high throughput genotyping that is required to elucidate greater molecular insights such as historical signatures of selection (Qanbari, Pausch, Jansen et al, 2014), phenotypic variations within livestock breeds (Groenen, Megens, Zare et al, 2011) as well as linkage disequilibrium over short physical distances (Kijas, Porto-Neto, Dominik et al, 2014) than any of the other molecular markers currently available. The availability and accessibility of comprehensive databases of genomic data for various uses has also facilitated population genetic studies globally for example; the National Centre for Biotechnology Information(NCBI) (Sayers, Barrett, Benson et al, 2011), Livestock Animal Quantitative Trait Loci (QTL) database (Hu, Park, Wu et al, 2013), and University of California Santa Cruz (UCSC) genome browser (Dreszer, Karolchik, Zweig et al, 2012).…”

Section: Modelling: the Way Forwardmentioning

confidence: 99%

Molecular identification of livestock breeds: a tool for modern conservation biology

et al. 2016

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Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census had indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12,000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been quantified. In spite of the importance, there have been a growing number of reports on the alarming erosion of domestic animal genetic Molecular Identification of Livestock Breeds: A Tool for Modern Conservation Biology 2 resources. This erosion of animal genetic resources is happening in spite of several global conservation initiatives designed to mitigate it. In this review, we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members within a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems.

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Linkage disequilibrium over short physical distances measured in sheep using a high‐density SNP chip

Cited by 104 publications

References 25 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 of a New Zealand multi-breed sheep population and composite breeds’ history revealed by a high-density SNP chip

Molecular identification of livestock breeds: a tool for modern conservation biology

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