AIPL RESEARCH REPORT
Imputation of Cow Genotypes and Adjustment of PTAsT.A. Cooper, M.E. Tooker, P.M. VanRaden, G.R. Wiggans, and J.B.Cole
Animal Improvement Programs Laboratory, ARS-USDA, Beltsville, MD 20705-2350
301-504-8334 (voice) ~ 301-504-8092 (fax) ~ http://aipl.arsusda.gov
As reported by [VanRaden (2010)], the imputed genotypes are, on average, between 96.6% and 97.9% accurate depending on breed. These values were tested using simulated data. The procedure was recently tested using a cow that was imputed for research purposes, and which was subsequently genotyped using the BovineSNP50 chip (Illumina, San Diego, CA). The imputed genotype and the genotype received from the chip were 98% similar.
|Breed||Number||% Correct Calls|
Genotyped cows usually are the most valuable cows in a dairy herd. These cows needed an adjustment because they were being over-evaluated. The high PTA values were causing the genomic predictions to suffer in accuracy because the marker effects were trying to explain a phenotype that was inflated compared to the bulls that carried those same genes. A study completed over a year ago showed that the added information from genotyped cows was not increasing reliability, indicating that some type of adjustment was necessary. By adjusting the over-evaluated cow PTA, it was possible to increase the accuracy of the genomic predictions. The following table shows the gains in reliability over PA when all genotyped animals were included in the predictor population, and when cows were excluded. Negative differences indicate traits where a greater gain in reliability is achieved when the females are not included in the predictor population.
|Gain difference||Reliability gain1
|Bulls Only||Bulls and Cows||Bulls Only||Bulls and Cows|
|Somatic cell score||22.0||23.1||1.1||5.9||7.5||1.6|
|Daughter pregnancy rate||27.0||27.7||0.7||10.4||10.6||0.2|
|1Reliability gain based on 2004 information to predict 2008 bull performance. 2010 Gains including imputed animals and adjustment.|
All genotyped cows, heifers, and imputed cows were adjusted by reducing the mean and variance of the traditional PTA. All genotyped animals including bulls, were affected by the adjustment made to the maternal portion of the parent average, regardless of the genotype status of the dam. The adjustments were made to milk, fat and protein and the percentage traits only. Brown Swiss adjustments where not implemented due to low numbers of genotyped cows.
Genomic evaluations are calculated using deregressed values from traditional PTA to estimate SNP effects. The upward bias of traditional cow PTA may be the reason for this. The direct genomic value (DGV) is the sum of an animal’s SNP effects. It should be consistent with traditional PTA which is true is for bulls. For cows, however, the traditional PTA is higher. To make the cow PTA more like those of the bulls for the yield traits (milk, fat and protein), mean and variance adjustments were calculated. Evaluations were stratified by reliability so cow PTA could be adjusted to be similar to bulls with the same reliability. The variance adjustment was the SD of deregressed Mendelian sampling within reliability group for bulls divided by the SD of deregressed Mendelian sampling within reliability group for cows. The mean adjustment is the difference between bull and cow evaluations after variance adjustment. Corrected PTA values were calculated from the adjusted deregressed Mendelian sampling values after reversing the deregression. Adjusted deregressed values were then used to calculate SNP effects. SNP effects are the contribution of that SNP to the total PTA for a given trait. This value can be positive or negative. The SNP effects are then applied to animals based on their genotype in combination with polygenic effects and the adjusted traditional values. This combined value is known as the genomic PTA. The following table shows the variance and mean adjustments applied to the deregressed values of the traditional cow PTA and maternal portion of the PA.
|Std. Deviation||Mean||Std. Deviation||Mean||Std. Deviation||Mean|
This table shows the gain in reliability for predicting the performance of young bulls using bulls and adjusted cows to predict SNP/marker effects verses using bulls and unadjusted cows. These gains in reliability are also observed in cows and heifers. The full paper is available [Wiggans et al.(2010)].
|Trait||Gain in Reliability|
Resulting genomic evaluations were more accurate when the rescaled cow PTAs were included in estimation of marker effects. Genomic evaluations for the top cows, top young bulls, and top heifers decreased by about 250 pounds for milk, 8 pounds for fat, and 5 pounds for protein, whereas genomic evaluations for the top bulls with daughters decreased only by about 70 pounds for milk, 3 pounds for fat, and 2 pounds for protein. Adjustments were largest for foreign bulls with a high proportion of genotyped daughters. The population average of all bulls with daughters decreased slightly by 40 pounds for milk, 1.5 pounds for fat, and 1.5 pounds for protein; standard deviations also decreased slightly by about 1%. Correlations between genomic evaluations before and after the adjustment were 0.997 for bulls with daughters and 0.990 for cows and young animals.
The PTA milk for Holstein cow A dropped from 1982 pounds in the January release to 381 pounds in the April release. She has several offspring, two are full sisters (whose sire is a high reliability (99%) bull) and will be used to illustrate the new changes.
Evaluation from January 2010 (all values are PTA milk pounds):
Both offspring are performing below parent average.
Evaluation from April 2010:
Genomic PTA = a + (b * Traditional PTA)
If you then want to see the effect changes to milk, fat, and protein have on $NM due to genotyping and the cow adjustment, use the value ($/PTA unit) Milk - $0.0001, Fat - $2.89, Protein - $3.41. Net Merit is affected by changes in many traits, the changes below strictly show those due to milk, fat and protein.
Genomic (Gen) $NM = Traditional (Trad) $NM - (Trad Milk PTA - Gen Milk PTA)*.0001 - (Trad Fat PTA - Gen Fat PTA)*2.89 - (Trad Protein PTA - Gen Protein PTA)*3.41
Holstein Cow Born in 2006 Traditional Evaluation:
Milk PTA = 1000 pounds
Fat PTA = 25 pounds
Protein PTA = 15 pounds
$NM = 400
Comparable Genomic PTA:
Genomic Milk PTA = -113 + (.76 * 1000) = 647
Genomic Fat PTA = 0 + (.70 * 25) = 17.5
Genomic Protein PTA = 1 + (.70 * 15) = 11.5
$NM = 400 - (1000 - 647)*.0001 - (25 - 17.5)*2.89 - (15 - 11.5)*3.41 = 366
|Trait||(Genomic PTA - Traditional PTA)|