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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.

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LD analyses of all 16 significant SNPs (p≤0.05 after FDR), intervening SNPs and haplotypes for the significant SNPs. The values in the boxes are pair wise SNP correlations (r2) and boxes without numbers indicate SNPs in complete LD. The 16 significant SNPs are shown in B. Haplotypes for these 16 SNPs are shown in C. Each line represents a haplotype and the frequency of the haplotype in this population is given at the end of the line. Haplotypes with a frequency below 2% are not included.
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Figure 2: LD analyses of all 16 significant SNPs (p≤0.05 after FDR), intervening SNPs and haplotypes for the significant SNPs. The values in the boxes are pair wise SNP correlations (r2) and boxes without numbers indicate SNPs in complete LD. The 16 significant SNPs are shown in B. Haplotypes for these 16 SNPs are shown in C. Each line represents a haplotype and the frequency of the haplotype in this population is given at the end of the line. Haplotypes with a frequency below 2% are not included.

Mentions: A total of 143 SNPs were located in the region encompassing the initial 6 Mb of SSC6. However, only 16 markers displayed significant associations with skatole in the pig population analyzed and showed three separate regions, two of them defining blocks of consecutive SNPs. In Figure 2A, the linkage disequilibrium (LD) between all the SNPs in the region between 0.64 and 3.9 Mb is shown. Figure 2B shows the LD for the 16 significant SNPs only. The first of these three regions contained two SNPs (MARC0019446 and ASGA0084674) that mapped consecutively to positions 0.63 and 0.65 Mb and show very high LD of r2 = 0.98 (Figure 2B, block 1). The second region spanned approximately 0.4 Mb, from 1.8 to 2.2 Mb, and is the largest block with seven consecutive significant SNP markers. Among all of these SNPs strong LD was detected (Figure 2B, block 2). The third region on SSC6 extended over approximately 0.6 Mb (from 3.3 to 3.9 Mb) and contained five significant SNPs. Unlike the regions discussed previously, there were several non significant SNP markers located between the five significant markers. Furthermore, the SNP MARC0067306 is not in LD with any of the other SNPs in this area (Figure 2B, block 3). This might be due to a wrong position of the SNPs because of a mistake in the build9 assembly. Finally, significant associations were also detected for two isolated markers located at 5.22 Mb (MARC0009863) and 5.9 Mb (ALGA0113531) which are clearly not in LD with any of the other significant SNPs (Figure 2B, SNP 15 and 16).


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)

LD analyses of all 16 significant SNPs (p≤0.05 after FDR), intervening SNPs and haplotypes for the significant SNPs. The values in the boxes are pair wise SNP correlations (r2) and boxes without numbers indicate SNPs in complete LD. The 16 significant SNPs are shown in B. Haplotypes for these 16 SNPs are shown in C. Each line represents a haplotype and the frequency of the haplotype in this population is given at the end of the line. Haplotypes with a frequency below 2% are not included.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: LD analyses of all 16 significant SNPs (p≤0.05 after FDR), intervening SNPs and haplotypes for the significant SNPs. The values in the boxes are pair wise SNP correlations (r2) and boxes without numbers indicate SNPs in complete LD. The 16 significant SNPs are shown in B. Haplotypes for these 16 SNPs are shown in C. Each line represents a haplotype and the frequency of the haplotype in this population is given at the end of the line. Haplotypes with a frequency below 2% are not included.
Mentions: A total of 143 SNPs were located in the region encompassing the initial 6 Mb of SSC6. However, only 16 markers displayed significant associations with skatole in the pig population analyzed and showed three separate regions, two of them defining blocks of consecutive SNPs. In Figure 2A, the linkage disequilibrium (LD) between all the SNPs in the region between 0.64 and 3.9 Mb is shown. Figure 2B shows the LD for the 16 significant SNPs only. The first of these three regions contained two SNPs (MARC0019446 and ASGA0084674) that mapped consecutively to positions 0.63 and 0.65 Mb and show very high LD of r2 = 0.98 (Figure 2B, block 1). The second region spanned approximately 0.4 Mb, from 1.8 to 2.2 Mb, and is the largest block with seven consecutive significant SNP markers. Among all of these SNPs strong LD was detected (Figure 2B, block 2). The third region on SSC6 extended over approximately 0.6 Mb (from 3.3 to 3.9 Mb) and contained five significant SNPs. Unlike the regions discussed previously, there were several non significant SNP markers located between the five significant markers. Furthermore, the SNP MARC0067306 is not in LD with any of the other SNPs in this area (Figure 2B, block 3). This might be due to a wrong position of the SNPs because of a mistake in the build9 assembly. Finally, significant associations were also detected for two isolated markers located at 5.22 Mb (MARC0009863) and 5.9 Mb (ALGA0113531) which are clearly not in LD with any of the other significant SNPs (Figure 2B, SNP 15 and 16).

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