got genomics?

1. got genomics? Joseph C. Dalton, PhD

2. Definitions • Genome: complete collection of hereditary information (DNA) • DNA: material that carries genetic information (The Wellcome Project)

3. Definitions • DNA is made up of two chains of nucleotide base subunits. • Nucleotide bases link together: • Adenine: Thymine • Cytosine: Guanine ~3 billion base pair sites in the bovine genome! (The Wellcome Project)

4. Definitions • Gene: • Basic unit of inheritance • A specific section (sequence of DNA) required to encode a particular protein • Proteins determine form and function (The Wellcome Project)

5. Definitions • Chromosome: A threadlike strand of DNA and associated proteins in the nucleus of cells that carries the genes and functions in the transmission of hereditary information.

6. DNA and genotyping • DNA can be collected from a blood, tissue, hair, or semen sample. • From a DNA sample it can be determined which of the four bases are located at ~ 40,000 sites (genotyping). (ABS Global, 2008)

7. Single nucleotide polymorphism • A single nucleotide polymorphism (AAGCCTA to AAGCTTA ) may produce a variation in an important trait. • Single nucleotide polymorphisms are also called SNP or SNIP.

8. What is a “SNP-CHIP?” • A tool to identify DNA markers for economically important traits in livestock. • A snip (SNP) is a change in a single location in the DNA structure (AAGCCTA to AAGCTTA ). (Illumina, Inc.)

9. How does a SNP-CHIP help estimate the breeding value of an animal? • Progeny tested sires were genotyped and associations were made between genotypes and traits (proofs). • Associations between key traits (proofs) and genotypes at the 40,000 base pair sites are used to define information in a bull’s genomic proof. (ABS Global, 2008)

10. How does a SNP-CHIP help estimate the breeding value of an animal? • In young animals, associations between key traits and marker genotypes are estimated using data from the animal's ancestors (progeny tested bulls).

11. Which traits? • Genomic traits that are estimated: • Production traits: milk, fat, protein, fat (%) and protein (%) • Health and fitness traits: PL, SCS, DPR, calving ease and stillbirth, type and linear conformation traits (ABS Global, 2008)

12. What does all this mean?

13. Genomic evaluation • Past: A young animal's genetic potential was based on parent average (PA). • PA = average of the predicted transmitting abilities (PTA’s) of its parents; reliability = 30-40% • Flaws: • No way to determine the sample of genes the young animal inherited from its parents. • Must wait 2 yr to measure performance of females, and five years (in the case of males) to measure the performance of its progeny. (Weigel, 2008)

14. Genomic evaluation • Present: Because of the relationships between SNP markers and important genes observed in an animal's ancestors, we can see what the future may hold for that animal. • For a young Holstein bull and heifer, a combination of the animal's PA with information from the SNP Chip = a “genomic PTA” with a reliability of 60 to 70%. (Weigel, 2008)

15. Genomic PTA • Heifers: Reliability ~ = to measuring several lactation records on the animal and its daughters. • Young cow: Information from the SNP Chip can be combined with its lactation records to obtain a more accurate estimate of its genetic merit. (Weigel, 2008)

16. Genomic PTA • Bull calf: Reliability = to that obtained by measuring performance on about a dozen daughters. • After performance data from 80 to 100 daughters is available (through progeny testing), information from the SNP Chip has relatively little value. (Weigel, 2008)

17. So what’s going on now? • Most young bulls entering N. American AI centers (and many potential bull dams) are tested with the SNP Chip. • Result: A higher success rate from progeny testing in the future, as we know prior to entry into an AI center that each young bull has received a good sample of genes from its parents. (Weigel, 2008)

18. Genomic-enhanced evaluations • Published by USDA-AIPL (beginning with the January 2009 Sire Summary) • unproven and proven sires • Holstein and Jersey breeds • Incorporate daughter information, genomic information, and traditional pedigree contributions.

19. Evaluation differences in a full brother group Which young bull would you select? (Adapted from ABS Global, 2008)

20. Benefits of genomics • Earlier information about genetic merit and fitness traits of young sires • Assists in parentage validation • More accurate inbreeding calculations • Testing of potential bull dams • Testing of animals in consignment sales • “First choice of flush” from embryo transfer (ABS Global, 2008; Weigel, 2008)

21. Will there be a need for progeny testing in the future? • Yes. Lactating cows are the true measure of a bull’s transmitting ability. • Progeny test information is required to generate genomic information.

22. What about genomic evaluation of other breeds (Brown Swiss)? • Gains in reliability for Brown Swiss have been negligible. Why? • Small population size (not as many progeny tested bulls are available for estimating the associations between SNP markers and important traits) • Is anything being done to increase the population size? Yes. • Through a combination of information from North American sires with key international sires. (Weigel, 2008)

23. Questions?

24. For more information • http://www.absglobal.com/dairy/genomics/ • http://www.selectsires.com/genomics_menu.aspx • http://agteamdirect.com/Genomics.aspx • http://genex.crinet.com/page1973/Genomics (Photo on title slide courtesy of ABS Global)