# Presentation: 714303

## Genomic History and New Genetic Principles 

## Genetic Markers: Changing GoalsPast and Future

**Determine if major genes exist ****(few)**
**Estimate sparse marker effects**
**Only within family analysis**
**Find causative mutations ****(DGAT1, ABCG2)**
**Estimate dense effects across families**
**Implement routine predictions**
**Increase REL**** with more genotypes**
**Decrease cost**** with a selected SNP subset**

## Genomic History at Beltsville

**174 markers, 1068 bulls, 8 sires**
**Illinois, Israel, and AIPL**
**1991-1999**
**367 markers, 1415 bulls, 10 sires**
**GEML, AIPL, Illinois, and Israel**
**1995-2004**
**38,416 markers, 16,646 animals**
**BFGL, AIPL, Missouri, Canada, and Illumina**
**Oct 2007- Oct 2008**

## 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 |

## Genetic Progress

**Assume 60% REL for net merit**
**Sires mostly ****2**** instead of ****6**** years old**
**Dams of sons mostly heifers with 60% REL instead of cows with phenotype and genotype (66% REL)**
**Progress could increase by ****>50%**
**0.37 vs. 0.23 genetic SD per year**
**Reduce generation interval more than accuracy**

## Genetic Terms

**Predicted transmitting ability and parent average**
**PTA**** required progeny or own records**
**PA**** included only parent data**
**Genomics blurs the distinction**
**Reliability**
**REL of PA**** could not exceed 50%**
**Genomics can predict the other 50%**
**REL**** limit for calves theoretically 99%**

## Positive or Negative Traits

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

## 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 |

## Conclusions

**100X**** more markers allows MAS across rather than within families**
**5X**** more bulls allows estimation of much smaller QTL effects (HO)**
**Reliability ****increases**** by tracing actual genes inherited instead of expected average from parents**

## Acknowledgments

**Genotyping and DNA extraction:**
**BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina**
**Computing:**** **
**AIPL staff (George Wiggans, Mel Tooker, Leigh Walton)**
**Funding:**** **
**National Research Initiative grants**
**2006-35205-16888, 2006-35205-16701**
**Agriculture Research Service**
**Contributors to Cooperative Dairy DNA Repository (CDDR)**

## CDDR Contributors

**National Association of Animal Breeders (NAAB, Columbia, MO)**
**ABS Global (DeForest, WI)**
**Accelerated Genetics (Baraboo, WI)**
**Alta (Balzac, AB)**
**Genex (Shawano, WI)**
**New Generation Genetics (Fort Atkinson, WI)**
**Select Sires (Plain City, OH)**
**Semex Alliance (Guelph, ON)**
**Taurus-Service (Mehoopany, PA)**