Swine Cluster 1

Development of new genomic tools to improve meat quality traits 

and production efficiency in pigs 

Project leaders

  • Brian Sullivan, Canadian Centre for Swine Improvement Inc (CCSI), Ottawa, Ontario
  • Mohsen Jafarikia, Canadian Centre for Swine Improvement Inc (CCSI), Ottawa, Ontario

Project objective

Develop new genomic tools to improve meat quality traits as well 

as enhance product differentiation and efficiency of pork production.

Summary of the project

Canadian Centre for Swine Improvement (CCSI) and Canadian swine genetic organizations are collaborating to evaluate a new genomic tool that has been available to the Canadian swine industry since January 2009 – the 60K SNP (single nucleotide polymorphism) panel. The SNP panel and its practical application are being evaluated in major Canadian swine breeds. Two station-test trials were conducted: Test 27 (April 2010) and Test 28 (November 2010). Pigs entering the test station were evaluated for growth, feed conversion, feeding behaviour, conformation and extensive meat quality measurements, as well as genotyped using the 60K SNP panel. Associated biochemical measures were also collected. Additionally, on-farm phenotypic data measured on relatives of station-tested pigs (more specifically: sires, dams and full-sibs) and DNA samples were and will continue to be collected by participating breeders to increase the size of the resource population and provide additional data for further genomic analyses. 

This is a unique opportunity provided by the Swine Science Cluster initiative to build a work team focused on developing new genomic tools to improve meat quality traits, enhancing product differentiation and improving the efficiency of pork production. This will be especially useful for traits that are difficult and/or expensive to measure such 

as meat quality.

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Significant achievements

Over 6900 tissue samples were collected in-station and on-farm. 

This includes: 706 blood samples, 1280 ear tags, 314 semen samples and 4622 tail tags that were sent to DNA LandMarks for storage in the ‘DNA repository’. The 60K genotypes of the 631 station-tested pigs and 81 sires and dams of station tested pigs were loaded into the CCSI database for analysis. Individual monitoring of pigs from the nursery phase to the end of the growing phase via electronic IDs was performed during station tests. A total of 671 animals had growth and feed intake collected during the station tests. 

Data records from 635 station-tested animals were included in subsequent analyses and a total of 635 animals were slaughtered in batches over a 6-week period. Carcass and meat quality traits were recorded at the plant. The carcass traits included: reconstituted half carcass weight, loin eye area, half carcass length, leg weight, loin weight, shoulder weight, belly weight, leg yield, loin yield, shoulder yield and belly yield. 

Conformation scores for the following traits were recorded on station-tested pigs at Deschambault: Number of functional teats, number of total teats, locomotion, scores for feet and legs including pasterns and toes as well as ham and loin conformation scores. In total, more than 15 traits related to conformation were evaluated. A total of 194 Duroc, 

196 Landrace and 246 Yorkshire pigs had conformation scores collected at the test station (total of 636 pigs). A total of 1592 relatives of station-tested pigs had teat count records collected on farms.

Sow productivity data was collected on dams, full-sisters and half-sisters of station-tested pigs. A total of 29323 litter records collected on 5060 on-farm female relatives (dams, half-sibs and full-sibs) were loaded into the CCSI database. The number of litters for dams, full-sibs and half-sibs is expected to continue to accumulate throughout the project.

Meat quality measures on 622 station tested pigs were collected at the plant and loaded in the CCSI database. AAFC collected muscle tissues on carcasses at the plant within 48 hours after slaughter. 

The parameters measured at FRDC are: muscle glycolytic potential, citrate synthase, lactate dehydrogenase and malic enzyme activities, 

myofibrillar fragmentation index, shear force, water loss as well as proximal analyses for humidity, fat and protein. The analyses on 

meat samples for pigs from test 27 (n=329) were completed for all parameters listed above. Meat sample analyses from test 28 pigs (n=295) are underway. Shear force and glycolytic potential analyses were completed. The myofibrillar fragmentation index was measured on 133 pigs. The proximal analyses for humidity fat and protein have been completed for 115 of the 295 pigs from test 28 and enzymatic activities analyses were started recently started (n=10 out of 295). Muscle fiber typing (I, IIA, IIX, IIB) was completed for 78 pigs identified as candidates for gene expression analyses.

The genotyping of eight SNPs in the ADIPOQ, ADIPOR1 and ADIPOR2 genes of 622 station-tested pigs were received at CCSI 

and were loaded into the CCSI database.

Station-tested pigs were genotyped for known markers (CAST, PRKAG3, MC4R, CPT1A, ESR, CCR7, HMGA1 and IGFBP1) 

and the results were loaded into the CCSI database in July 2011. 

Preliminary data analyses on SNPs from the 64K SNP panel were carried out. Minor allele frequencies of SNPs, Hardy-Weinberg equilibrium as well as linkage disequilibrium between SNPs in the breeds under study were investigated.

Approaches on genomic evaluation were investigated and preliminary association analyses in backfat on the Yorkshire breed were carried out using SNP data collected from the current project and from previous ones as well. Additional preliminary analyses were carried 

out in the Yorkshire breed with regards to number of piglets born.


Associated documents  

Building a better bacon-Genomics Tools for Pork Quality