Changes to evaluation system (August
2009)
Brown Swiss genomic
evaluations
By George Wiggans, Paul VanRaden, Tad Sonstegard, and Curt Van
Tassell
Official genomic evaluations were computed for 906 Brown Swiss
animals. Reliability was improved over initial tests by genotyping additional
bulls not previously available in the Cooperative Dairy DNA Repository and by
trading genotypes for 115 bulls with the Swiss Brown Cattle Breeders'
Federation in Switzerland in a trade arranged by Dan Gilbert and Jürg
Moll. For young animals, genomic reliabilities average about 12% above parent
average reliability, as compared to 20% for Jerseys and 30% for Holsteins. The
U.S. Brown Swiss Association will distribute evaluations for both males and
females. They offer testing of females and young bulls because testing of bulls
is not restricted to NAAB members in this breed.
Revised marker set used in genomic
predictions
By Paul VanRaden, George Wiggans, Mel Tooker, Jana Hutchison, and
Lillian Bacheller
An expanded set of 43,385 markers was used to compute genomic
evaluations for all three breeds. Previously, markers were required to have
minor allele frequency > 0.05 for Holsteins and > 0.03 for other breeds
(Wiggans et al,
2009), and numbers used were 38,416 for Holsteins, 31,628 for Jerseys, and
34,593 in preliminary tests of Brown Swiss. Single-nucleotide polymorphisms
(SNPs) with low minor allele frequency or even monomorphic SNP were included
after edits to remove SNP that had many missing genotypes or parent-progeny
conflicts. Observed gains in reliability from using the new SNP set were mostly
positive but < 1%. Research on evaluations and relationships across breeds
has begun using the common SNP set. While reprocessing previously called
genotypes, missing parentage markers from the set recommended by
Heaton et al
(2007) were recovered for use in verifying parentage of genotyped animals
worldwide.
All laboratories now report called genotypes rather than only
intensity files. AIPL has discontinued calling genotypes after verifying
consistent genotyping among the laboratories. Genotypes are edited and stored
in AIPL's database as received, allowing pedigree conflicts or quality problems
to be resolved sooner and simplifying recovery of genotypes after conflicts
have been resolved. Marker quality remains excellent. Less than 0.4% of
genotypes have missing values, and 75% of the 43,385 markers have no
parent-progeny conflicts among the 32,234 genotyped animals in the
database.
Blending of genomic and current
Interbull evaluations
By Paul VanRaden and Jay Megonigal
Aug 14 UPDATE: The previously
announced blending of genomic and current Interbull data in the final selection
index will not be implemented in August, partially because of time constraints
caused by receiving corrected Interbull files later than anticipated. August
2009 evaluations will use the same methods as in April of comparing
reliabilities to determine if the current Interbull evaluation is official or
the genomic evaluation estimated from current domestic evaluations and previous
Interbull evaluations . An exception is that the blending procedure was used
for Holstein type traits, as in April. The second proposed change, that genomic
evaluations replace traditional evaluations for genotyped animals even if the
reliability did not increase by >1%, was implemented for August evaluations.
Previously, traditional evaluations were official if genomic reliability was
not at least 1% higher, for example if traditional reliability was 99%. AIPL
regrets any inconvenience this may cause.