Genomics garners much attention at Holstein Convention

Tom Lawlor, Holstein USA's geneticist, spoke before a near capacity crowd at the 125th gathering of the nation's Holstein breeders. Based on the crowd size, it was clear breeders still have many questions following April's genetic evaluations.

During Lawlor's presentation, he told Holstein breeders that there were 1,471 cows that had imputed proofs this April . . . proofs derived from genomic test information from over five offspring. Since then, that number has risen to 2,004 cows as more animals enter the genomic database. Lawlor estimates that breeders saved some $500,000 in testing costs due in part to the imputed genomic proofs.

When it came to two hotly debated issues from the April evaluations, Lawlor told those in attendance that 98 percent of indexes went down when genomic evaluations were rescaled to more closely reflect bull evaluations. Meanwhile, when evaluations were imputed, 56 percent of indexes went up while 44 percent went down. It was the combination of these two events which caused all the turmoil. When rescaled evaluations and imputed proofs were added together, 83 percent of cow indexes dropped with only 17 percent going up.

Lawlor went on to tell breeders about two new genomic tests that were coming soon involving the 3K and 860K chips which will be in addition to the current 52K test. Lastly, Lawlor said that the rescaled indexes should be back on the same base by April 2011 as USDA geneticists hope to have all genomically tested cows on the same base as females with traditional evaluations.

Genomics rapidly evolving; unanswered questions remain

The latest USDA genetic evaluations ushered in numerous changes just three months after January's major base change. Among them were imputed female evaluations and cow evaluation adjustments which put genomically tested female evaluations on a more even playing field with genomically tested male counterparts.

While all these changes might have been scientifically sound, they came as a surprise to most breeders since there was little advance notice regarding the changes prior to the April release. The lack of notice combined with the fact that the majority of genomically tested females dropped due to the corrections caused a great deal of frustration for owners of elite cattle. On top of that, cow adjustments created a multiple currency system which now sees genomically tested cows on a different genetic scale than those with traditional genetic evaluations. In our May 10 issue, AIPL scientists answer some questions regarding imputed proofs and cow adjustments. We are attaching a PDF of that article to help answer these questions.
hdm-2010-05-10-0-343.pdf

At the latest Council on Dairy Cattle Breeding meeting in Baltimore, Md., on April 27 and 28, genomics continued to be a leading topic of conversation. Information shared with industry partners included:

• Full sibling do not share equal amount of genes from parents. In the past, it was thought that 50 percent of the genes came from the dam and 50 percent came from the sire. Genomic testing tells us that the number of genes in common between full siblings can range from 35 to 65 percent.

• The genomic evaluations for bulls with 99 percent reliability will change over time because scientists are learning more about the relationships within the Brown Swiss, Holstein, and Jersey breeds every month as more genomic data comes into the system.

• There are 50,119 animals with genotypes as of April 2010.

•North America is no longer in the lead for accuracy of genomic evaluations. A group of European countries (Germany, Holland, France, and Scandinavia — Denmark, Sweden, and Finland) have each contributed 4,000 genotypes for Holstein bulls to create a database of some 16,000 animals. The sharing system has created higher reliabilities — 5 percent higher — than those in the U.S. and Canada. German reliabilities are even a bit higher than other European countries because they tested an additional 1,000 bulls.

• The cow adjustments allowed genomically tested females to contribute to young bull evaluations. In Holsteins, the improvement in reliability went up 2.6 to 3.1 percent for yield traits. The improvement was greater for Jerseys at 7.7 to 9.4 percent. No adjustments were made in the Brown Swiss breed due to smaller population size.

To view the actual presentations from USDA scientists, click on the title to this blog and it will take you to the AIPL presentations.