The Cost analysis of breeding to improve eating quality of beef using genetic marker panels

Summary

Meat Standards Australia Australia (MSA) is an eating quality assurance program underpinned by a large body of consumer tests (Watson et al., 2008). The MSA grading system is unique in the world in that it assigns a palatability score to every cut/cook combination. To achieve this it uses empirical prediction equations to estimate eating quality from commercial inputs collected at grading. Previous MLA research has shown that individual gene markers (i.e. T1, T2, T3 and T4) and MVP predictions impacted on beef palatability (i.e. MQ4 score) for a range of muscles(Cafe et al., 2010b; Greenwood et al., 2013; Thompson, 2011; Weaber and Lusk, 2010; White et al., 2005). However the pathway to application and its use in genetic improvement is unclear. The first step in incorporating these results in MSA pathways is to examine the potential returns for using MVP predictions for harvesting and in selection of superior sires.
Existing data sets were used to estimate the effect of the tenderness gene markers on palatability across the musculature of the carcass. These estimates were used to calculate the expected effect of the tenderness gene markers on the MSA Index for the 39 muscles in the MSA model. In addition the economic impact of the tenderness gene marker will be estimated for an enterprise where cuts were simply harvested from a population. The economic impact of selection for tenderness gene markers in open and closed breeding systems was also be evaluated.
The cost of currently testing the SNP for the tenderness genes is currently of the order of $40/head. The fixed costs of testing are of the order of $7/head so it would be unlikely that a commercial service would be offered at less than $20/head. It was found that harvesting cuts based on the tenderness MVP without selection was unlikely to increase returns unless the average of the group had substantially lower MVPs than the across breed base (MVP at least 0.26 below). Selection of sires with improved MVPs could increase the carcass value of future progeny. It was estimated that selection of elite sire from within the example dataset could increase the carcass value by $11.3, $19.2, 23.9 and $29.1 with 30%, 10% 5% and 1$ of sires selected respectively. Therefore it is only with a high selection differential (greater than 5%) that one generation of testing would be likely to cover the cost testing.
Prior to any implementation better estimates of the relationship between tenderness MVP and MQ4 for the 39 muscles in the MSA model are required. It is suggested that increased consumer testing is required to cover the full musculature or a better means of predicting the regression coefficients for individual muscles as a function of MQ4 be developed. To this end a more strategic approach may be to invest in experiments to better understand the relationship with ageing rate and the mechanisms by which gene markers influence palatability.
Using either the current 4 markers or the 56 SNP panel it was predicted that response to selection based on the tenderness MVP would plateau as the genes became fixed in the population after 3 to 4 generations of selection. To avoid this better genomic functions need to be estimated using the full number of available SNPs. It is suggested that the current BIN resource be used to develop genomic predictions that are focused on using current sires.
In conclusion it is unlikely that producers could benefit from harvesting cuts based on MVPs, however this depends where the base for the MVP is set. Currently it is set at the mean of MVPs across all breeds. Therefore breeds with lower than average MVP would be penalized if they tested and reported MVPs on their animals. It was clear from the modeling exercises that selection for a tenderness MVP would lead to short to medium term improvements in MQ4 of selected animals. If the tenderness MVP is to be an input in the MSA model there are limited ways to defray the relatively high per animal testing costs. At $20/head the testing costs were of the order of 0.10$/kg carcass weight, whereas this would be effectively reduced by increasing carcass weight. Alternatively if used within a closed supply chain where product is marketed under a brand it may not be necessary to test individual progeny, rather the assumption is that a higher frequency of favourable tenderness SNPs will further promote the brand in terms of consumer satisfaction.
Given the finite lifespan of the current MVP which is based largely on the 4 tenderness SNPs (it was predicted that response to selection would plateau in 3 to 4 generations) it was suggested that the current beef information nucleus projects be harnessed to provide prediction equations using new closely spaced markers.​