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Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight.

Al-Mamun HA, Kwan P, Clark SA, Ferdosi MH, Tellam R, Gondro C - Genet. Sel. Evol. (2015)

Bottom Line: One region on sheep (Ovis aries) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (P = 2.37 × 10(-16)) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW.The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6.In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry.

View Article: PubMed Central - PubMed

Affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia. hawlader.almamun@une.edu.au.

ABSTRACT

Background: Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep.

Methods: A total of 1781 Australian Merino sheep were genotyped using the medium-density Illumina Ovine SNP50 BeadChip. Among the 53 862 single nucleotide polymorphisms (SNPs) on this array, 48 640 were used to perform a GWAS using a linear mixed model approach. Genotypes were phased with hsphase; to estimate SNP haplotype effects, linkage disequilibrium blocks were identified in the detected QTL region.

Results: Thirty-nine SNPs were associated with BW at a Bonferroni-corrected genome-wide significance threshold of 1 %. One region on sheep (Ovis aries) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (P = 2.37 × 10(-16)) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW. The region that surrounds this association signal on OAR6 contains three genes: leucine aminopeptidase 3 (LAP3), which is involved in the processing of the oxytocin precursor; NCAPG non-SMC condensin I complex, subunit G (NCAPG), which is associated with foetal growth and carcass size in cattle; and ligand dependent nuclear receptor corepressor-like (LCORL), which is associated with height in humans and cattle.

Conclusions: The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6. In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry. These findings should facilitate the discovery of causative variants for BW and contribute to marker-assisted selection.

No MeSH data available.


Linkage disequilibrium (LD) map. Extent of LD across the 2.41 Mb region between 36.15 and 38.56 Mb on OAR6. At the top of the figure, the 13 significant SNPs identified in this region are highlighted in red by order of significance. The haplotype block of 104 kb containing four SNPs is shown in bold black
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Fig3: Linkage disequilibrium (LD) map. Extent of LD across the 2.41 Mb region between 36.15 and 38.56 Mb on OAR6. At the top of the figure, the 13 significant SNPs identified in this region are highlighted in red by order of significance. The haplotype block of 104 kb containing four SNPs is shown in bold black

Mentions: The patterns of LD in the region between 36.15 and 38.56 Mb on OAR6 were investigated using /D’/ (Fig. 3). One clear LD block of 104 kb was detected, with LD blocks defined following the criteria described in [32]). This block contained one of the genome-wide significant SNPs (7th ranked), while the second most significant SNP was on its border (Fig. 3).Fig. 3


Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight.

Al-Mamun HA, Kwan P, Clark SA, Ferdosi MH, Tellam R, Gondro C - Genet. Sel. Evol. (2015)

Linkage disequilibrium (LD) map. Extent of LD across the 2.41 Mb region between 36.15 and 38.56 Mb on OAR6. At the top of the figure, the 13 significant SNPs identified in this region are highlighted in red by order of significance. The haplotype block of 104 kb containing four SNPs is shown in bold black
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4536601&req=5

Fig3: Linkage disequilibrium (LD) map. Extent of LD across the 2.41 Mb region between 36.15 and 38.56 Mb on OAR6. At the top of the figure, the 13 significant SNPs identified in this region are highlighted in red by order of significance. The haplotype block of 104 kb containing four SNPs is shown in bold black
Mentions: The patterns of LD in the region between 36.15 and 38.56 Mb on OAR6 were investigated using /D’/ (Fig. 3). One clear LD block of 104 kb was detected, with LD blocks defined following the criteria described in [32]). This block contained one of the genome-wide significant SNPs (7th ranked), while the second most significant SNP was on its border (Fig. 3).Fig. 3

Bottom Line: One region on sheep (Ovis aries) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (P = 2.37 × 10(-16)) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW.The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6.In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry.

View Article: PubMed Central - PubMed

Affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia. hawlader.almamun@une.edu.au.

ABSTRACT

Background: Body weight (BW) is an important trait for meat production in sheep. Although over the past few years, numerous quantitative trait loci (QTL) have been detected for production traits in cattle, few QTL studies have been reported for sheep, with even fewer on meat production traits. Our objective was to perform a genome-wide association study (GWAS) with the medium-density Illumina Ovine SNP50 BeadChip to identify genomic regions and corresponding haplotypes associated with BW in Australian Merino sheep.

Methods: A total of 1781 Australian Merino sheep were genotyped using the medium-density Illumina Ovine SNP50 BeadChip. Among the 53 862 single nucleotide polymorphisms (SNPs) on this array, 48 640 were used to perform a GWAS using a linear mixed model approach. Genotypes were phased with hsphase; to estimate SNP haplotype effects, linkage disequilibrium blocks were identified in the detected QTL region.

Results: Thirty-nine SNPs were associated with BW at a Bonferroni-corrected genome-wide significance threshold of 1 %. One region on sheep (Ovis aries) chromosome 6 (OAR6) between 36.15 and 38.56 Mb, included 13 significant SNPs that were associated with BW; the most significant SNP was OAR6_41936490.1 (P = 2.37 × 10(-16)) at 37.69 Mb with an allele substitution effect of 2.12 kg, which corresponds to 0.248 phenotypic standard deviations for BW. The region that surrounds this association signal on OAR6 contains three genes: leucine aminopeptidase 3 (LAP3), which is involved in the processing of the oxytocin precursor; NCAPG non-SMC condensin I complex, subunit G (NCAPG), which is associated with foetal growth and carcass size in cattle; and ligand dependent nuclear receptor corepressor-like (LCORL), which is associated with height in humans and cattle.

Conclusions: The GWAS analysis detected 39 SNPs associated with BW in sheep and a major QTL region was identified on OAR6. In several other mammalian species, regions that are syntenic with this region have been found to be associated with body size traits, which may reflect that the underlying biological mechanisms share a common ancestry. These findings should facilitate the discovery of causative variants for BW and contribute to marker-assisted selection.

No MeSH data available.