SNP Based Parentage Assignment in Sheep: Application in Australian Flocks PART 2: James Kijas 1 , Julius van der Werf 6,7 , Mohammad Ferdosi 6,7 , Amy Bell 1,6 , Sam Gill 6,8 , Klint Gore 6 , Jill Maddox 3 and John Henshall 1,6 . 1 CSIRO Livestock Industries, Australia. 2 AgResearch, New Zealand. 3 Port Melbourne, Australia. 4 USDA, USA. , PART 1: James Kijas 1 , John McEwan 2 , Shannon Clarke 2 , Hannah Henry 2 , Jill Maddox 3 , Mike Heaton 4 , for the International Sheep Genomics Consortium 5 CSIRO Livestock Industries, Australia. AgResearch, New Zealand. Port Melbourne, Australia. USDA, USA. , Australia. 5 www.sheephapmpa.org. 6 Sheep Cooperative Research Center, Australia. 7 University of New England, Australia. 8 Meat Livestock Australia. ? ? ?
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SNP Based Parentage Assignment in Sheep: Application in Australian Flocks
PART 2: James Kijas 1, Julius van der Werf 6,7, Mohammad Ferdosi 6,7, Amy Bell 1,6, Sam Gill 6,8, Klint Gore 6, Jill Maddox 3 and John Henshall1,6.
1 CSIRO Livestock Industries, Australia. 2 AgResearch, New Zealand. 3 Port Melbourne, Australia. 4 USDA, USA. ,
PART 1: James Kijas 1, John McEwan 2, Shannon Clarke 2, Hannah Henry 2, Jill Maddox 3, Mike Heaton 4, for the International Sheep Genomics Consortium 5
CSIRO Livestock Industries, Australia. AgResearch, New Zealand. Port Melbourne, Australia. USDA, USA. ,Australia. 5 www.sheephapmpa.org. 6 Sheep Cooperative Research Center, Australia. 7 University of New England,Australia. 8 Meat Livestock Australia.
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Background and Aims
Current Industry Practises:
1. Syndicate matings- no information about paternity in large management groups- inability to track sire merit through progeny performance
2. Single Sire matings- requires dedicated infrastructure (eg fences)
3. Mothering up to construct dam pedigree- labour intensive (costly)- not that accurate
Aims for development of a SNP Panel for Parentage:
1. Develop a Core Panel of SNP with international application- robust on multiple genotyping platforms- high MAF across many sheep breeds- promote to ISAG
2. Trial a panel of Core + Performance SNP within Australian flocks- test needs to be $10 / animal to drive industry adoption- high exclusion in populations with high relatedness (sires and ewe base)
Outline
PART 1: Technical Development of a Core Panel of SNP
PART 2: Trialling a Core + Performance Panel of SNP within Australian Flocks
International Sheep Genomics Consortium
History of developing tools for the sheep genome
- reference genome assembly (now v3.0 !)- SNP50 BeadChip- HD SNP by January 2013
- Additional ‘filler’ SNP to make up the number of 383
Collected samples from 1600 animals (blood cards)
- 5 industry flocks (progeny, ewes, sires)
- mainly Merino
Genotyped using all 6 SQ plexs: assessed power
Defined assignment thresholds using simulation
- 1000 simulated lambs, each with one correct sire- LOD is the log of ratio (likelihood correct/incorrect)- the most likely sire given mLOD1(blue if correct, red if wrong)
- difference between mLOD1 and the next best sire is ∆1
- second most likely sire given mLOD2 (light blue)
2 SQ plexes
127 SNP (64 core)
Sires with high mLOD and Δ1
These all correct (no red dots)
2 SQ plexes
127 SNP (64 core)
Most likely sire is correct sire, however
the next best is very nearly as likely (low Δ)
The next best sire (light blue) would get
selected as the true sire in some cases
3 SQ plexes
190 SNP (84 core)Using 3 plexes makes big difference !
The next best sire (light blue) is never
selected as the true sire using the
defined threshold
Very high confidence for analysis
of the real data
Progeny that are unlikely to have
a sire in the group genotyped.
Producer confirmed this was possible
Most assignments made
where next best sire
is not very likely (Δ well
above threshold)
Simulated Data Real Data
Conclusions
1. Technical Development of the Core Panel of SNP
- identified technically robust SNP- suitable for use across sheep breeds- promoting the core panel to ISAG for accreditation
2. Trialling a Core + Performance Panel within Australian Flocks
- in our flocks, 190 SNP gives good confidence in assignment- expect to release a commercial test in 2013
Acknowledgements
Core Panel
John McEwanShannon ClarkeHannah HenryJill MaddoxMike HeatonThe International Sheep Genomics Consortium
Testing in Australian Flocks
Julius van der WerfDaniel Pomp and JeremyMohammad FerdosiAmy BellSam GillKlint GoreJill Maddox and John Henshall