Enabling genetic evaluations of dairy, beef, pigs and chicken with large number of genotyped animals

Summary

Methodology for inclusion of genomic information used for the calculation of genetic values in farm animals had a computing limit of about 100,000 genotyped animals. We developed a method that removed that limit while increasing accuracy. The method is becoming standard in commercial applications.

Situation

Genomic selection has become a valuable tool in animal breeding because it can increase the genetic gain while reducing the generation interval. Early methods to incorporate the DNA information in multiple steps were complicated and often inaccurate. A different method developed at UGA called single-step GBLUP considers all the available information: DNA, pedigrees and phenotypes jointly. The method is accurate and simple to use but had a size limitation of about 100,000 genotyped animals. Over a million Holsteins and a quarter millions Angus cattle have been genotyped, with the numbers increasing fast.

Response

We derived a new algorithm called APY for inversion of the genomic relationship matrix. This algorithm is based on an observation that farm animals are closely bred and DNA in any animal contains large similar blocks from common ancestors. Subsequently, instead of considering possibly millions of DNA components (SNP), it is sufficient to account only for a small number of blocks of DNA. About 10,000 blocks are present in Holstein and Angus Cattle, with less than 5,000 blocks in pigs and broiler chicken. With the APY algorithm, we successfully concluded an evaluation of Holsteins with 720,000 genotyped animals. Computations took hours instead of weeks, and the genetic evaluations were more accurate

Impact

The single-step method using the APY algorithm allows the industry to incorporate the DNA information efficiently and reliably, without any limit on the number of animals with DNA. With this development, genomic selection is becoming a routine methodology, putting UGA in forefront of research in genetic evaluation worldwide.

State Issue

Agricultural Profitability and Sustainability

Details

• Year: 2016
• Geographic Scope: International
• County: Clarke
• Program Areas:
  • Agriculture & Natural Resources