1. 1 Application of Molecular Technologies in Beef Production Dan W. Moser, Ph.D Department of Animal Sciences and Industry Kansas State University, Manhattan

2. 2 Molecular Technologies DNA assessment of identity and parentage Selection for specific genes Marker assisted selection

3. 3 Genes and Chromosomes Chromosome –Structure in cell nucleus which stores and transmits genetic information in the form of DNA Gene –Sequence of DNA bases on a chromosome that causes a characteristic

4. 4 Genes and Chromosomes Any chromosome contains many genes, but parts of the chromosome may contain no genes The precise locations of most genes are unknown Current estimates place the number of human genes at 50,000; bovine, perhaps 30,000

5. 5 Genes and Chromosomes Chromosomes are arranged into homologous pairs, chromosomes of similar size and structure that contain genes for the same traits With 60 chromosomes, cattle have 30 homologous pairs A parent contributes one randomly chosen chromosome from each homologous pair to its offspring

6. 6 Genes and Chromosomes The various possible forms of a gene are called alleles When an individual has two identical alleles for the same trait, they are homozygous (AA, bb, etc.) When an individual has two contrasting alleles for the same trait, they are heterozygous (Aa, Bb, etc.)

7. 7 DNA Typing May be used to establish identity or parentage Useful in determining animal origin May become a component of national ID programs Particularly beneficial in seedstock operations

8. 8 DNA Typing for Parentage Confirm parentage for pedigree records and genetic evaluation Quality control for carcass data collection Identify sires of calves from multiple sire pastures Allow multiple sires to be used simultaneously in embryo transfer

9. 9 Qualitative Traits Qualitative traits fall into a few distinct classes –Red or black –Diluted or non-diluted –Horned or polled –Double-muscled or normal Qualitative traits are determined by a one or a few genes These genes usually affect one trait

10. 10 Qualitative Traits Since few genes are involved, those genes should be easier to discover Some genetic tests for qualitative traits are available –Red/Black coat color –Double-muscling –Numerous breed-specific genetic diseases

11. 11 Quantitative Traits Quantitative traits are those that show a continuous distribution –Weights and measures –All performance traits Quantitative traits are influenced by multiple genes Each gene has a relatively small effect

12. 12 Quantitative Traits Quantitative traits are the result of genes for factors that control growth, development, reproduction, lactation, fat deposition, etc. –Hormones –Hormone receptors –Growth factors –Other proteins

13. 13 Quantitative Traits At least four gene tests for beef cattle are commercially available: –GeneSTAR marbling (Thyroglobulin) –GeneSTAR tenderness (Calpastatin) –TenderGENE tenderness (Calpain) –Merial igenity L appetite (Leptin) Expect the number of such tests to continue to increase

14. 14 Potential Pitfalls The effects of alleles may vary under different environmental conditions Alleles may interact with alleles at other locations One allele may be partially or completely dominant to the other

15. 15 Potential Pitfalls Nearly every gene will likely have an effect on more than one trait Some alleles with favorable effects for one trait may have unfavorable effects for other traits Not all alleles may be detected

16. 16 Multiple Alleles from Thallman, 2001

17. 17 Genes vs. Markers These tests are direct tests, tests for variation in the genes that have been proven to have a certain effect Direct tests will work for all animals, and can identify animals as homozygous favorable, heterozygous, or homozygous unfavorable

18. 18 Genetic Markers Markers – known sequences believed to be near actual genes Statistically associated with a phenotype Markers are used to find genes, but could be used in some cases for selection before the gene is known

19. 19 Chromosomes Paternal Chromosome Maternal Chromosome

20. 20 Genes on Chromosomes Genes

21. 21 Genes on Chromosomes Heterozygous Homozygous

22. 22 Markers on Chromosomes Markers

23. 23 Markers Flanking a Gene Markers flanking a gene

24. 24 Genetic Markers Once a marker has been shown to have an effect for a particular sire, his progeny can be sorted into those that received the favorable or unfavorable allele Marker-assisted selection is useful only for progeny of heterozygous sires

25. 25 Compare Progeny Groups

26. 26 Compare Progeny Groups TenderTough

27. 27 Using Marker Results tender tough

28. 28 Genetic Markers Markers work well within families, but may not have the same effect in other families or breeds, due to recombination (crossover) The closer the marker is to the gene, the more consistent its effect

29. 29 Recombination Paternal Maternal

30. 30 Recombination Worst-case Scenario Tough gene “Tender” markers

31. 31 Implementing Marker- Assisted Selection Collect DNA on sire Collect DNA and phenotypes on (50?) progeny Determine markers that have significant effects for that sire Select future progeny of sire based on marker results

32. 32 Genetic Markers Marker-assisted selection is being used in the swine and dairy industries AI companies could test their most popular bulls for various markers, and report which marker tests can be used on progeny of those bulls

33. 33 Interpreting Test Results     0

34. 34 Interpreting Test Results GeneSTAR Marb  GeneSTAR Tnd   TenderGENE - -igenity L T t NCBA Tndr3 - -LeanGene1 + + CAB/OSU Marb + -LeanGene2 + - MeanGene + +LeanGene3 + + Ov. Rate 1 + -GrowGene A + + CalvEze + -GrowGene B - -

35. 35 Interpreting Test Results Calving Ease EPD2.9.45 Wean Wt EPD39.65 Milk EPD25.50 Yearling Wt EPD80.65 Carc Wt EPD14.65 Marb EPD0.31.65 %RP EPD0.14.75

36. 36 Interpreting Test Results The most logical and useful way to report test results is to include tests in EPD calculation Direct gene and/or marker tests can be included in National Cattle Evaluation (NCE) programs Raises issues as to which tests should or should not be used in NCE

37. 37 Gene-Adjusted EPDs More accurate, especially for young animals Require that gene test results for all tested animals be available, not just those with favorable results Require independent, unbiased evaluation of the test Selecting which tests to use will be difficult

38. 38 Gene or Marker Selection Most beneficial for traits that are difficult to measure, and for evaluating young animals EPDs evaluate the effects of all genes on a trait Bulls with desirable, high accuracy EPDs should not be discounted because of a “bad” gene test result