In 2019, age at first calving is on course to be added to the Net Merit Index, and residual feed intake may not be far behind.
Earlier this year, measures for disease resistance – genetic evaluation for resistance to milk fever, displaced abomasum, ketosis, mastitis, metritis and retained placenta – were assigned economic values and incorporated into Net Merit, Cheese Merit, Fluid Merit and Grazing Merit Indices.
Paul VanRaden, research geneticist at the USDA Animal Genomics and Improvement Lab (AGIL), says age at first calving is also being assigned economic values and will be incorporated into the merit values, probably in 2019, and residual feed intake sometime further in the future.
He says the Council on Dairy Cattle Breeding (CDCB) normally lets breeders see the predicted transmitting abilities for new traits before including them in indexes.
VanRaden and his colleagues place a value of $2.50 per day for earlier calving. The economic emphasis could be about 3 percent of the Net Merit Index, which removes some of the emphasis from heifer conception rate.
The approximately 31 million records available nationwide for the age at first calving trait helped them to calculate a heritability for age at first calving of 2.7 percent and a predicted transmitting ability (PTA) standard deviation of “only about three days.”
He added the genomic reliability (measure of accuracy or degree of confidence in the genetic index for a particular animal) is 66 percent for Holsteins, allowing accurate selection even for newborn calves.
Back in 2017, VanRaden and colleagues starting taking a closer look at age at first calving to improve dairy cattle efficiency. “Since age at first calving is a phenotypic trait recorded on U.S. dairy farms, we investigated the feasibility of using this data in genomic selection. Favorable correlations with fertility and lifetime production traits, in addition to high sire reliabilities, suggested that age at first calving could be implemented as a new trait in genomic selection indices.”
The team determined the optimal age at first calving (without negative effects of calving too young, such as stillbirths) for Holstein and Brown Swiss cows is 21 to 22 months. Most Brown Swiss cows are calving five months later than optimum, and Holsteins are calving two months later than optimum.
Their initial studies suggest the genomic PTA values for age at first calving showed an improvement of greater than 20 percentage points in genomic young bulls compared to parent averages in Holsteins.
Feed efficiency
Although net merit rankings have indirectly accounted for feed intake by subtracting feed costs correlated with yield and bodyweight composite, the new addition of the residual feed intake economic value measures if a cow ate more or less feed than expected from her yield and bodyweight (independent of traits that were already included in the index).
VanRaden says although researchers and producers have long wanted to measure and select for feed efficiency, a higher reliability will require more research herds or international cooperation. Direct use in net merit can begin when formal agreements are established for more herds to supply ongoing feed intake data to CDCB, he notes.
Accuracy of evaluations
As VanRaden and others at the USDA Animal Genomics and Improvement Lab (AGIL) include new traits on the merit indices, they are very cautious of double-counting costs. He explained that sick cows have lower yield, fertility and productive life, and those traits already account for most of the expense. Therefore, when they added the new traits of resistance to illness, they were careful to avoid double-counting any of the costs.
He explains that some elite bulls now have all daughters genotyped with parentage always confirmed, while other sires may have 10 percent misidentified daughters. “The researchers found only small advantages in genetic rankings by accounting for accuracy of parentage. Bigger advantages may occur from adding more discovered ancestors of calves to their pedigrees, including 200,000 maternal grandsires and 200,000 maternal great-grandsires. These could be added using substitute IDs for the non-genotyped dams and granddams that are not known.”
AGIL has been working on revising DNA mapping. Using updated knowledge about single nucleotide polymorphisms (known as SNP, defined as a variation in a single base pair in a DNA sequence), researchers are restructuring the maps and increasing accuracy by “substituting more informative SNP for less informative ones, adding causative variants as they are discovered and eliminating SNP found to contribute mostly noise,” VanRaden said. “Inclusion of gene tests in haplotypes allows more precise tracking of the lethal recessives that cause embryo or calf losses when both parents contribute a defective allele.”
Researchers benefit from using the same standardized maps because it lets everyone track genetic differences using a common language while showing where the genes are and how the DNA encodes the proteins.
“Genomic selection is very successful,” VanRaden says, especially for previously recorded traits with large databases. The methods are constantly being refined to provide improved predictions for more traits. 
Kelli Boylen is a freelance writer based in northeast Iowa.
