Limits...
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.


Related in: MedlinePlus

Ensembl alignments of the sequence for the 1 Mb region surrounding the genes NCAPG and LCORL. The Ovis aries reference genome (Oar_v3.1 assembly) was aligned against (from top to bottom) bovine (UMD v3.1 assembly), porcine (Sscrofa 10.2 assembly) and human (GRCh37 assembly) genomes. Code colour for genes: brown – protein coding, grey – pseudo gene, blue – processed transcript, yellow – merged Ensembl/Havana and purple – RNA gene. Triangles: black – breakpoint between different chromosomes, blue – inversion in chromosome, brown – breakpoint on chromosome and red – gap between two underlying slices
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Ensembl alignments of the sequence for the 1 Mb region surrounding the genes NCAPG and LCORL. The Ovis aries reference genome (Oar_v3.1 assembly) was aligned against (from top to bottom) bovine (UMD v3.1 assembly), porcine (Sscrofa 10.2 assembly) and human (GRCh37 assembly) genomes. Code colour for genes: brown – protein coding, grey – pseudo gene, blue – processed transcript, yellow – merged Ensembl/Havana and purple – RNA gene. Triangles: black – breakpoint between different chromosomes, blue – inversion in chromosome, brown – breakpoint on chromosome and red – gap between two underlying slices

Mentions: Based on the Ovis aries reference genome assembly (Oar_v3.1), the region between 36.15 and 38.56 Mb on OAR6 contains 14 genes. These include NCAPG non-SMC condensin I complex, subunit G (NCAPG), which is associated with foetal growth and carcass size in cattle [33], and ligand dependent nuclear receptor corepressor-like (LCORL), which is associated with height in humans and cattle [14, 15] (Table 2 and Fig. 4). The contig tracks in Fig. 5 show that a high level of sequence conservation was found between the 1.0 Mb sequence of the OAR6 region around NCAPG and LCORL and the syntenic regions on BTA6, HSA4 (HSA for Homo sapiens chromosome) and SSC8 (SSC for Sus scrofa chromosome). When considering a larger 2.41 Mb region (Table 2), more genes were identified, as well as 12 previously reported QTL using different sheep breeds [21] (Table 3). These included QTL for average daily gain, body weight, milk yield, milk lactose yield, and milk fat percentage.Table 2


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)

Ensembl alignments of the sequence for the 1 Mb region surrounding the genes NCAPG and LCORL. The Ovis aries reference genome (Oar_v3.1 assembly) was aligned against (from top to bottom) bovine (UMD v3.1 assembly), porcine (Sscrofa 10.2 assembly) and human (GRCh37 assembly) genomes. Code colour for genes: brown – protein coding, grey – pseudo gene, blue – processed transcript, yellow – merged Ensembl/Havana and purple – RNA gene. Triangles: black – breakpoint between different chromosomes, blue – inversion in chromosome, brown – breakpoint on chromosome and red – gap between two underlying slices
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Ensembl alignments of the sequence for the 1 Mb region surrounding the genes NCAPG and LCORL. The Ovis aries reference genome (Oar_v3.1 assembly) was aligned against (from top to bottom) bovine (UMD v3.1 assembly), porcine (Sscrofa 10.2 assembly) and human (GRCh37 assembly) genomes. Code colour for genes: brown – protein coding, grey – pseudo gene, blue – processed transcript, yellow – merged Ensembl/Havana and purple – RNA gene. Triangles: black – breakpoint between different chromosomes, blue – inversion in chromosome, brown – breakpoint on chromosome and red – gap between two underlying slices
Mentions: Based on the Ovis aries reference genome assembly (Oar_v3.1), the region between 36.15 and 38.56 Mb on OAR6 contains 14 genes. These include NCAPG non-SMC condensin I complex, subunit G (NCAPG), which is associated with foetal growth and carcass size in cattle [33], and ligand dependent nuclear receptor corepressor-like (LCORL), which is associated with height in humans and cattle [14, 15] (Table 2 and Fig. 4). The contig tracks in Fig. 5 show that a high level of sequence conservation was found between the 1.0 Mb sequence of the OAR6 region around NCAPG and LCORL and the syntenic regions on BTA6, HSA4 (HSA for Homo sapiens chromosome) and SSC8 (SSC for Sus scrofa chromosome). When considering a larger 2.41 Mb region (Table 2), more genes were identified, as well as 12 previously reported QTL using different sheep breeds [21] (Table 3). These included QTL for average daily gain, body weight, milk yield, milk lactose yield, and milk fat percentage.Table 2

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.


Related in: MedlinePlus