1. The Impact of the 1000 Bull Genomes Project and its Future
Amanda Chamberlain, Christy Vander Jagt, Ruidong Xiang, Mike Goddard, Iona MacLeod, Robert Schnabel, Ben Hayes, Hans Daetwyler
Founded in 2011 at Sir Mark Oliphant Genomics Conference

2. Hayes and Daetwyler 2019. Annual Review of Animal Biosciences. 7:89-102
1000 bull genomes
Founded in 2011 at Sir Mark Oliphant Genomics Conference
Largest impact on discovery of deleterious mutations
Glass-eyed albino
Dominant red
Neurocristopathy
Osteogenesis imperfecta type 2
Bulldog calf syndrome
Holstein Haplotype 3
Weaver syndrome
Progressive retinal degeneration
Oculocutaneous albinism
Lethal chondrodysplasia
Belted
Familial renal syndrome
Recessive embryonic lethal

3. Hayes and Daetwyler 2019. Annual Review of Animal Biosciences. 7:89-102
1000 bull genomes
Founded in 2011 at Sir Mark Oliphant Genomics Conference
Largest impact on discovery of deleterious mutations
Facilitated GWAS for complex traits using imputed sequence data
Accurate identification of causative genes
Improvements to accuracy of genomic predictions
Largest gains in multibreed populations
Best results from preselecting variants based on GWAS
Bigger improvements will come from identification of mutations of small effect
Computationally efficient methods that can utilise full sequence
Utilising biological information

4. Run 7 – New Assembly
ARS-UCD1.2 + Btau4 Y

5. Run 7 – New Pipeline
GATKv3.8 best practises
.bam and g.vcf submission

6. 40 Partner Institutes

7. 3817 animals
Average 12x

9. Taurus Taurus-Indicus 106 breeds 171 breeds 3103 animals 3817 animals
13.5 million INDEL
90.2 million SNP
Taurus-Indicus
171 breeds
3817 animals
19 million INDEL
132.3 million SNP
2012
2014
2013
2015
2017
2019

10. 1.9%

11. Identifying Causative Variants for Improved Genomic Prediction (Run6)
Identifying Causative Variants for Improved Genomic Prediction (Run6)
30 sources of multi-omic information:
Phenotypes from 44,000+ dairy cattle with 17.7 million variants:
Priority ‘FAETH’ List
Chr19:
Chr4:
Chr14:
Chr23:
Chr10: …
Chr5:
40K
10K-XT

12. Per-variant Impact on 34 Dairy Traits
Conserved sites across 100 vertebrate species

13. Per-variant Impact on 34 Dairy Traits
Polar lipid content mQTL

14. Per-variant Impact on 34 Dairy Traits
Expression QTL

15. Genomic Prediction: 50K-XT vs 50K
Genotypes:
- real & imputed Standard 50K genotypes
- imputed XT-50K genotypes (disadvantaged! VS. Std 50K)
Phenotypes:
- milk, fat & protein yield
- fertility & Somatic Cell Count (SCS)
Reference/Training set = Aust. mixed-breed, Bulls & Cows:
29,200 animals (~26,000 Hol, ~3000 Jer, ~400 Aust Red)
Validation = animals not in Ruidong’s analyses:
Holstein, Jersey, Aust Red (bulls and cows)
NZ Crossbreds

16. Genomic Prediction: 50K-XT vs 50K

17. Acknowledgements

18. Acknowledgements
1000 bulls pipeline Christy Vander Jagt Hans Daetwyler Robert Schnabel
Variant Selection for Australian Dairy Ruidong Xiang Iona Macleod Mike Goddard