Limits...
The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars.

Ramos AM, Duijvesteijn N, Knol EF, Merks JW, Bovenhuis H, Crooijmans RP, Groenen MA, Harlizius B - BMC Genet. (2011)

Bottom Line: The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels.This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p.These markers defined three independent clusters in the region, which contain a low number of protein-coding genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.

ABSTRACT

Background: Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the economic and animal welfare concerns there is interest in developing genetic markers that could be used in selection schemes to decrease the incidence of boar taint. The Porcine 60 K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected.

Results: The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome.

Conclusions: This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs.

Show MeSH
Association between skatole levels and 2,418 SNPs located on SSC6. On the y-axis are -log10(p-values) and on the x-axis are the physical positions of the SNPs. The significance threshold used was 3.50, which corresponds to a chromosome-wide FDR q-value of 0.05.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3111395&req=5

Figure 1: Association between skatole levels and 2,418 SNPs located on SSC6. On the y-axis are -log10(p-values) and on the x-axis are the physical positions of the SNPs. The significance threshold used was 3.50, which corresponds to a chromosome-wide FDR q-value of 0.05.

Mentions: A total of 16 SNPs were significantly associated with skatole levels at the chromosome-wide q-value ≤ 0.05 (Table 1). These markers were all located on SSC6 in the initial 6 Mb of this chromosome (Figure 1). All the remaining SNPs located in other regions of the genome were not significantly associated with skatole.


The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars.

Ramos AM, Duijvesteijn N, Knol EF, Merks JW, Bovenhuis H, Crooijmans RP, Groenen MA, Harlizius B - BMC Genet. (2011)

Association between skatole levels and 2,418 SNPs located on SSC6. On the y-axis are -log10(p-values) and on the x-axis are the physical positions of the SNPs. The significance threshold used was 3.50, which corresponds to a chromosome-wide FDR q-value of 0.05.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3111395&req=5

Figure 1: Association between skatole levels and 2,418 SNPs located on SSC6. On the y-axis are -log10(p-values) and on the x-axis are the physical positions of the SNPs. The significance threshold used was 3.50, which corresponds to a chromosome-wide FDR q-value of 0.05.
Mentions: A total of 16 SNPs were significantly associated with skatole levels at the chromosome-wide q-value ≤ 0.05 (Table 1). These markers were all located on SSC6 in the initial 6 Mb of this chromosome (Figure 1). All the remaining SNPs located in other regions of the genome were not significantly associated with skatole.

Bottom Line: The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels.This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p.These markers defined three independent clusters in the region, which contain a low number of protein-coding genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.

ABSTRACT

Background: Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the economic and animal welfare concerns there is interest in developing genetic markers that could be used in selection schemes to decrease the incidence of boar taint. The Porcine 60 K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected.

Results: The genome-wide association study revealed that 16 SNPs (single nucleotide polymorphisms) located on the proximal region of chromosome 6 were significantly associated with skatole levels. These SNPs are grouped in three separate clusters located in the initial 6 Mb region of chromosome 6. The differences observed between the homozygote genotypes for SNPs in the three clusters were substantial, including a difference of 102.8 ng/g skatole in melted fat between the homozygotes for the ALGA0107039 marker. Single SNPs explain up to 22% of the phenotypic variance. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome.

Conclusions: This study demonstrated new SNP markers significantly associated with skatole levels in the distal region of chromosome 6p. These markers defined three independent clusters in the region, which contain a low number of protein-coding genes. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs.

Show MeSH