# Presentation: 897389

## Update on All-breed Model, Fertility, Genomics

## Test Day Model - Potential Benefits

**Increased accuracy of evaluations **
**Account for lactation curve differences**
**Account for genetic differences by parity**
**Evaluate persistency, rate of maturity**
**Include milk-only records if multi-trait**
**Possible earlier selection of bull dams**
**Promote as state-of-the-art system **
**Management effects more accurate**
**Could provide to DRPCs and herd owners**

## All-Breed PTAs – March Test Run

**Genetic correlations mostly same**
**JE increase .02 for PL and .01 for SCS**
**BS decrease .01 for fat and SCS**
**AY increase .01 for PL**
**USA bulls in top 100 differ little**
**Numbers are averages across all scales**
**JE improve for SCS, fat (26 vs 25)**
**JE decline for milk, protein (59 vs 62)**
**BS decline for yield (10 vs 15)**
**HO improve for yield (17 vs 16)**

## Jersey and Swiss PTAs

**Base cow means changed little**
**Base cow SD changed little**
**Top bulls for protein dropped by ~9 lbs, bottom bulls dropped by ~4 lbs in both breeds**
**Unknown parent grouping, heterosis may be responsible**

## All-breed Trend Validation

**85 tests, 6 were significant (.05)**
**None significant for milk or SCS**
**1 of 15 for fat and for protein**
**2 of 15 for PL and for DPR**
**Increase in DPR repeatability made trend more negative, helped tests**

## DPR Results – March Test Run Holstein genetic correlations

| Eval | Model | BEL | DFS | ESP | GBR | IRL | ITA | NLD | NZL |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Mar | All breed | 86 | 89 | 93 | 83 | 76 | 90 | 86 | 62 |
| Feb | Within breed | 85 | ... | 93 | 83 | 72 | 86 | 85 | 60 |
| Diff |  | +1 | ... | 0 | 0 | +4 | +4 | +1 | +2 |

**March model also included an increase in repeatability**

## DPR - Top 100 bullsBorn in last 12 years, March 2007 test run

|  | Country with most daughters |  |  |  |  |  |  |  |
| --- | --- | --- | --- | --- | --- | --- | --- | --- |
| Scale | DFS | ESP | GBR | IRL | ITA | NLD | NZL | USA |
| BEL | 14 | 4 | 10 | 6 | 1 | 6 | 54 | 4 |
| DFS | 29 | 3 | 11 | 6 | 3 | 17 | 27 | 3 |
| ESP | 15 | 5 | 10 | 4 | 1 | 5 | 52 | 8 |
| GBR | 18 | 7 | 13 | 7 | 4 | 11 | 30 | 7 |
| IRL | 12 | 3 | 10 | 10 | 1 | 5 | 58 | 0 |
| ITA | 18 | 3 | 8 | 3 | 3 | 8 | 55 | 2 |
| NLD | 18 | 4 | 10 | 4 | 1 | 22 | 38 | 3 |
| NZL | 1 | 0 | 0 | 1 | 0 | 0 | 97 | 0 |
| USA | 17 | 4 | 8 | 3 | 2 | 6 | 53 | 7 |
| Total | 142 | 33 | 80 | 44 | 16 | 80 | 464 | 34 |

## Bulls to Genotype60,000 SNP Project

**Choose HO bulls with semen at BFGL**
**Genotype 1777 proven bulls**
**Born 1994-1996 with >75% REL NM**
**Plus 172 ancestor bulls born 1952-1993**
**Predict 500 bulls sampled later**
**Born 2001 with >75% REL NM**
**Include other bulls in gap years?**
**Born 1997-2000 (proven) or >2002 (waiting)**

## Birth Years of Bulls to Genotype

**Data cutoff**

## Contributors of DNA500 CDDR bulls to predict, born in 2001

| AI Organization | Code | Number of bulls chosen |
| --- | --- | --- |
| CRI / Genex | 1 | 126 |
| Select Sires | 7 | 107 |
| Alta Genetics | 11 | 67 |
| Accelerated | 14 | 44 |
| ABS Global | 29 | 120 |
| Semex | 200 | 32 |

## Potential ResultsSimulation of 10,000 SNPs

**QTLs normally distributed, n = 100**
**Reliability vs parent average REL **
**58% vs 36% if QTLs are between SNPs**
**71% vs 36% if QTLs are located at SNPs**
**Higher REL if major loci and Bayesian methods used, lower if many loci (>100) affect trait**

## Alleles Shared by Sibs

| Indep-endent Loci | Percentage of alleles shared |  |  |  |
| --- | --- | --- | --- | --- |
|  | Full sibs |  | Half sibs |  |
|  | Mean | SD | Mean | SD |
| 1 | 50 | 35.4 | 25 | 17.7 |
| 5 | 50 | 15.8 | 25 | 7.9 |
| 10 | 50 | 11.2 | 25 | 5.6 |
| 50 | 50 | 5.0 | 25 | 2.5 |
| 100 | 50 | 3.5 | 25 | 1.8 |
| Infinite | 50 | 0.0 | 25 | 0.0 |

## Reliability from Full SibsMarker and QTL positions identical, sib REL = 99%

|  | Reliability Obtained From: |  |  |
| --- | --- | --- | --- |
| Full Sibs | 
A | 60 QTLs
G | 30,000 QTLs
G |
| 1 | .250 | .250 | .250 |
| 10 | .454 | .494 | .470 |
| 100 | .495 | .907 | .624 |
| Infinite | .500 | 1.000 | 1.000 |

**A**** = traditional additive relationships, ****G**** = genomic relationships**