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SNPs of high utility within European commercial pig breeds

Final Report Summary - PIGSNP (SNPs of high utility within European commercial pig breeds)

SNP discovery was done in close collaboration with activities in other projects funded by the EU and the USDA. Most sequencing and SNP identification activities were performed at WU who also coordinated the SNP discovery and the design of the Illumina porcine 60K+ iSelect Beadchip. A total of 158 DNA samples were collected from five pig breeds, including Duroc, Pietrain, Landrace, Large White and Wild Boar. These samples were representative of the worldwide distribution of each breed. Sequencing was done on 3 different Reduced representation libraries (RRLs) together comprising around 10 % of the porcine genome. After application of a number of different filtering criteria to reduce the number of false positives, a total of 372 886 high confidence SNPs were identified. This number clearly surpassed our initial goal of generating around 40 thousand SNPs.

In addition to the SNPs identified in our research, SNPs deriving from other sources were also collected to form a database comprising a total of 549 282 SNPs. These were then used to design the Illumina Porcine 60K+ iSelect Beadchip, commercially available as the PorcineSNP60 beadchip. A total of 64 232 SNPs were included on the Beadchip, and 43 582 of the SNPs were identified at Wageningen University.

Further validation was performed by genotyping with the Beadchip the 158 individuals that had originally been sequenced. Results showed that the overall SNP call rate was high (97.5 %) and that of the 62 621 SNPs that could be reliably scored, 58 994 were polymorphic, yielding a SNP conversion success rate of 94.5 %. The MAF for all SNPs that could be scored was 0.274. The PorcineSNP60 beadchip was made freely available to the scientific community and chips surpassing 40 000 assays have been used worldwide.

We also used the RRL sequences obtained within WP1 for the identification of breed specific SNPs within the five breeds sequenced. Around 29 000 SNPs were identified as potential breed specific SNPs and 4 441 of these had been included on the Porcine SNP60 beadchip. Of these 4441 SNPs 193 SNPs were confirmed to be breed specific.

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 60K SNP Beadchip was used to genotype 891 pigs from a composite Duroc sire line, for which skatole levels in fat had been collected.

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 106.9 ng / g of melted fat between the homozygotes for the MARC0044930 marker. No obvious candidate genes could be pinpointed in the region, which may be due to the need of further annotation of the pig genome. The considerable differences observed between the homozygous genotypes for several SNPs may be used in future selection schemes to reduce skatole levels in pigs.

Our study clearly demonstrates the usefulness of the Porcine SNP60 beadchip we designed, in genome-wide association studies.