PIGSNP

SNPs of high utility within European commercial pig breeds

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 Obiettivo del progetto (Objective)

'Within the PigSNP project SNPs will be identified that are known to be segregating within commercial European pig breeds. Using the Solexa sequencing technique a representation of the genome is directly sequenced to high redundancy. This is achieved by digesting the DNA with a restriction enzyme and sequencing fragments within a specific size range (i.e. 250 bp). The strategy used is based on sequencing a mixture of the DNA from 5 individuals of a single commercial breed to 20 X depth. Furthermore, the use of 5 individuals per breed (10 haplotypes) will ensure the identification of SNPs with high minor allele frequencies. This approach ensures that SNPs identified will be informative within the commercial line and therefore will be useful not only in experimental QTL crosses but also for genomic selection in current commercial breeding lines. The combination of new generation sequence technology (Solexa) combined with WITHIN breed SNP identification of major SNPs is particular innovative and timely. The SNPs identified will be available to be included in high density SNP panels (within existing international ongoing collaborations) that will be used to genotype available commercial pig breeds. This will aid in the further fine mapping of previously identified QTL within these commercial crosses. Within the project we will use the identified SNPs for fine mapping 2-3 previously identified QTL on chromosomes 2 and 4 identified within an experimental MeishanxEuropean white cross and within a commercial finisher population respectively. Both populations have been used extensively for the identification of several QTL for fatness, carcass and meat quality traits. Within the project it is aimed to identify between 10 and 20 thousand SNPs each for 4 different commercial breeds. QTL fine mapping will be done using the Illumina Golden Gate assay.'

Introduzione (Teaser)

Despite major advances in fine gene mapping, undesirable genes still lurk in the genomes of commercial breeds of animal. EU-funded research has analysed the pig genome down to the single nucleotide to identify useful genes while eliminating the bad guys.

Descrizione progetto (Article)

The revolution in genomics and mapping techniques is playing a role in improving nearly every production efficiency trait evaluated in livestock. Advances mean that pig breeders and commercial pork breeders can now avail of gene marker technology once thought to be the domain of high-tech laboratories.

The 'SNPs of high utility within European commercial pig breeds' (Pigsnp) project aimed to really narrow down the search for useful traits in commercial pig breeds by using a new technique to look for single nucleotide polymorphisms (SNPs). As the name suggests, SNPs occur when there is a difference in only one nucleotide or base pair in the DNA strand.

The implications of SNP identification are very significant indeed. The variation to be found in genomes of all species is astronomical in scale and animal and plant breeders can tailor their programmes to the exact recipe of traits required.

Pigsnp looked at 158 samples of DNA collected from five major pig breeds, Duroc, Pietrain, Landrace, Large White and Wild Boar. They availed of the high-throughput Illumina Solex sequencing technology that provides a large surface area for many thousands of parallel chemical reactions. Over 350,000 high confidence SNPs were isolated and, together with polymorphisms from other sources, a database with more than half a million SNPs has been constructed.

Using the PorcineSNP60 beadchip to validate the SNPs and determine genetic merit, Pigsnp achieved some 43,000 SNPs that were identified and these have been made freely available to the scientific community for research purposes. Of these, almost 4,500 were confirmed to be breed specific.

On a practical basis, one genetic trait that breeders want to eliminate from their stock is boar taint which confers an unpleasant taste to the meat due to certain testicular anabolic hormones. The beadchip was used to genotype pigs for potential boar taint. Use of genetic markers will eliminate the need to castrate animals, to date the only way of making sure that the meat will not taste unpleasant.

Although the pig genome requires additional analysis and annotation for precise genes to be pinpointed for undesirable traits, the PorcineSNP60 beadchip designed by Pigsnp has undeniable practical uses in the pig breeding industry. Extending the boundaries of genotyping to that of the single nucleotide can no doubt be extended to other breeding programmes and genomic study generally.