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Meat - Next Generation Project - Biology & Production Pathways

Project Leader

Dr Matthew McDonagh
Department of Primary Industries, Victoria
Tel: 03 9217 4385
Email -

This project has been completed.

Photo: Courtesy MLA
Photo: Courtesy MLA

About the Project

The objectives of this project are:
• Consumer eating quality and new mechanistic phenotypes for omega 3 fatty acid content, will be measured on animals from the INF
• Genes of large effect on muscle omega 3 levels and eating quality will be discovered
• SNP close to genes of large effect on these phenotypes will form a crucial part of commercial tests for genetic selection of animals for omega 3 and eating quality

Business Case

Promoting lamb based on levels of iron, zinc and omega-3 fatty acids that reach official dietetic claims (i.e. a nutritional source) has been a key marketing strategy by Meat & Livestock Australia’s (MLA) human health and marketing division within the last year. The current information in data bases held by MLA suggests Zn levels are adequate but that Fe and Omega 3 could be improved – the improvement required is some 10-20%, in other words we believe quiet achievable.

The work on consumer eating quality is associated with understanding how the genetic interactions between production and meat traits will influence the eating quality of the loin and topside – a large muscle in the back leg of lambs. An added benefit of this work is that we aim to understand genetic variation in the eating quality of the topside. In the current Meat Standards Australia recommendations, the topside cannot be sold as a separate cut since it fails as a grill or roast because it is tough. However as lamb carcase weight increases to around 23kg and above, boning rooms wish to not only extract the round and rump (leaving a traditional easy carve leg) but also the topside so as the remaining ‘new easy carve leg’ is of a better portion size for retail purchase. Further to this, analyses of eating quality data from the INF has
demonstrated that the progeny means for some sires are close to unacceptable levels. Variation around these means shows that a significant proportion of animals are delivering unacceptable levels of meat toughness. This problem has been identified as critical to address by MLA and the subprogram.


The project aims to improve the market value and productivity of lamb through mechanistic understanding of how mineral and Omega-3 fatty acids develop in different muscles of high productivity animals and how variation in these phenotypes and meat tenderness influences consumer perceptions of eating quality. We have 3 main work area aims, 1) To identify variation in narrow genomic regions in close association with genes of large effect on the mechanisms underlying these phenotypes and use this genetic variation to improve these lambs, 2) To determine the relationships between variation in objective measures of meat tenderness and omega 3 levels with consumer evaluations of meat quality parameters, and 3) To expedite the analysis and interpretation of INF meat quality mineral and meat quality data.

Work area 1) We propose that narrow gene regions that have large effects on nutritional quality and eating quality phenotypes are already known and that SNP coverage across these loci on the 50K chip is not sufficient to explain their influence. Whole genome associations using the INF data and the 50K SNP chip show that the 50K SNP chip has low coverage of the Calpain (CAPN) and Fatty Acid Desaturase (FADS) loci and that the SNP that are present do not associate significantly with tenderness or with omega 3 content. Deep sequencing has been conducted on 30 sires from the INF, which were chosen based on divergence in tenderness and omega 3 phenotypes in their progeny. We have discovered 7000 new SNP within the CAPN and FADS loci, of which 192 SNP have been made into a research SNP assay for meat tenderness and omega 3 content. The 192 CAPN and FADS loci SNP were chosen based on even spacing across the CAPN and FADS gene regions and good representation across breeds. Both the discovery of SNP relevant to the INF population and increasing our understanding of these genes will strongly underpin the new molecular technologies for gene marker assisted selection in these difficult to measure traits. These loci have been demonstrated to explain a large proportion of variation in these traits in other meat species and incorporation of predictive markers from the 192 CAPN and FADS loci SNP will improve predictive accuracy of the 50K SNP chip.

We have genotyped 700 progeny from the 2007 INF flock for the 192 CAPN and FADS loci SNP. These progeny are related to the sires from which the 192 CAPN and FADS loci SNP were identified. A further 700 progeny from the 2010 INF will also be genotyped prior to 30 June 2011 with the 192 CAPN and FADS loci SNP. The 2010 INF progeny have been selected based on availability of core INF meat traits and consumer eating quality data on 2 muscle types.

The new work proposed for 2010/2011 was to complete the SNP association analysis of the 192 CAPN and FADS loci SNP with INF meat traits and with consumer eating quality assessment data. This work will involve computational analysis time to complete the SNP associations and to determine the relationship between the research 192 CAPN and FADS loci SNP and the 50K SNP chip. We hypothesise that the predictive ability of the 192 CAPN and FADS loci SNP will provide significant additional predictive capacity to the 50K SNP chip. If accurate imputation of the dense 192 CAPN and FADS loci SNP is possible based on association with SNP on the 50K chip, we may be able to improve prediction for tenderness and omega 3 content across the broader INF.

Work area 2) We have completed collection and processing of loin and topside samples from 750 lambs of the 2009/2010 drop Kirby and Katanning INF sites. These samples have had sensory evaluation completed and our preliminary analysis demonstrate that genotype has asignificant influence on consumer perceptions of tenderness and overall liking.

The new work proposed for the 2011/12 financial year will be to complete sample collection and preparation for consumer testing of loin and topside muscles from 750 WA Katanning and NSW Kirby 2010/2011 INF drop lambs. These cuts will be collected, shipped, prepared and stored for later consumer testing. This data will contribute to new work on Omega 3 fatty acids plus also underpin the objective meat science measures being undertaken in 3.1.

Work area 3) Muscle mineral (Fe, Zn and myoglobin) data and intramuscular fatness (IMF) data from the 2007 and 2008 drop INF lambs has now been curated and analysed. This analysis has shown that IMF is associated with more aerobic muscle profiles. Preliminary estimates of associations between myoglobin and aerobicity appear to follow a similar trend to IMF. Large sire effects were observed for iron and zinc levels and although selection for muscling (PEMD) reduced zinc levels in muscle, it had no influence on iron.

Summary of Work Program

  • Bioinformatic analysis for SNP association in causative genes and related regulatory genomic regions that control omega 3 synthesis and meat quality will be undertaken (0. 5 post doc). This will include analyses to enable imputation of predictive SNP across all animals that have been genotyped with the 50K Chip
  • Completion of sample collection and data analysis from the 2010/11 WA Katanning and NSW Kirby INF site will be overseen for the consumer eating quality project.
  • Data analysis of the meat science phenotypes will be conducted to establish phenotypic and genetic correlations in collaboration with the Information Nucleus program (0.5 post doc) and 'Range of new meat phenotypes measured' project.

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