# Presentation: 660824

## AIPL Update

## Genotyped animals (October 2008)

| Breed | Bulls | Cows | Predictors |
| --- | --- | --- | --- |
| Holstein | 12,275 | 2,445 | 7,821 |
| Jersey | 1,205 | 369 | 1,428 |
| Brown Swiss | 365 | 3 | 359 |

## Experimental DesignHolstein, Jersey, and Brown Swiss breeds

|  | HO | JE | BS |
| --- | --- | --- | --- |
| Predictor: |  |  |  |
| Bulls born <1999 | 3,576 | 743 | 225 |
| Cows with data |  | 202 |  |
|  |  |  |  |
| Predictee: |  |  |  |
| Bulls born >1999 | 1,759 | 425 | 118 |

**Data from 2003 used to predict independent data from 2008**

## Reliability Gain1 by BreedYield traits and NM$

| Trait | HO | JE | BS |
| --- | --- | --- | --- |
| Net merit | 23 | 9 | 3 |
| Milk | 23 | 11 | 0 |
| Fat | 33 | 15 | 5 |
| Protein | 22 | 4 | 1 |
| Fat % | 43 | 41 | 10 |
| Protein % | 34 | 29 | 5 |

**1****Gain above parent average reliability ~35%**

## Reliability Gain by BreedHealth and type traits

| Trait | HO | JE | BS |
| --- | --- | --- | --- |
| Productive life | 18 | 12 | 2 |
| Somatic cell score | 21 | 1 | 16 |
| Dtr pregnancy rate | 16 | 5 | - |
| Final score | 18 | 6 | - |
| Udder depth | 35 | 13 | 3 |
| Foot angle | 14 | 10 | - |
| Stature | 26 | 9 | 3 |

## New Genetic Terms

**Actual vs. expected genetic similarity**
**Genomic relationships and inbreeding**
**Genomic future inbreeding (****GFI****) vs. ****EFI**
**Daughter merit vs. son merit**
**Haplotyping and imputation**
**Which allele is from sire vs. dam?**
**Which alleles are linked together?**
**Can missing genotypes be predicted?**

## Genomic vs. PedigreeInbreeding

| Bull | Pedigree F |  | Genomic F |
| --- | --- | --- | --- |
| O Man | 4.5 |  | 15.8 |
| Ramos | 2.3 |  | 11.5 |
| Shottle | 5.6 |  | 11.9 |
| Planet | 6.7 |  | 18.8 |
| Earnit | 6.2 |  | 12.8 |
| Nifty | 3.1 |  | 11.7 |

**Correlation = .68**

## Genomic vs. Expected Future Inbreeding

| Bull | EFI |  | GFI |
| --- | --- | --- | --- |
| Blackstar | 7.9 |  | 7.9 |
| Elevation | 7.6 |  | 7.4 |
| Chief | 7.1 |  | 6.8 |
| Emory | 7.0 |  | 6.9 |
| RC Matt | 7.0 |  | 6.7 |
| Juror | 7.0 |  | 6.7 |

## Net Merit by ChromosomePlanet - high Net Merit bull

## Schedule

**Calculate SNP effects with each of 3 annual traditional evaluations**
**Calculate genomic evaluations once or more between traditional evaluations, monthly?**
**Recalculate SNP effects if significant number of predictor animals added**
**Use existing SNP effects if only young animals added**

## Official release in 2009

**Information from genomic evaluations propagated to evaluations of descendents without genotypes**
**NAAB to manage bull-owner notification and sharing among AI organizations**
**Public release of genomic evaluations**
**Cows soon after calculated**
**Bulls when enrolled with NAAB or Canadian AI organization**
**Shared by agreement with owner**

## Low cost genotyping research

**Develop a genetic test that is cheap enough to enable use on most animals**
**Provide parentage verification/discovery**
**Provide a genetic estimate useful for first stage screening**
**384 SNP proposed for first test**
**High throughput procedures being developed**

## Reliability of evaluations

**Reliability from inverse of a matrix with order the number of genotyped animals**
**Approximation necessary as number of genotyped animals increases**
**Daughter equivalents discounted by 0.6 to represent better the reliability of 2003 data in predicting bulls first evaluated in 2008**

## Plans to increase accuracy

**Genotype more predictor bulls**
**Reach 1,500 Brown Swiss, possibly through foreign collaboration**
**Increase genotyped Jerseys from both domestic animals and possible foreign collaboration **
**Investigate across-breed analysis so Holstein data can improve accuracy for Jerseys and Brown Swiss**

## Haplotyping

**Haplotyping may increase accuracy**
**Even a SNP very close to a QTL may have a different allele frequency**
**Haplotype allele may have higher correlation with the QTL**
**May assist in imputation of genotypes of missing SNP and perhaps whole animals**

## International implications

**All major dairy countries are investigating genomic selection**
**Interbull meeting in January on integration of genomic evaluations**
**Studs must balance competitive benefit from treating genotypes as proprietary with benefits from sharing**

## Interbull

**Genomics contribution to accuracy should be reported**
**Avoid double counting when submitted by multiple countries**
**Could be processed similar to parent contribution**
**Change in 10-herd requirement needed to allow marketing bulls with only genomic information in countries without genomic evaluations**

## Query example

## Dystocia Complex

**Markers on ****BTA 18**** had the largest effects for several traits:**
**Dystocia: ****Sire and daughter calving ease**
**Conformation: ****rump width, stature, strength, and body depth**
**Efficiency: ****longevity and net merit**
**Large calves contribute to shorter PL and decreased NM$**

## Slide 20

## Markers on BTA18 with large effects

**Markers on BTA18 with large effects**

## SIGLEC proteins

**Human Siglec-9 highly expressed in the placenta (Foussias, 2000).**
**Human Siglec-6 may be involved in initiation of parturition (Brinkman-Van der Linden et al., 2007).**
**Siglec-6 binds and sequesters leptin (Brinkman-Van der Linden et al., 2007).**

## Proposed mode of action

**Leptin-deficient mice delay parturition (Mounzih et al., 1998).**
**Homozygotes may express high levels of Siglec-6, resulting in leptin deficiency and delayed parturition.**
**ss86324977**** may result in increased calf size associated with longer gestation lengths.**

## Interbull fertility traits

**Heifer conception as a rate (****heifer conception rate****)****‏****.**
**Ability to recycle after calving (****days to first breeding****)****‏****.**
**Cow conception as a r****ate (****cow conception rate****) and interval (****first breeding to conception****)****‏****.**
**Calving to conception (****days open****)****‏****.**

## Status of fertility traits

**Traits 1 ****and**** 3**** (heifer and cow conception rates) submitted to Sept. 2008 test run.**
**Work on ****Trait 2**** (days to first breeding) is underway.**
**Trait 4**** (ability to conceive as an interval) is now required.**
**We already report ****Trait 5**** (DPR).**

## Heifer and cow conception rate

**Heifer conception rate (****HCR****) is the percentage of inseminated heifers that become pregnant at each service.**
**Cow conception rate (****CCR****) is defined as the percentage of inseminated cows that become pregnant at each service.**

## Conception rate variance components

## Correlations among fertility PTA

- Correlations among PTA for bulls with at least100 CR daughters.

## Distribution of Heifer CR PTA

## Distribution of Cow CR PTA

## Top bulls – Heifer CR

## Bottom bulls – Heifer CR

## Top bulls – Cow CR

## Bottom bulls – Cow CR

## Acknowledgments

**Genomics work supported by NRI Grants 2006-35205-16888 and 2006-35205-16701 and by NAAB.**
**Much of the work on heifer and cow CR was carried out by Dr. Melvin Kuhn while he was at AIPL.**