Q. What risks do you see for individual cow-calf producers in the wise and profitable application of DNA tests?

Q. With regard to the application of DNA tests in selection, what challenges do see ahead for:

  1. BIF?
  2. Breed Associations?
  3. Public research institutions (i.e., Land Grant Universities and USDA-ARS)?
  4. Genomic Companies?
  5. Seedstock breeders?
  6. Cow-calf producers?
  7. AI companies (Bull Studs)?

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  1. bifdna said

    I see a major challenge for breed associations regarding DNA tests. If the DNA test information is to be added to the other information available on an animal (pedigree, individual performance, etc), which it certainly must be in order to be properly considered when calculating EPDs, the associations are challenged to modify or add to their databases. Sounds easy, but isn’t. Moreover, as the DNA tests evolve over time, there could be information stored from “Generation 1” DNA tests, all the way up to “Generation 10” DNA tests. In other words, a DNA test is not a static thing. The current tests will certainly be expanded and improved over time. A test for marbling, for instance, may currently involve 3 markers. Five years from now, the DNA test for marbling might involve 10 markers — or 100 markers. So, if I was an association database designer, should I structure the database to accommodate 3 markers, 10 markers, or 100 markers?
    Database gurus — please tell me. Do you see this as a major hurdle?

  2. Technically no. It is not a problem to develop an “open ended” data base where each new or added markers can be accommodated in new tables as they are discovered. Any modern data base building tool based on OBDC (object based data connectivity) can relatively easy accommodate the layering on of additional tables. MS access, sequel, dbase etc all are built on this MS standard. However the more tables the more redundant the data and the more space and computing power that is needed. Also the more potential for error as the linking of tables of data could grow exponentially. But at this point computing power and data storage capacities are growing at a faster rate than known DNA markers. The real question is what do we think we know about the markers and their effects on phenotype, their interactions with each other, and the combined effects, this part of the equation will be the real test. Each new SNP multiplies the potential combinations by a factor of 3 (homozygous positive, homozygous negative, and heterozygous) three markers have 3x3x3 possible combinations or 27 different genotypes. If you add one more you get 81 etc. with 100 markers you get 3e100 or 515,377,520,732,011,000,000,000,000,000,000,000,000,000,000,000
    potential individual combinations of Genotypes. Thus the storage of the markers is not near as complicated as calculating the potential effects of all the possible combinations, This will take some real programing & logic power.

  3. bifdna said

    Seedstock producers readily share performance data with their breed association(s). If they didn’t, they would not receive the full benefit of their association’s genetic evaluation programs. Producers seem to have no qualms sharing these data. And yet, some of the discussion about DNA marker data relates to “test result confidentiality”. If a producer is willing to share data about the entire genotype of an animal (as estimated through EPDs), why would that same producer be reluctant to share data about the specific genotype at a few loci?

  4. Sam Johnson said

    RE: Sharing of Data. Not all data is shared only that which the producer wants to send in. Just look at all of the catalogs with just interim EPDs listed whenever you see this you know that producer doesn’t share the data and is content to sell projected EPDs calculated from the parentage only. EPDS and or indexes require that you send in the data or you will not get the information (EPDs) not all producers were happy to do this till they could not sell their cattle without them. DNA through private companies is a different issue. You do not need the cooperation of the breed association or its other members to get and use DNA info. Thus this information is just like any other data it is the option of the owner if he wants to make it public just as phenotypic data. Information is power and if I have information which helps or hurts me competitively I am not obligated to share this with anyone. The same is true for any industry! Just try to get the formula for Coke or the 11 herbs & spices from Kentucky Fried Chicken or the source code for any Microsoft computer program.

  5. Graybull said

    Interesting question………risks for the cow-calf producer in regard to the “WISE and PROFITABLE” use of DNA tests/market assisted selection.

    No risk……….IF and that is a big IF……tests are used wisely and profitably.

    Easiest prediction in the entire realm of DNA testing……..the tests will NOT be wisely and profitably used. Greater chance they will be “profitably” used…….. as in “profitably” used for marketing purposes rather than genetic advancement purposes……..just as is happening today.

    If you figure out a way to get the average cowman to use DNA testing wisely…… me.

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