Limousin Information Nucleus and Young Sire Testing Project

Summary

DNA marker discovery was moving from searching for genes of large effect and small marker panels to the use of high density Single Nucleotide Polymorphism (SNP) panels to discover many SNPs with small effects. In order to validate the predictions from the currently available small marker panels marketed by genomic companies and to enable Genome Wide Scans (GWS) to search for informative SNPs for production traits the availability of a large number of animals phenotyped for a wide range of traits became important. It also became increasingly evident that prediction equations from the high density SNP panels were likely to be breed specific.

For the Limousin breed to take advantage of new genomic technologies it was essential to establish a database of Limousin or Limousin cross animals with known pedigree,a comprehensive phenotypic profile and stored DNA.
The most effective way to produce the database was an Information Nucleus which involved a progeny test of young bulls where all progeny are grown out and slaughtered. Additional advantages of the progeny test model are that some young bulls would gain accurate genetic information (EBVs) for a wide range of traits and could be utilised to increase the genetic progress of the breed.

The project ran over three cohorts of calves each sired by 10 young Limousin sires, a group of Charolais bulls and a group of Shorthorn bulls mated predominantly to mature Angus cows Some high content Limousin cows which were mated only to the Limousin bulls in each cohort. All progeny were backgrounded on pasture or forage oats after weaning and were finished in a commercial feedlot or the Tullimba research feedlot for a minimum of 100 days except for cohort 1 heifers (finished on grass).
An extensive range of phenotypic measures was taken on each calf including birth traits, growth traits, carcase traits docility and MSA and laboratory eating quality traits. All progeny and their measurements were recorded in the ABRI crossbred register. Those traits currently analysed by BREEDPLAN were routinely analysed in the Limousin BREEDPLAN analysis. High quality DNA extracted from blood was stored at the University of Queensland Animal Genetics Laboratory for all sires and progeny.

Progeny from the first cohort were tested with an Illumina 50K genomic test by the CRC for Beef Genetic Technologies. Along with the genotypes from 345 influential Limousin sires the genomic results for cohort 1 progeny were used to test the veracity of the CRC multibreed genomic prediction equations for the Limousin breed and also to test prediction equations developed for the Limousin breed in the USA by Merial through their subsidiary,Igenity. In both cases the the prediction equations were not sufficiently accurate to justify the inclusion of genotype predictions into the Limousin BREEDPLAN analysis.

Benefits to industry

The industry benefit of this project is that the accurately measured and genotyped animals along with 345 genotyped influential sires will allow the Limousin breed to take advantage of the Single Step BREEDPLAN Genetics and genomics which utilises genomic test results to increase the accuracy of EBVs and Indexes and to get EBVs for hard or expensive to measure traits such a NFI and carcase traits. This will increase the rate of genetic gain for Limousin seedstock herds which will in turn benefit the Australian beef industry.