CDCB changes to evaluation system (December 2018)
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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 |
|