Genomics-based tools for the American mink

2. Genomics-based tools for the American mink Bernhard Benkel Nova Scotia Agricultural College

3. Genomics-based Tools for the American Mink • Background • Breed improvement • Traditional vs DNA marker-assisted • Genomics toolset • What is it and how do we get there • Applications • DNA markers • Whole genome selection • Implementation • Who, when, and where

4. Breed Improvement

5. Breed Improvement 28 days Broilers: days to market from 34 d in 1998 to 28 d in 2008

6. Breed Improvement Milk production: from 7,500 kg per cow in 1990 to 10,000 kg today

7. Traditional versus Genomics-assisted • Classical selection can be very effective, but takes time • Molecular markers preferred for: • Late onset traits • Traits that are expensive to measure • Low heritability traits • Speed, cost

8. Genomics Source: DOE/HGMIS

9. DNA Sequence

10. Genome Information Content

11. How Much is 1 Billion bp? 300 volumes of “Methods in Enzymology”

12. Single Nucleotide Polymorphism (SNP) ATT GGACAGAAC CGG- Q ATT GGACACAAC CGG– H * Genome Mapping Tools • Single Nucleotide Polymorphism (SNP) mapping panels • coverage, density, economy/automation 1 million SNPs

13. Complete Genome Sequences

14. SNPs • Find the SNPs…. 1/1000 in humans = 3 million between individuals • Find the ‘causative’ SNPs… a single SNP in some cases

15. A Home-grown Example • NS mink rancher imports black male(s) with ‘silky’ fur • Silky males bred to NS black females for a number of years • Eventually litters containing black and ‘marbled’ pups appear

16. Himalayan mink • HM: IFEQWLRRHHPLQEVYPEAN • WT: IFEQWLRRHHPLQEVYPEAN • HM: APIGQNRESYMVPFIPLYRN • WT: APIGHNRESYMVPFIPLYRN • HM: GDFFISSRDLGYDYSNLQES • WT: GDFFISSRDLGYDYSNLQES SNP in exon 4 of tyrosinase gene… one nucleotide out of 2.5 billion

17. Simple vs Complex Traits • Simple = most of genetic variation in trait due to a single gene • Complex = trait controlled by a number of genes each… major and minor genes

18. Distribution Tails • High versus low performers • Size, color, behaviour, etc

19. Cost of Sequencing a Complex Genome Human 2001 $1 billion Mouse 2002 $200 million Cow 2005 $50 million 2010 $100,000 2015 $10,000

20. Next Generation Sequencing • Massively parallel • Solexa • Solid • Single molecule • Helicos • Mobius • Archon X-prize = $10 million • 10 human genomes for < $10K per genome

21. Toward DNA-based Selection in Mink • Mink genome sequencing • Reference genome assembly • Re-sequencing on divergent mink • SNP marker discovery • SNP panels (whole genome/targeted) • Primary tools for association studies

22. DNA Tests: Beef Cattle

23. Genomic evaluations have arrived for Holsteins! • Canadian Dairy Network (CDN) has released the August 2009 genetic evaluations for all breeds that can be easily accessed by clicking on the Genetic Evaluation link and selecting the preformatted pdf files for printing reports, top lists, etc. or by going further and clicking on Data Files to choose files to download to your computer. • For genotyped Holsteins, a new Genomic Evaluation Details page is linked to their Genetic Evaluation Summary and all genomic evaluations are labelled with a “G” prefix to the proof type label of PA, EBV or MACE. • CDN is pleased to provide the information accessible on this web site as part of its continued commitment to providing valuable genetic evaluation and selection information.

24. Applications in Mink • Breed improvement in mink • Disease resistance • e.g. Aleutian Disease • Coat quality • Hair density, length, color • Reproduction • Feed efficiency

25. Budget & Time Lines • NGS sequencing for prototype genome sequence development • Library construction: 3 paired-end libraries each with a different fragment size at $1,200 per library = $3,600 • NGS sequencing: 5 slides x 7 lanes/slide = 35 lanes at $2,250/lane = $78,750 • Sequence assembly for prototype genome sequence development • Bioinformatics, sequence assembly = $25,000 • NGS sequencing for SNP discovery • Library construction: 4 libraries at $1,100 each = $4,400 • NGS sequencing: 20 lanes at $1,200 each = $24,000 • SNP discovery • Bioinformatics, SNP discovery = $10,000 • Total budget: approximately $175,000 CDN over 18 to 24 months with 20% from NS Dept of Agriculture; 40% from the mink industry and 40% from Canadian granting agency, NSERC

26. Collaborators • NSAC (Bernhard Benkel) • NIH/Laboratory of Genomic Diversity (Stephen O’Brien) • Université de Montréal (Bruce Murphy)

27. Your Role • Six months down the road... provide financial support • Immediately… start collecting phenotypes and samples

29. Followup • Whole genome association in livestock • How does it work, what does it cost, why is it popular? • (www.semex.com/downloads/Genomaxbrocure_ART_LR.pdf) • Genome sequencing • Implications for medicine of the $1000 genome sequence? • Complex traits and prediction of phenotype from genome sequence info

30. Applications • Whole Genome Scan to identify genes controlling important traits • coronary artery disease in humans • type 2 diabetes in humans • feed efficiency in cattle • Whole Genome Selection • black box approach • marker assisted selection

31. Gene Order Validation

32. Using Genomic Info for Breed Improvement • Discover genetic variation by sequencing • Single nucleotide polymorphisms (SNPs) • 1/1000 between individuals (human) • Develop SNP panels for: • Whole genome association studies • Shotgun or black box approach • Functional candidate gene approach • Surgical strike - do you feel lucky?