Genomic Service Operation

Transcription

1 IRISH CATTLE BREEDING FEDERATION Genomic Service Operation Mary McCarthy, Karl O Connell & Francis Kearney ICBF ICAR 2012 Session P3 Thursday 31 st May

2 Introduction The economic breeding index (EBI) is a profit based index used to identify genetically elite animals for Irish production systems. Genomic Selection supplements this traditional method. GS commenced in Ireland in Currently 7,081 bulls in reference population. It uses the DNA profile of an animal as well as ancestry and performance to increase data reliability. 2

3 Genomic Selection Uptake of Genomically Selected (GS) bulls very high in Ireland since GS bulls accounted for 47% of inseminations in These bulls are recommended to be used in teams, lower reliability than Irish daughter proven bulls. Table 1. Bull Proof type, percentage inseminations, average number of bulls used and average genetic merit and reliability for AI bulls used on Irish farms in 2011 Type of Proof % Use on farm Av Bulls/Herd EBI* (Rel) DP-IRL (75) DP-INT (47) GS (57) * EBI =Economic Breeding Index 3

4 Genomic Service History The ICBF Genomic Service is focused on providing genomic evaluations for dairy animals. It was launched in February 2011 based on the Illumina Bovine 3K chip, male animals mainly. In December 2011 we advanced to the Bovine LD chip at no extra cost. Spring 2012 service launched for genotyping females. 4

5 Service Benefits It gives a more accurate estimate of the genetic merit of an animal at a younger age Speeds rate of genetic gain The increase in reliability of a genomic proof over parent average is 10 25% This is equivalent to daughters in milk production Helps identify correct parents Female genotypes provide a large amount of accurate information for the reference population and help farmers make better breeding decisions. 5

6 Service Process ICBF DATABASE 6

7 Service Products Illumina Bovine3K (2,900 SNPs) 50 (all inclusive) Holstein Friesian Illumina BovineLD (6,900 SNPs) 50 Holstein Friesian/Pure Friesian Special offer on female genomics 30 (Full cohorts) Illumina Bovine SNP50 (~54,000 SNPs) 94 Pure Friesians/Sire not already genotyped. Illumina BovineHD (777,000 SNPs) 300 Beef animals reference population. 7

8 Female Genomics Goal is to use females in the reference population in the future Need both genotypes and phenotypes Reduction in cost where farmer genotypes a complete cohort of animals (e.g., all 2011 born females) To help prevent bias in future reference population if only selected females were genotyped Farmer can use genomics to make breeding decisions 8

9 Projects to date Dairy reference population 2008 present. BovineSNP50 & Limited HD Beef reference population 2011 present. Bovine HD Young bull calves BovineSNP50 in 2009,2010 Bovine3k in 2011 BovineLD in 2012 Females 2012 to present. BovineLD 9

10 Number of animals genotyped 3k 2011 LD k HD s-beef Reference population 50k-Dairy Reference population Farmers AI Companies TOTAL

11 Current criteria Animals must be Holstein or Friesian and not more than 6.25% of a third breed. The reference population consists only of these breeds. Sire and maternal grandsire must be recorded in the ICBF database. Pure Friesians can be genotyped on the 7k chip if the sire has already been done on the 50k panel. 11

12 Users Artificial Insemination Companies. A file of recently registered male calves is sent from ICBF each week. Animals are selected for genotyping with a view to purchase for entry into an AI station. Herd owners signed up to HerdPlus This is ICBF s breeding information service. Breed Societies. 12

13 To order genotypes the user logs into ICBF with User name and Password 13

14 AI Company Genotype Request Screen Enter animal number to validate tag choose chip type and sample type and submit order. This generates a request for a sample kit to be issued from ICBF. 14

15 HerdPlus User screen Select Genomics Link and Place Order 15

16 HerdPlus User genotype request screen. Tick the required eligible animal from this online profile. 16

17 Payment Methods Once you have selected the animals you confirm and pay by credit card or Laser card. Orders can be taken in the HerdPlus office on and payment can also be made by cheque. 17

18 Genotype Orders Following submission of orders, hair sample kits are mailed directly to the herd owner from ICBF. Kits contain: Hair sampling cards, 1 per animal, barcoded with the full Interbull number. Cover letter. Hair collection instructions, follicles from end of tail. Return to ICBF prepaid envelopes. 18

19 Hair collection instructions 19

20 AI Company Contracts Genotype requests can be submitted for the same animal by a number of AI companies. In this case one sample card and a multiple request letter and contract from each AI company is sent to the herd owner. The owner returns one contract per animal. This indicates the organisation that is to receive the genotype. 20

21 Sample Receipt Hair samples and contracts where necessary are returned by mail from the herd owner to ICBF. The hair cards and contracts are scanned into the database

22 GENOTYPING LABORATORIES WEATHERBY S IRELAND. NEOGEN USA. Samples are sent on a weekly basis. An electronic file of the sample details is also sent. 22

23 Results The laboratory automatically transmits the results to the ICBF database. File is loaded, animals validated and tracking updated. Animals with low call rates <90% are removed and reissued. Valid animals and valid genotypes are loaded to the IGenoP database. Different animal groups are extracted for evaluation. ICBF also caters for breeding companies who make their own genotyping arrangements and wish to receive genomic EBI s. 23

24 Genotype Tracking All the different stages from date requested to genotype published can be tracked by the user who placed the order. 24

25 Evaluations Each week genotypes are extracted from the database, imputed and genomic breeding values are computed. Genomic EBI s are distributed to the customer who placed the order. All results for male calves are made available on the ICBF public bull search two weeks after evaluations. Genomic evaluation reports are available via the ICBF website or by post. Results can be viewed in the herd owners EBI and genomics profiles. 25

26 Incorrect Sires Animals that have incorrect sires are identified. Currently 6.5% error rate on sire. These are checked against the sires on file. Reduces error rate down to 1.5%. Changes are made and farmers and Breed Society notified. 26

27 Genomic Evaluation Report Clients receive a report for each animal 27

28 Conclusions The genomic service infrastructure has worked very well. Large uptake, high level of interest in service. Excellent call rates >99%. Quick turnaround time approx. 3 weeks from sample submission to genomic result with a fully traceable integrated system. Research on providing genomic breeding values for other dairy breeds and beef cattle is underway, preliminary results later this year. 28

29 Thank you 29