# Presentation: 167820

## Genetic trends in dairy cattle

**	**

**Genetic trends in dairy cattle**
**over the next 25 years ...**
**	****where are we**
**	****headed and how**
**	****will we get there**

## National Dairy Genetic Evaluation Program

**AIPL**

**CDCB**

**NAAB**

**PDCA**

**DHI**

**Universities**

**AIPL**** ****	****Animal Improvement Programs Lab., USDA**
**CDCB****	****Council on Dairy Cattle Breeding**
**DHI****	****Dairy Herd Improvement (milk recording organizations)**
**NAAB****	****National Association of Animal Breeders (AI)**
**PDCA****	****Purebred Dairy Cattle Association (breed registries)**

## DHI statistics (2007)

**4.4 million cows**
**98% fat recorded**
**95% protein recorded**
**94% somatic cell count recorded**
**23,500 herds**
**184 cows per herd**
**23,560 pounds milk per cow**
**3.69% fat**
**3.09% (true) protein**

## Traits evaluated

**Yield (milk, fat, protein volume; component percentages)**
**Type/conformation**
**Productive life/longevity**
**Somatic cell score (SCS)/mastitis resistance**
**Fertility**
**Daughter pregnancy rate (DPR; cow)**
**Estimated relative conception rate (bull)**
**Calving ease/dystocia (service sire, daughter)**

## Evaluation methods

**Animal model ****(linear)****	****Heritability**
**Yield (milk, fat, protein)****	****25–40%**
**Type (Ayrshire, Brown Swiss, ****	****7–54%**
**	****Guernsey, Jersey)**
**Productive life****	****8.5%**
**SCS****	****12%**
**DPR****	****4%**
**Sire-maternal grandsire model**** ****(threshold)**
**Service sire calving ease****	****8.6%**
**Daughter calving ease****	****3.6%**

## Dairy cattle breeding

**Long generation interval –**** 5 years**
**High value of individuals –**
**	****$2,000 per cow**
**Intensive management –**
**	****milking 2–3 times per day**
**Bull semen suitable for dilution –**
**	****500 doses per collection day)**

## U.S. progeny-test bulls (2006)

**Major and marketing-only AI organizations plus breeder proven**
**Breeds**
**Ayrshire –**** 13**
**Brown Swiss –**** 30**
**Guernsey –**** 12**
**Holstein –**** 1,493**
**Jersey –**** 151**
**Milking Shorthorn –**** 8**
**260 new bulls returned to service per year**

## Genetic-economic indexes

| Trait | Relative value (%) |  |  |
| --- | --- | --- | --- |
|  | Cheese merit | Net
merit | Fluid merit |
| Protein (lb) | 36 | 33 | 9 |
| Fat (lb) | 18 | 22 | 22 |
| Milk (lb) | –10 | 0 | 24 |
| Productive life (mo) | 9 | 11 | 11 |
| SCS (log base 2) | –7 | –9 | –9 |
| Udder composite | 6 | 7 | 7 |
| Feet/legs composite | 3 | 4 | 4 |
| Body size composite | –2 | –3 | –3 |
| DPR (%) | 5 | 7 | 7 |
| Service sire calving difficulty (%) | –2 | –2 | –2 |
| Daughter calving difficulty (%) | –2 | –2 | –2 |

## Index changes

| PTA traits included | Relative emphasis on traits in index (%) |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- |
|  | PD$
1971 | MFP$
1976 | CY
1984 | NM
1994 | NM
2000 | NM
2003 |
| Milk (lb) | 52 | 27 | –2 | 6 | 5 | 0 |
| Fat (lb) | 48 | 46 | 45 | 25 | 21 | 22 |
| Protein (lb) | ... | 27 | 53 | 43 | 36 | 33 |
| Productive life | ... | ... | ... | 20 | 14 | 11 |
| SCS | ... | ... | ... | –6 | –9 | –9 |
| Udder composite | ... | ... | ... | ... | 7 | 7 |
| Feet/legs composite | ... | ... | ... | ... | 4 | 4 |
| Body size composite | ... | ... | ... | ... | –4 | –3 |
| DPR | ... | ... | ... | ... | ... | 7 |
| Service sire 
     calving difficulty | ... | ... | ... | ... | ... | –2 |
| Daughter
     calving difficulty | ... | ... | ... | ... | ... | –2 |

## International reach

**Semen and embryos marketed internationally**
**Interbull Evaluation Centre (Sweden) ranks all bulls for each participating country**
**Correlations between countries of <1 accommodated**
**Some foreign bulls used as sires of sons**
**U.S. and Canadian semen used widely in South America**
**Red breeds more popular in Europe than in North America**

## PTA milk prediction

## Net merit prediction

**Net merit prediction**

## PTA DPR prediction (curvilinear)

## PTA DPR prediction (linear)

## Holstein milk yield

## Goals beyond increased yield

**Improve fertility**
**Increase herdlife**
**Improve disease resistance**
**Reduce calving difficulty**
**Improve efficiency**

## Options for increasing progress

**Crossbreeding**
**Increased selection intensity**
**Adoption of new technologies**

## Crossbreds

**Increasing interest**
**Way to increase fertility**
**Scandinavian Red breeds proposed**
**Hybrid vigor observed**

## All-breed animal model

**Purebreds and crossbreds together**
**Unknown parents grouped by breed**
**Variance adjustments by breed**
**Age adjusted to 36 months, not maturity**

## Genomics

**Genotype calves**
**Calculate genomic evaluation**
**Select intensively**
**Reduce cost of finding top bulls**
**Increase rate of genetic progress**

## Getting started

**Select animals to genotype**
**Assign identification to animals**
**Collect tissue samples**
**Extract DNA**
**Check DNA quality and standardize concentration**
**Begin 3-day genotyping process**

## Genomic evaluation workflow

**Check genotypes for inheritance errors**
**Calculate genomic relationships**
**Infer missing genotypes**
**Estimate single-nucleotide polymorphism (SNP) effects**

## Evaluation workflow – cont.

**Combine genomic information with parent average**
**Based on gain from genomics over parent average for animals with genotypes**
**Apply to all traits**
**Distribute results**

## First genomic evaluation

**750 animals nominated for genotyping**
**Over 5,285 predictor bulls from United States and Canada**
**Embryo flushes**
**AI organization that arranged for genotyping have first choice**
**More information at **_**[http://aipl.arsusda.gov/reference/changes/eval0804.html](http://aipl.arsusda.gov/reference/changes/eval0804.html)**_

## Reliabilities and squared correlations

|  | Squared correlation
× 100 |  |  | Reliability (%) |  |  |
| --- | --- | --- | --- | --- | --- | --- |
|  |  |  |  | Tradi-tional | Genomic |  |
| Trait | PA | Genomic |  | PA | Realized | Gain |
| Net merit | 11 | 28 |  | 30 | 53 | 23 |
| Milk (lb) | 28 | 49 |  | 35 | 58 | 23 |
| Fat (lb) | 15 | 44 |  | 35 | 68 | 33 |
| Protein (lb) | 27 | 47 |  | 35 | 57 | 22 |
| Fat (%)  | 25 | 63 |  | 35 | 78 | 43 |
| Protein (%) | 28 | 58 |  | 35 | 69 | 34 |
| Productive life  | 17 | 27 |  | 27 | 45 | 18 |
| SCS | 23 | 38 |  | 30 | 51 | 21 |
| DPR | 20 | 29 |  | 25 | 41 | 16 |
| Service sire calving ease | 27 | 29 |  | 28 | 31 | 3 |
| Daughter calving ease | 14 | 22 |  | 25 | 40 | 15 |
| Final score | 23 | 36 |  | 24 | 42 | 18 |

## Marker effects for net merit

## SNP density comparison

|  | PA reliability (%) | Genomic reliability (%) |  |  |
| --- | --- | --- | --- | --- |
| Trait |  | 10K | 20K | 40K |
| Net merit | 30 | 48 | 50 | 53 |
| Milk (lb) | 35 | 53 | 56 | 58 |
| Fat (lb) | 35 | 64 | 66 | 68 |
| Protein (lb) | 35 | 54 | 56 | 57 |
| Productive life | 27 | 38 | 41 | 45 |
| SCS | 30 | 45 | 47 | 51 |
| DPR | 25 | 37 | 39 | 41 |

## Conclusions

**Genomic predictions significantly better than parent average (P < .0001) for all 26 traits tested**
**Gains in reliability equivalent on average to ****11**** daughters with records **
**Analysis used ****3,576**** historical bulls **
**Current data includes ****5,285**** proven bulls **
**Larger populations require more SNPs**

## Current status

**Field test results distributed for 750 nominated animals**
**Extension to Jersey and Brown Swiss in progress**
**Transition to commercial genotyping labs**
**Extension to cows planned for June**

## SNP project outcomes

**Genome-wide selection**
**Parentage verification and traceability panels**
**Enhanced mapping for quantitative trait loci and gene discovery**

## Future plans

**Evaluations of animals not genotyped updated using genomic information (3 times per year)**
**Genomic evaluations calculated and released more frequently (monthly? weekly?)**
**Bull evaluations made public when bull enrolled with NAAB**
**Cow evaluations made public immediately at USDA web site**
**January 2009 target for public release**

## Genomic selection (New Zealand)

**Identify top 30,000 bull calves annually based on parent average**
**Genotype by 6 days old with 768 SNP**
**Genotype top 500 bull calves with 50K SNP chip**
**Keep top 100 bull calves**

## Genomic selection (NZ) – cont.

**At 1 year, limited progeny test to check for undesirable recessives**
**At 2 years, market as part of DNA team**
**When progeny tested, graduate best to progeny-proven team**

## Research topics

**Differential inclusion of X-chromosome effects to predict bulls versus cows**
**Contribution of cows to accuracy of genomic prediction**
**Benefit of genotyping more predictor bulls**
**Optimum methods for combining genomic and current evaluation**

## Research topics – cont.

**Practicality of screening and parentage verification with low-cost, low-SNP number assay**
**Potential of freely sharing enough SNP for accurate parentage discovery**
**Computational methods to improve accuracy, such as haplotyping**

## Summary

**Genomic prediction has great promise**
**Extensive changes in bull acquisition and marketing and in cow selection expected**
**Routine genotyping and validation will become industry rather than research responsibilities**

## Where do we go from here

**Economic indexes adjusted as conditions change**
**Traits added as their collection becomes feasible and value demonstrated**
**Dairies increase in size and technological sophistication**
**Selection adapts the cow to meet human needs**

## Senior research staff