Changes to evaluation system (August
2010)
Mexican cow records
By Paul VanRaden, George Wiggans, and Lillian Bacheller
July 6 update: Records from cows in some
Mexican herds are now included in USDA evaluations. Records included must meet
the same quality control standards required for U.S. herds, with inspection of
meter centers, laboratories, service providers, and processing centers
conducted by Quality
Certification Services, Inc. Records with state code 66 (Mexico) are
grouped in the southwest region to determine age adjustment factors and
heterogeneous variance adjustments. The Council on Dairy Cattle Breeding
approved this policy for including foreign data already in October 2003.
Mexican cows are not double counted in international evaluations because Mexico
does not send its own national evaluations to Interbull. From 1976-1996, the
Mexican national evaluations for milk yield were computed by USDA but were
separate from U.S. evaluations. The new approach of combined records should be
more accurate by including progeny across both countries. As numbers of records
increase, methods to account for genotype by environment interaction could
become more important in the future.
Validation of genomic
evaluations
By Katie Olson, Paul VanRaden, Mel Tooker, and Tabatha
Cooper
July 6 update: This
additional report provides statistics from the
validation.
Genomic evaluations were validated using tests developed and approved
by Interbull (Mantysaari et al.,
2010). Those tests are required before countries participate in genomic
multitrait across-country evaluation (Sullivan
and VanRaden, 2010) and before young bulls can be marketed in some European
countries. The validation is very similar to previous tests applied to U.S.
data (VanRaden et
al., 2009). August 2006 input data and genotypes of 5,822 proven Holstein
bulls and 2,200 cows with records were used to compute the predictions using
the latest software, cow adjustments, and imputed dam genotypes introduced in
April 2010. August 2006 predictions were also computed using genotypes of 1,616
proven Jersey bulls and 343 cows with records and 973 proven Brown Swiss bulls
and 83 cows with records. Regressions and reliability gains were computed by
predicting only bulls first proven in the United States after 2006. The numbers
of bulls used to test the predictions were 2,038 Holsteins, 313 Jerseys, and
103 Brown Swiss. Selective genotyping of the predicted bulls reduces observed
regressions and correlations as compared to true prediction ability in an
unselected population (Henderson et al., 1959;
Mantysaari et
al., 2010). Thus, the Interbull validation compares observed regressions
with expected regressions instead of with the theoretical value of 1 in an
unselected population.
Improvements to imputed dam
genotypes
By Paul VanRaden
Imputed dams have a genomic indicator code of 3 in
format 105 to
indicate that the cow's genotype was imputed from progeny DNA instead of
directly observed from her own DNA (code 1). In April, imputed dams had a
genomic indicator code of 1. Code 2 continues to indicate a nongenotyped
progeny with an evaluation that was recalculated to include information from
genotyped parents or imputed parents.
Technical refinements were introduced for determining genotypes of
dams from their genotyped progeny. Previously, progeny haplotypes were
determined by checking known parental haplotypes first and then searching the
list of population haplotypes in descending frequency order. The new strategy
also checks grandparental haplotypes if either parent was not genotyped. When
crossovers are detected, known alleles within maternal and paternal haplotypes
of the parent are used to impute any remaining unknown alleles within the
progeny's haplotype. Current instead of base population allele frequencies are
used for markers that could not be imputed from progeny genotypes. This change
has the largest impact and increases the genetic evaluations of imputed dams by
an average of $40 for net merit, 115 pounds for milk, 5 pounds for fat, 4
pounds for protein, and 0.3 months for productive life and decreases
evaluations for daughter pregnancy rate by 0.2 percentage units. Correlations
between imputed dam evaluations before and after these changes are about 0.96.
Correlation of genomic with traditional evaluation for milk increased to 0.87
from 0.84. Dams imputed for the first time in May or later updates were already
affected by these changes, whereas evaluations of dams previously imputed in
April remained official until the release of official evaluations in August.
In August, marker genotypes with one known allele and one unknown
allele have the known allele used in the evaluation and the current population
frequency substituted for the other allele. Previously, marker genotypes were
used only if both alleles were known. Also, the two most popular haplotypes
inherited by progeny are stored for each dam instead of only the first two
haplotypes encountered. This improved the genotype accuracy and made the
imputation resistant to incorrect pedigree data. With this greater accuracy,
imputed genotypes now are used to exclude progeny that have conflicts with
their dam at more than 1,000 SNP. Improvement of imputation will be continued
because this step is essential for combining different marker densities.
Preliminary evaluations using
3,000 markers
By George Wiggans, Paul VanRaden, and Curt Van Tassell
A 3,000 (3K) marker panel developed by
Illumina (San Diego, CA) in cooperation
with the
Bovine
Functional Genomics Laboratory (Beltsville, MD) may be available soon.
Current plans are to include 3K genotypes in monthly genomic updates and
distribute them to breeders as unofficial. Distribution files will include a
new field to indicate that an evaluation was based on a 3K genotype. Although
3K evaluations are not included in the August official evaluation, they could
become official in December pending industry review. The new programs for
haplotyping and imputation implemented in April 2010 allow multiple marker sets
to be included in the same evaluation. Use of 3,000 instead of 43,000 markers
for young animals results in 80% of the gain in reliability on average, with
slightly better results if parents are genotyped and worse if not. For example,
if genomic reliability with 43,000 markers is 70% and parent average
reliability is 35%, average reliability expected for a 3K evaluation is
0.80(70% − 35%) + 35% = 63%. Although cows and bulls with 3K genotypes
can add to the reference population, they contribute about 20% less information
than do animals with genotypes based on 43,000 markers.
Conception rate evaluations for
males and females
By Duane Norman, Paul VanRaden, Gary Fok, and Jana
Hutchison
Heifer conception rate (HCR) and cow conception rate
(CCR) are provided for females in bytes 374–397 of
format 105 beginning
in August. Parent averages for HCR and CCR of bulls have been added in bytes
604–615 of format
38 because dam evaluations are now available. Predicted transmitting
abilities for HCR and CCR were previously provided only for bulls (format 38
since January 2010 and a separate file during 2009). Neither trait is included
yet in net merit or evaluated genomically, but both options are possible in the
future as numbers of fertility records increase. Bulls and cows without HCR or
CCR records receive multitrait predictions of HCR and CCR from correlated
traits such as daughter pregnancy rate, and the two new traits are now used in
multitrait prediction of productive life.
Evaluation of sire conception rate resumed following a temporary
suspension in April and a new agreement among industry partners on data
transfer. Only requested herds are provided and used in the evaluation. The
Council on Dairy Cattle Breeding's efforts to promote a continuing supply of
data for research on fertility and other important traits are appreciated.