Identifying chromosomal selection‐sweep regions in facial eczema selection‐line animals using an ovine 50<scp>K</scp>‐<scp>SNP</scp> array

Phua, S. H.; Bräuning, Rüdiger; Baird, Hayley; Dodds, K. G.

doi:10.1111/age.12122

Cited by 7 publications

(5 citation statements)

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“…A total of 49 517 SNPs, 91.30% of SNPs on the chip, met the quality-control measures and had a MAF >0.01 across all samples. These results are similar to other ovine studies, which reported >98% and >90% for sample and SNP loci call rates, respectively Shariflou et al, 2012;Våge et al, 2013;Phua et al, 2014).…”

supporting

confidence: 91%

“…The RRS was carried out on 60 individuals from 15 breeds . The SNP chip has been validated in more than 75 international sheep breeds and has been used in a wide range of applications, which include the elucidation of quantitative trait loci and selection strategies (Miller et al, 2011;Kijas et al, 2012;Demars et al, 2013;Liu et al, 2013;Våge et al, 2013;Gutiérrez-Gil et al, 2014;Phua et al, 2014). SNP panels developed from a limited number of individuals or breeds are not necessarily representative of the polymorphisms and frequency distribution of alleles in the genome of all members of the species, this being referred to as ascertainment bias (Nielsen & Signorovitch, 2003;Morin et al, 2004).…”

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confidence: 99%

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Evaluation of the OvineSNP50 chip for use in four South African sheep breeds

et al. 2016

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Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua Afrikaner (NA), South African Merino (SA Merino) and South African Mutton Merino (SAMM) were genotyped to determine the utility of the OvineSNP50 chip for these important South African sheep breeds. After quality control measures had been implemented, 85 SA Merino, 20 Dorper, 20 NA and 19 SAMM samples remained, with an average call rate of 99.72%. A total of 49 517 (91.30%) SNPs on the chip met quality control measures and were included in downstream analyses. The NA had the fewest polymorphic loci, 69.20%, while the SAMM, Dorper and SA Merino had between 81.16% and 86.85% polymorphic loci. Most loci of the SA Merino, Dorper and SAMM had a MAF greater than or equal to 0.3. In contrast, the NA exhibited a large number of rare alleles (MAF < 0.1) and a uniform distribution of other loci across the MAF range (0.1 < MAF ≤ 0.5). The NA exhibited the least genetic diversity and had the greatest inbreeding coefficient among the four breeds. The results of the Dorper, SA Merino, and SAMM compare favourably with those of international breeds and thus demonstrate the utility of the OvineSNP50 chip for these breeds. Effects of SNP ascertainment bias, however, could be seen in the number of non-polymorphic loci and MAF distribution of the three commercial breeds in comparison with those of the NA. The implementation of methods to reduce the effect of SNP ascertainment bias and to ensure unbiased interpretation of genotype results should therefore be considered for future studies using OvineSNP50 chip genotype results.

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confidence: 91%

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confidence: 99%

Evaluation of the OvineSNP50 chip for use in four South African sheep breeds

et al. 2016

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“…) and screening for selection signatures on the genomes of FE‐resistant and susceptible genetic‐line animals (Phua et al . ). To date, eight putative loci located on different chromosomes have been identified to be involved in the disease trait (Phua & Dodds ).…”

Section: Introductionmentioning

confidence: 97%

Towards genomic selection for facial eczema disease tolerance in the New Zealand sheep industry

et al. 2014

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Pithomycotoxicosis, more commonly known as facial eczema (FE), is a liver disease that occurs predominantly in New Zealand because of its toxigenic Pithomyces chartarum strains. The first reported case was in sheep in 1887. Since the 1930s, a number of studies have been conducted in an attempt to mitigate the problems FE has on the sheep and dairy industries. The research in these studies included work on fungicide and biological control of the saprophytic fungus, use of different pasture plants to inhibit fungal growth, stock management with respect to pasture fungal spore counts and the use of zinc prophylaxis on animals. The finding that there was a genetic basis in FE sensitivity in sheep prompted research for a genetic approach to mitigation in the form of a diagnostic DNA test for susceptibility to the disease. Recently, we have used the Illumina OvineSNP50 BeadChip to develop a genome-enabled prediction approach to screen for FE-tolerant sheep. Our current best genomic prediction for FE is for the Romney breed and has an accuracy of 0.38. This prediction accuracy is not as high as the individual accuracy gained by an artificial challenge test (0.64). However, it has the advantage of being a non-invasive test and can be provided as part of genomic testing for other traits at minimal cost.

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“…Several approaches have been used to search for causative genes or loci underlying FE tolerance, including a candidate gene approach [31,32], genome-wide scans for quantitative trait loci (QTL) [33,34] and scanning for selective sweep signatures [35]. There was limited concordance between the results of the studies, with only two of the selective sweep regions, on chromosomes OAR1 and OAR13, found within suggestive (F-statistic value>10.2) QTL regions.…”

Section: Introductionmentioning

confidence: 99%

Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep

McRae

Rowe

Johnson

et al. 2021

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Facial eczema (FE) is a significant metabolic disease that affects New Zealand ruminants. Ingestion of the mycotoxin sporidesmin leads to liver and bile duct damage, which can result in photosensitisation, reduced productivity and death. Strategies used to manage the incidence and severity of the disease include breeding. In sheep, there is considerable genetic variation in the response to FE. A commercial testing program is available for ram breeders who aim to increase tolerance, determined by the concentration of the serum enzyme, γ-glutamyltransferase 21 days after a measured sporidesmin challenge (GGT21). Genome-wide association studies were carried out to determine regions of the genome associated with GGT21. Two regions on chromosomes 15 and 24 are reported, which explain 5% and 1% of the phenotypic variance in the response to FE, respectively. The region on chromosome 15 contains the β-globin locus. Of the significant SNPs in the region, one is a missense variant within the haemoglobin subunit β (HBB) gene. Mass spectrometry of haemoglobin from animals with differing genotypes at this locus indicated that genotypes are associated with different forms of adult β-globin. Haemoglobin haplotypes have previously been associated with variation in several health-related traits in sheep and warrant further investigation regarding their role in tolerance to FE in sheep. We show a strategic approach to the identification of regions of importance for commercial breeding programs with a combination of discovery, statistical and biological validation. This study highlights the power of using increased density genotyping for the identification of influential genomic regions, combined with subsequent inclusion on lower density genotyping platforms.

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Identifying chromosomal selection‐sweep regions in facial eczema selection‐line animals using an ovine 50K‐SNP array

Cited by 7 publications

References 19 publications

Evaluation of the OvineSNP50 chip for use in four South African sheep breeds

Evaluation of the OvineSNP50 chip for use in four South African sheep breeds

Towards genomic selection for facial eczema disease tolerance in the New Zealand sheep industry

Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep

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