Changes to evaluation system (January
Genomic evaluations become
By Paul VanRaden*, George Wiggans*, Tad Sonstegard†, Curt
Van Tassell†, and Leigh Walton*
Improvement Programs Laboratory, †Bovine Functional Genomics
|UPDATE (January 12, 2009) – The previously announced plans for December 2008 and January 2009 calculations were modified as follows. On December 18, lactation records were updated and new evaluations computed using an additional 3 weeks of data for cows and more data for bulls than at the November 30 cutoff used to prepare files for the December 9 Interbull deadline. However, genomic evaluations that were released on December 1 were not recomputed in mid-December as anticipated. The genomic evaluations from December 1, 2008, are official unless 1) the bull's reliability for net merit was higher in the traditional evaluation from December 18, 2008, or 2) the bull had foreign daughters, in which case the Interbull multitrait, across-country evaluation is official. Counts of daughters and herds are from December 18, 2008, for domestic bulls and from November 30, 2008, for bulls with foreign daughters even though only daughter data from July 26 (August 2008 evaluation data) were included in genomic evaluations. Among previously active AI bulls, only 20% gained a sufficient number of daughters for their December 18 traditional evaluation to replace the December 1 genomic evaluation. For future evaluations, AIPL plans to include all new phenotypic information in genomic calculations.|
|UPDATE (January 22, 2009) – Tables summarizing differences between December 2008 genomic and traditional evaluations are available for active AI bulls and for young bulls.
Genomic predictions of genetic merit become official in January 2009.
Predicted transmitting abilities (PTAs) use genomic data derived from DNA in
addition to traditional phenotypic and pedigree data. Genotypes for 38,416
single-nucleotide polymorphisms evenly distributed across all 30 chromosomes
document which genes each animal inherited and provide a new source of
information for genetic evaluations. Formats
genotyped status in bytes 547 and 190, respectively. Codes are 0 for
traditional evaluations, 1 for genotyped animals, and 2 for descendants of
genotyped animals with reliabilities that increased by at least 1% because of
inclusion of genomic information in the parent average (PA). Descendants of
genotyped animals have updated PAs and PTAs using the same methods developed
previously to include information from foreign parents. Ancestors are not
updated because programs are not yet available to transfer genomic information
from a genotyped calf to its nongenotyped dam, for example.
Genotyped heifers are eligible for elite status and have records in
the format-105 files. Genotyped young bulls are not eligible for active
artificial-insemination (AI) status. However, genomically tested bulls that
will be marketed are identified as G status. Format-38 files include a record
for each bull with a National Association of
Animal Breeders (NAAB; Columbia, MO) code, and the genomic PTA is listed as
official for genotyped bull calves only after they receive an NAAB code because
of NAAB's 5-year exclusive license or after they reach 24 months of age.
Domestic test files for
format 105 and for
format 38 are
available for inspection. Evaluations contained in these files are not from the
latest December calculations but rather from an earlier test in October. A
U.S.-only version of format 38 without genomic information added is provided so
that genomic adjustments can be better understood. Genomic equations are solved
using data from the previous multitrait, across-country evaluation from the
Interbull Centre (Uppsala, Sweden).
The official PTA for each proven bull includes the extra information from
genomics or from new daughters added since the last evaluation, but not both,
because recalculating genomic predictions after the arrival of Interbull data
on the Thursday prior to Tuesday release is not feasible.
Calving-trait and type files also include genomic evaluations as
official, and programming to include those records has begun. Breed
associations and NAAB continue to distribute calving-trait and type files.
Genomic predictions are available for 16 linear traits but not feet/legs score,
rear-teat placement, or rear-udder width. Currently, genomic net merit is
obtained by directly analyzing net merit as a trait, because genomic results
were not available for all individual traits. Genomic evaluations for
stillbirth began in October 2008. In the future, genomic net merit could be
obtained as a sum of individual genomic PTAs as is done for breed association
composites and indexes.
Genomic predictions for Holsteins have been computed about every 2
months since April 1, 2008. Initially, letters to owners and computer files
labeled as unofficial were distributed directly from the Animal Improvement
Programs Laboratory (AIPL), but breed associations and NAAB now provide those
services. Jersey genomic PTAs were tested in June, found to be significantly
better than PAs, and distributed unofficially to owners in October 2008.
Because of limited numbers of genotyped bulls, Brown Swiss predictions were not
much better than PAs and were not distributed. Negotiations have begun on
obtaining more Brown Swiss genotypes from Europe. As of October 2008, the USDA
database includes 368 Brown Swiss, 1,558 Jersey, and 14,720 Holstein
Genomic inbreeding coefficients and genomic estimates of future
inbreeding (GFI) analogous to expected future inbreeding (EFI) are now included
in computer files for genotyped animals. Genotypes allow measuring actual
homozygosity and percentages of genes in common instead of the expected
fractions computed from pedigrees by
formulas. For GFI, the reference population is all genotyped animals born
in the last 10 years. For EFI, the reference population is a sample of females
born in the last 5 years. Thus, GFI and EFI should have nearly the same
interpretation and, in fact, are similar numerically. Genomic inbreeding is
about 2% higher for males than for females because the X chromosome is coded as
homozygous in males.
Reliability of PA for young Holstein bulls and heifers averaged 36%
for net merit but increased to 66% when genomic information was included.
Theoretical reliabilities were reported initially but now have been reduced by
multiplying the theoretical gain in daughter equivalents by 0.6. For young
bulls, genomic PTAs for some traits average a little lower than PAs because
upward biases in PA are being corrected. For example, genomic net merit
averaged $388 compared with $420 for traditional PA; genomic PTA protein
averaged 34 pounds compared with 39 pounds for traditional PA. For active AI
bulls, genomic evaluations had significantly higher reliabilities than
traditional evaluations for nearly all traits and were distributed unofficially
on the AIPL web site beginning in August 2008.
Further explanation of the methods for calculating
evaluations are available.
By John Cole, Dan Null, and Paul VanRaden
Milk, fat, and protein lactation records were computed jointly by
multitrait best prediction instead of separately by single-trait best
prediction. Somatic cell score evaluations continue to be on a single-trait
basis. Best prediction recently has been enhanced by the addition of improved
lactation curve functions, new estimates of correlations among test days, and
the ability to accommodate lactations longer than 305 days.
Gains in reliability for milk and components yields were expected
because of the change to multitrait best prediction, particularly for bulls
with many daughters in alternative test plans, because estimates of missing
test-day yields can be calculated through correlations with other traits.
Reliabilities for PTA protein of active AI sires increased as expected for all
breeds, with gains ranging from 4.2% (Brown Swiss) to 7.5% (Jersey).
Reliabilities for PTA milk increased slightly (~1%) for Guernseys, Jerseys,
Holsteins, and Milking Shorthorns but were unchanged for Ayrshires and Brown
Swiss. Records from milk-only herds were examined, and quality of data was
found to be poor; those records continue to be excluded from routine
Further explanation of the methods for calculating
best predictions of
lactation yield are available.
Cow and heifer conception
By Jana Hutchison and Paul VanRaden
Genetic evaluations of bulls for cow conception rate (CCR) and heifer
conception rate (HCR) are being released for the first time in January 2009.
The CCR is based on data and a model similar to those introduced for
rate (SCR) in August 2008; HCR is based on previous research reported by
Kuhn et al.
For CCR, PTA ranged from −8% to +8%; HCR PTA
ranged from −5% to +5%. Models and edits for CCR and HCR are described in
GE along with daughter pregnancy rate. For Holsteins, genetic correlations
with traits similar to CCR from 10 other countries ranged from 0.50 to 0.90 and
averaged 0.73. Correlations of HCR ranged from 0.76 to 0.91 with 5 other
countries and averaged 0.83. Interbull correlations for CCR averaged 0.62 for
Jerseys, 0.69 for Brown Swiss, and 0.78 for Guernseys; correlations for HCR
averaged 0.88 for Jerseys, but other breeds had insufficient data for analysis
because conception records were stored only after 2003. Evaluations for CCR and
HCR are not yet included in net merit or in format-38 files. Instead, the 2 new
traits are available in a separate, downloadable file
that includes both domestic and foreign bulls.
Acknowledgement: Development of
genetic evaluations for CCR and HCR was completed primarily by former AIPL
scientist Dr. Melvin Kuhn, and we thank him very much for his contribution.