BRAHMAN NEWS SEPTEMBER 2008 Issue #160
The “SmartGene for Beef” project is providing valuable information to further develop genetic evaluation in the Australian beef industry, provide new EBVs and increase the accuracy of some existing BREEDPLAN EBVs.
By integrating DNA marker information with BREEDPLAN phenotypic data and pedigree information to calculate marker-assisted Estimated Breeding Values “SmartGene for Beef” aims to help producers select more efficiently for economically important traits.
Tenderness was the key trait targeted by “SmartGene for Beef” because no EBV is available yet, and the trait cannot be directly measured on live animals. Tenderness is the most significant characteristic in consumer taste panel tests. Research has shown that it is a major limitation particularly for tropical adapted beef breeds consistently meeting eating quality standards.
The SmartGene results for tenderness are very consistent. Of the four GeneSTAR tenderness markers examined, T1 and T2 consistently showed significant effects in British breeds and T1, T2 and T3 showed effects in tropically-adapted breeds of cattle. These markers will be the major components of BREEDPLAN trial Tenderness EBVs to be released in October 2008.
Marker-assisted EBVs will allow producers to identify animals that are genetically pre-disposed to producing more tender meat. This will not only provide significant benefits to the Queensland (and the Australian) beef industry but also to our global customers.
The project was undertaken in three distinct stages:
Genotyping was performed by Catapult Genetics using ~12,000 DNA samples from Beef CRCI and II animals plus two industry projects. All animals were tested for the 12 commercially available GeneSTAR DNA tests (4 markers each for tenderness, marbling and feed efficiency). Results from the testing were transferred to the Beef CRC’s database.
The Animal Genetics and Breeding Unit (AGBU) then undertook analyses. DNA test results and performance measures (phenotypic measures of tenderness, intramuscular fat or IMF, marbling and feed efficiency in fully pedigreed animals) were analysed to estimate the full range of parameters required to calculate marker-assisted EBVs. Specifically this research estimated gene frequencies and evaluated the effects of each marker individually as well as sets of markers (T1-T4, M1-M4 & FE1-FE4) on each trait. The amount of variation accounted for by each DNA marker in each cattle population was estimated using these gene frequencies & gene effects.
Software development is now being done by AGBU (funded by MLA) to calculate trial BREEDPLAN marker-assisted EBVs. They will combine the DNA test results from Stage 1, the DNA test results from seedstock animals already reported with BREEDPLAN, the genetic parameters from Stage 2 and the phenotypic records collected in CRC-I and II to deliver the marker-assisted EBV methodology to BREEDPLAN.
Animals tested in “SmartGene for Beef” project came from two Beef CRC projects conducted over the past 15 years and two field experiments conducted by breed associations. These projects are summarised below.
Catapult Genetics supplied the DNA tests. Results were reported as 0, 1 or 2 ‘stars’ for each marker. A result of 0, 1 or 2 ‘stars’ means the animal carries zero, one or two copies (alleles) of the ‘favourable’ form of each gene or marker.
Comparing the allele frequencies of different experiments for the same breed showed only small differences. Where extreme frequencies exist (i.e. where fewer than 5% of animals have two copies of a particular allele or where >95% of animals have the same combination of genes for the marker of interest), a larger number of tested animals with phenotypes are required to establish the marker effects with confidence. Even when the effects can be established, they may have little utility as the markers with extreme frequency explain only a small amount of the genetic variation in that population, particularly if the favourable marker is at very high frequency.
Extensive analyses were done within each trait (tenderness, marbling and NFI). The performance measures (phenotype) and DNA test results were analysed extensively to determine the effects of each individual marker, as well as collectively as the total effect of all of the markers applicable to the trait. Each trait had a panel of 4 markers with the total number of favourable “stars” for each trait potentially ranging from 0 to 8 “stars”. A brief outline of the key results are presented here. More detailed results will be available from the websites of the SmartGene partners.
BEEF CRCI These data comprise seven purebred breeds, 4 temperate breeds (Angus, Hereford, Murray Grey and Shorthorn) (n=3,229) and 3 tropically adapted breeds (Brahman, Santa Gertrudis and Belmont Red) (n=3,615)
BEEF CRCII These data are from the CRCII northern breeding project focussed on tropically adapted cattle - including purebred Brahman (n=2,039) as one breed and Tropical Composites (from various pastoral companies) as another (n=2,400).
ANGUS PROGENY TEST Angus Australia progeny test program conducted using the NSW DPI Trangie Angus herd as dams (n=415).
DURHAM PROGENY TEST The Shorthorn Beef progeny test program conducted in Durham herd (n=347), Orange, NSW.
Figure 1: The average effect of increasing ‘stars’ on ld shear force
Figure 1 shows the average effect of increasing numbers of “stars” on beef tenderness when measured as longissimus dorsi (LD; loin muscle) shear force.
Shear force is a mechanical measure that can be likened to how much force a person needs to chew a piece of steak. The lower the shear force value, the more tender the beef.
The effect of increasing numbers of “stars” was statistically significant (P<0.05) in each of the populations tested. Key points in the tenderness results include:
The marker effect as either individual markers or as increasing ‘stars’ was neither statistically significant (P>0.05) or consistent for IMF, MSA marble score or AUS-MEAT marble score in any of the populations tested, including the Angus progeny test animals. Points to note with respect to the IMF and marbling results include:
Net feed intake (NFI) is a measure of how much an animal eats relative to an expected amount for its weight and growth rate. The lower the NFI value, the less the animal eats for its weight and growth rate and the greater the animal’s feed efficiency.
The effect of increasing number of ‘stars’ was statistically significant for NFI (P<0.05) in the CRC1 temperate breed population, but not statistically significant in any other population. The effects of the markers on other traits associated with feed efficiency (e.g. daily feed intake and feed conversion ratio) were very similar to the effects on NFI.
Because the feed efficiency (FE) markers were discovered from research on some of the CRCI temperate and tropically adapted animals it was expected the effect of the markers would be statistically significant in that population. However, the marker effects were not statistically significant in any other population, showing that when tested in totally independent populations, the estimated marker effects were not consistent or informative. Points to note with respect to the NFI results include:
The project is funded by the Queensland Department of Tourism, Regional Development and Industry. Partners in the project, include Catapult Genetics, Animal Genetics and Breeding Unit, Agricultural Business Research Institute, Cooperative Research Centre for Beef Technologies and Meat and Livestock Australia in Australia and Cornell University in the USA. Catapult Genetics, Beef CRC, MLA, AGBU and ABRI and Cornell co-fund the project by direct and/or in-kind- contributions.