Developing a Large Scale Data Platform. Dr Rod Polkinghorne, OAM

Transcription

1 Developing a Large Scale Data Platform Dr Rod Polkinghorne, OAM

2 BIG DATA Coming from many sources NIR, Hyperspectral Vision systems, FLIR CT, DEXA Whole genome sequencing Too much DATA Need to identify the useful core Needed for Genomic application Phenotypic data Fertility, growth, yield, marbling Eating quality Data intensive & much more needed

3 WALES 180 IRELAND WHAT DATA DO WE HAVE on EQ? International Beef EQ Consumer Studies 180 JAPAN 1, , NORTHERN IRELAND 9, FRANCE 1, POLAND 7, KOREA 720 USA 10,980 SOUTH AFRICA 360 AUSTRALIA 2,400 NEW ZEALAND ,200 3,960

4 Environmental & Genetic Variation New Zealand Bulls Sth Africa Nth Ireland Ireland Euro s Bulls Harsh Environment Pastures & Supplements Bos Indicus Australia France Cows nn Animal Data Poland Dairy x Marbling Japan Wagyu Fully Fed & Housed Marbling Hanwoo HGP s USA Grain Feeding Korea

5 Agreed Concept For Global EQ Data Collaboration APPLICATION DATABASE WITH STANDARDISED TOOLS UNDERPINNING RESEARCH TRIALS POLISH RESEARCH TRIAL IRISH RESEARCH TRIAL AUST. RESEARCH TRIAL DATAbank COMPANY B POLAND FRANCE Northern IRELAND IRELAND COMPANY A AUSTRALIA INDEPENDENTLY OWNED DATA HOUSED IN A COMMON DATABASE Shared Data RESEARCH ACCESS TRIAL RESEARCH, PUBLICATIONS, ANALYSIS, MODEL DEVELOPMENT,

6 What Phenotypic data exists? MSA - All with EQ, Very limited phenotypic data USDA MARC - Outstanding phenotypic data, No EQ data ICBF - All Irish Beef & Dairy cattle, No EQ ICBF An Inspirational Model

7 AI Companies Genetic Evaluation System Milk Recording Herd Books Ped. Certs & Linears Dairy & Beef Farmers Calf reg & movement

8 AI Companies Genetic Evaluation System Less paper, more profit! Milk Recording Herd Books Ped. Certs & Linears Calf reg & movement ICBF Database Animal Events Dairy & Beef Farmers

9 700k MR recs/yr AI Companies Milk Recording 1m AI recs/yr Genetic 30m animals with 100m+ records. Evaluation System Teagasc Research Schemes, e.g., BVD, BGDP, Origin Green 2.3 m birth recs/yr Herd Books 1.6 m carcass recs/yr Slaughter Factories Ped. Certs & Linears Calf reg & movements 100k farmers are now serviced from the database. ICBF Database Animal Events 2.3m BVD recs/yr Vets & vet labs. Dairy & Beef Farmers Marts & auctioneers 7.0 m movement records/yr Milk Co-ops Bulk Tank Reports Teagasc & ACA Advisors Genotypes & gen labs. 500k genotype recs/yr

10 Where do we stand? A trickle down genetic model! Breed society dominated structure Pedigree augmented by genotyping Purebred progeny performance recorded 15 mo old bulls sold DATA to BREEDPLAN RECORDING DISCONNECT Commercial pure & cross bred progeny Carcase including MSA data DATA LOST Genetic application severely restricted by structure which doesn t access this data

11 Some personal experience.. DAIRY 1000 AI bred heifers from 3 Australian states Recips Feedlot feeding system Low milk & fat cows Elite sires ET donors Genetic Limitation Production doubled within 2 generations

12 Some personal experience.. BEEF Charlton Feedlot Individual animal records from documented $200/Hd difference based on growth alone within individual lots Polkinghornes Paddock to Plate Retail Brand Grade Weight Percentage of HSCW Value of Product by Grade Bones, $0.93 Individual muscle, fat & bone weights on 5,000 carcasses Individual muscle EQ score Direct VBM 40% of retail $0.50 to $1/Kg HSCW difference in carcase values in every mob Bone, 18.4% Fat, 12.2% N.F.S., 0.0% Ungrd, 0.0% 3 Star, 13.8% 4 Star, 18.2% 5 Star, 2.2% Trim, 33.6% Trim, $ Star, $93.68 Fat, $1.23 N.F.S., $0.00 Ungrd, $ Star, $ Star, $426.14

13 Some personal experience.. BEEF MARRINYA Enterprises 500 Breeding cows (2-10yrs old) Rotational 3-way cross - Angus, Shorthorn, Composite Single sire joining, birth weighing & ID 3 calving seasons Autumn, Winter, Spring Comprehensive data for genetics, DNA, production, carcase & retail value Which cows should be culled? Which cows should be ET donors? Sire Ranking? Absolutely no idea as couldn t access reliable analysis! Current systems fail to evaluate commercial multi-breed cattle

14 The Opportunity FROM: Trickle DOWN Registered Purebred records TO: GENOMIC PREDICTION Utilising Australian & Global Data SIRE, DAM & PROGENY RATINGS 15 Mo old sire with EBV s Carcase yield & EQ (MSA) results + Reproduction & Growth data (Any breed combination) UNKNOWN COMMERCIAL PROGENY Outcome UP The NLGC outcome should be a revolution in cattle industry efficiency & genetic progress enabled by collaborative global data sharing and incentivised by VBM