• Home
  • Breed
    • Brown Swiss Breed
    • World Conference 2021
    • Annual Report
    • Genetics
    • History
    • BS Historical Society
    • Brown Swiss Bulletin
    • Research
    • Sales
    • Latest News
  • Programs
    • Calendar of Events
    • All American Contest
    • BSA
    • BEST Program
    • Classification
    • Cow Recognition
    • Membership
    • Fees
    • National Awards
    • National Convention
      • 2020 Convention Minutes
    • Records
    • Shows
  • Youth
    • Junior Programs
    • Junior Contests
    • Youth Spotlight
    • Show Rules
    • State News
    • 2020 Jr Newsletter
  • Spotlight
    • All-American
    • Breeder Profile
    • Performance Awards
    • Individual Awards
    • 2019 National Shows
    • Outside our Borders
    • 94 & 95-Point Cows
  • Register
    • Why Register?
    • Identity Enrollment
    • Database Instructions
    • Reg & Embryo Rules
    • Embryo Flush Recording
    • Fee Schedule
    • Parentage Verification
    • Pedigree Description
    • Tattoos or Eartags
  • Applications
    • Registration
    • Membership
    • Subscription
    • Programs
    • Genetic/DNA Testing
  • Contacts-Links
    • Staff
    • Board of Directors
    • Committee Members
    • State Secretaries
    • Industry Links
    • Breeder Links
    • Brown Cow Talk
    • Facebook
Brown Swiss Association
25 Latest Articles Current Articles | Archives | Search

CDCB Changes to Evaluation System (Dec 2018)

CDCB changes to evaluation system (December 2018)

.

Changes in Haplotype Distribution in Holstein, Brown Swiss and Jersey

By Paul VanRaden and Daniel Null

Previous Brown Swiss and Jersey haplotypes BH1 and JH2 will be discontinued effective with the December 2018 run. Several European bulls are homozygous for BH1, and its fertility effect is no longer significant. Thus, US and European Brown Swiss associations have decided to discontinue reporting BH1.

Haplotypes BH1 and JH2 met the initial statistical tests for publication in 2011 and 2013, with no homozygous animals found at that time. The new ARS-UCD reference map makes JH2 very difficult to trace. The fertility losses from BH1 and from JH2 carrier matings were retested using the most current four years of data, and neither were significant. As causative mutations were not found for either BH1 or JH2, both haplotypes will no longer be reported.

A new recessive haplotype in Holsteins (HH6) was discovered in France on chromosome 16, and will now be listed. The fertility effects of HH6 were confirmed with a 9% drop in conception rate.

New Reference Genome Assembly in Use at CDCB

By Dan Null, Derek Birckhart, Paul VanRaden, Lillian Bacheller, John Cole, Jeff O’Connell & Ben Rosen

An updated genome sequencing reference map – called the genome assembly – has been adopted for CDCB evaluations, effective with the December 2018 run.

USDA-AGIL and USDA-ARS researchers, in cooperation with the University of California-Davis, released a new version of the cattle reference genome assembly named ARS-UCD1 (Rosen et al., 2018), replacing the University of Maryland version used since 2009 (UMD3) as the common language worldwide for tracking variation in cattle. The updated assembly has led to a new SNP list for genomic evaluations, and adoption is expected to improve genotype imputation accuracy and recessive haplotype calculation.

ARS-UCD1 showed improved imputation of genotypes, alignment of sequence from other animals and annotation of gene structure. The new map better matches true DNA sequences with improved marker order. The ARS-UCD assembly represents a vast improvement in the continuity of the bovine Genome.

Genomic Evaluations Using an 80k SNP Set

By George Wiggans, Daniel Null, Lillian Bacheller and Paul VanRaden

Effective December 2018, the number of markers used in genomic predictions increased to 79,276 (or 80k) from the previous 60,671 used since 2014. The revised list includes more exact gene tests added recently to chips, removes poorer performing markers, adds new variants with larger effects on traits and changes the marker order based on the new map. Reliability gains averaged 1.4% using HD chips including gene tests. One important mutation controlling about 30% of fat yield is now directly included (DGAT1; Gautier et al., 2007). The largest individual PTA changes in each breed were observed on foreign animals that are less connected to the US population, animals with less complete pedigrees, and animals genotyped with the lowest density chips.

Large Number of Gene Tests Added to Haplotype Determination

By Daniel Null and Paul VanRaden

Numbers of SNPs, inclusion of gene tests and presence or absence of nearby SNPs with poorer quality can affect carrier status for fertility haplotypes. The new 80k SNP set now contains many more gene tests that were added to recent chips and provided to CDCB, primarily from Neogen. Those tests help impute carrier status for all other animals.

Six gene tests were added for Holstein, two for Ayrshires, and one for Brown Swiss, and one test was corrected for Jersey. Comparisons of carrier status from the new versus old list reveal that most haplotypes are very stable, but a few more animals switched to being carrier than to being non-carrier. That may result from the gene tests revealing additional families not previously known to be carriers or from better haplotype inheritance with the new map and more rigorous SNP edits.

 Brown Swiss

Haplotype Same
status
Changed to
carrier (%)
Changed to
non-carrier (%)
Haplotype
frequency
Comment
 BH1 n/a .00 16.09 .00 Discontinued haplotype
 BH2 99.4 .42 .20 13.3 Gene test added
 BHD 98.7 .92 .37 3.0
 BHM 99.3 .66 .06 4.0
 BHP 99.6 .07 .31 2.5
 BHW 99.9 .07 .06 1.2
Share |
Copyright 2014 by Brown Swiss Association
Privacy Statement | Terms Of Use | Login |