Bull Controlling Country list (File 734)

Purpose

Defining which country controls a given AI bull that is used in multiple countries has always been a challenge for Interbull service users, given that country of registration only implies the origin of the animal, not where it actually is located. For progeny tested bulls included in MACE, the country with the larger number of daughters included in the national genetic evaluation usually is a reliable indicator of the controlling country, but this additional information is not available for the young genomically evaluated bulls that are included in GMACE. Therefore, the Interbull SC has decided to request additional information from the service users regarding which bulls are controlled by companies/stud within the area of influence of each country participating in Interbull international comparisons (MACE & GMACE). This information will have strategic use for interpreting all types of results distributed by Interbull and it will play an important role on the GMACE publication policy.

Implementation

  1. All countries sending data for GMACE have the option to send a list of bulls which they claim to have the control over until Feb 28, 2014.
  2. The lists received will be merged and made available to all participating countries, shortly after data reception, allowing potential conflicts to be resolved before distribution.
  3. For bulls included in the supplied controlling country list, publication status declared by the controlling country will take preference regardless of publication status in other countries.
  4. The previously distributed ”ownership” list will be renamed as ”publication status" list and will contain a list of bulls which comply with the following criteria for the controlling country:
    1. Status of bull = 10 (AI bull)
    2. Publication status = Y (bull meets the national standards for official publication)
  5. For any bull not included in any user-supplied controlling country file, the bull will be considered publishable in routine runs if at least one GEBV record included in GMACE, for any population and any trait, has
    1. Status of bull = 10 (AI bull)
    2. Publication status = Y (bull meets the national standards for official publication)
  6. Given that the Feb 2014 GMACE test run determines which changes can be implemented in both the April and August runs the publication policy adopted by participating countries must reflect the national policy to be adopted in both following runs.

This format is designed for uploading information about which animals have been genotyped, usually using whole genome SNP chips. Note that the file has semi-colon field separators (exactly eight) and the column positions allow for these separators. 

Column Field description                                   Format       Notes
1      Record type                                         Character 3  733
5      Breed of evaluation                                 Character 3  Notes 1 and 3.
9      Population of evaluation                            Character 3  Notes 2 and 3.
13     International animal ID                             Character19  Note 4.
33     Genotyping chip code                                Character10  Note 5.
44     Genotype status code (U/P/A/G/T/)                   Character 1  Note 6.
46     Share code (right to share genotype (Y/N))          Character 1  Note 7.
48     Tissue code (Availability of tissue for genotyping) Character 1  Note 8.
50     Publish code (right to publish thi info (Y/N)       Character 1  Note 9.

Notes:

  1. Breed of evaluation must be one of BSW, GUE, JER, HOL, RDC or SIM if the animal is submitted for Interbull evaluations or UUU otherwise.

  2. The population code must be an upper case population code assigned by the Interbull Centre. It is generally the same as the country code of the organization submitting the data except in the cases of multi-country evaluations (eg. "DEA" and "DFS") or multiple populations within a country participating in the same international evaluation (eg. "CHE"/"CHR", "FRA"/"FRR"/"FRM"). If the animal will not be submitted to Interbull evaluations use code "UUU". i.e., not submitted for MACE

  3. The breed-population combination must be among the combinations for which your organization is authorized to submit bull evaluations for MACE for dairy production traits, or "UUU;UUU" for animals which will not be submitted to Interbull evaluations.
  4. The 19-character international animal ID must be valid according to the rules specified for pedigree files (breed*3, country*3, sex*1, id*12). (The animal must exist in the Interbull pedigree database and a pedigree record must have been uploaded.)

  5. The "chip" code must be among the foreseen list present in the DB (eg., None, Parentage, Illu3K, IlluLD, Illu50K, Illu50K2, CRV60K, CRV60K2, IlluHD, AffyHD, Sequence, GGP9K, Unknown)

  6. The allowed "status codes" are: U=unavailable, P=genotyping in progress A=available but not yet used for GEBVs, G=used for GEBVs but not yet used in training, T=used for training for protein yield.
  7. The allowed "share codes" are: Y=yes, the country submitting the data is considering sharing or N=no, the country submitting the data is not considering sharing
  8. The foreseen "tissue codes" are: N=none, B=blood, S=semen, H=hair bulbs, E=ear punch, M=multiple or U=unknown. This field is available to signal access to biological material on animals which may be of interest to others.
  9. The allowed "publish codes" are: Y=yes or No. This field indicates whether the information in this specific record may be made available to other organizations (Y) or only to the Interbull Centre (N).

Sample records: 

733;BSW;ITA;BSWAUTM012345678900;Illu50K   ;G;Y;U;Y
733;BSW;ITA;BSWITAM000123456789;IlluLD    ;T;Y;U;Y
733;BSW;ITA;BSWITAM000987654321;Illu50K2  ;G;Y;U;Y
733;BSW;ITA;BSWITAM000987654322;None      ;U;N;B;Y
733;BSW;ITA;BSWITAM000987654323;Sequence  ;P;Y;S;Y