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Genomic Test

Genetic Visions - Genomics Update: What Does The Future Hold For Genomic Evaluations And You

By: Dr. Michael Cowan, Vice President Research, Accelerated Genetics, General Manager, Genetic Visions, Inc.

January 2009, marked the start of genomic evaluations in the USA as an official genetic evaluation for dairy cattle. The Holstein breed provided the foundation for this new method of estimating the genetic merit of individual animals by assigning economic values to changes in the animal's DNA structure. Over the past year, sufficient animals in the Jersey and Brown Swiss breeds have been genotyped to include them as part of official genomic evaluations issued by USDA-AIPL. Collectively, nearly 40,000 animals have provided single nucleotide polymorphism (SNP) genotypes to the US database, a database that is shared, through cooperative agreements, with Canada for the Holstein breed.

The North American Collaboration consists of genomic evaluation services provided by USDA-AIPL and Canadian Dairy Network (CDN). Several years earlier, a Canadian AI organization became part of the Cooperative Dairy DNA Repository (CDDR), a DNA reference source and depository for the major US AI organizations. The current exchange of data largely stems from that association and the mutual use of Holstein sires as sires of sons for both countries' dairy industries. In August, 2009, CDN published its first official genetic evaluation for the Holstein breed, genomic information was included in the calculation and released monthly. Unfortunately, the base change in 2010 along with staffing shortages have since hindered monthly publication of genomic evaluations in the US. Through the dairy industry's funding of additional staffing positions, the USDA-AIPL has indicated that monthly publications will likely resume as early as February, 2010.

Other countries or geographic regions are actively establishing a system to utilize genomic information based on the contributions of USDA-AIPL scientists. Last year saw the launch of genomic estimated breeding values for Holstein cattle in Ireland. Currently a consortium of European countries is underway to share genotypic data from reference populations while establishing genomic evaluations for each country based on trait values within each country and breed of dairy cattle. AI companies in Holland and New Zealand also calculate genomic proofs from SNP data which may differ from the used in the US and Canada.

A new high density SNP beadChip from Illumina, manufacturer of the current bovine SNP would follow what has side; new, larger often 10-fold increases in SNP number population comprehensive assays introductions. If this happens, several steps will need to be considered. For instance-

  1. The reference populations used to predict genomic evaluations will most likely need to be re-genotyped with the new assay, but at whose expense?
  2. Does the increase in SNP number in the high density SNP panel focus on non-dairy cattle population and as such furnish limited new information?
  3. More SNPs means fewer samples per testing device thus expanded time frames required to test the same number of samples.
  4. Additional SNP genotypes per animal means larger data files and more computing capacity to handle data and corresponding processes.
  5. When predicting the true genetic merit of individuals, what is the increase in accuracy achieved by expanding the SNP numbers over current platform and does it offset the associated costs?
  6. How will this impact the low density SNP technology currently in development? These are but a few of the questions that will surface as bovine SNP technology advances and new devices are offered.

Genomic selection represents a significant improvement over traditional pedigree selection, moreover, the reason for the global incorporation of genomics in cattle breeding programs. Like any new technology, time is needed to best understand how to apply it and how it can best fit into the dairy industry.

Accelerated Genetics is in a unique position to evaluate several aspects of genomics and how it can better serve our customers and cooperative members.

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