Genomics-based tools for the Genomics-based tools for the American minkAmerican mink

Bernhard BenkelBernhard BenkelNova Scotia Agricultural CollegeNova Scotia Agricultural College

BackgroundBackground• Breed improvementBreed improvement• Traditional vs DNA marker-assistedTraditional vs DNA marker-assisted

Genomics toolsetGenomics toolset• What is it and how do we get thereWhat is it and how do we get there

ApplicationsApplications• DNA markersDNA markers• Whole genome selectionWhole genome selection

ImplementationImplementation• Who, when, and whereWho, when, and where

Genomics-based Tools for the Genomics-based Tools for the American MinkAmerican Mink

Breed ImprovementBreed Improvement

Breed ImprovementBreed Improvement

28 days

Broilers: days to market from Broilers: days to market from 34 d34 d in 1998 to in 1998 to 28 d28 d in 2008 in 2008

Breed ImprovementBreed Improvement

Milk production: from Milk production: from 7,500 kg7,500 kg per cow per cow in 1990 to in 1990 to 10,000 kg10,000 kg today today

Traditional versus Genomics-Traditional versus Genomics-assistedassisted

Classical selection can be very Classical selection can be very effective, but takes timeeffective, but takes time

Molecular markers preferred for:Molecular markers preferred for:• Late onset traitsLate onset traits• Traits that are expensive to measureTraits that are expensive to measure• Low heritability traitsLow heritability traits• Speed, costSpeed, cost

GenomicsGenomics

Source: DOE/HGMIS

DNA SequenceDNA Sequence

Genome Information ContentGenome Information Content

Size (bp)Size (bp) GenesGenes

HumanHuman 3.2 x 103.2 x 1099

(Billion)(Billion)~35,000~35,000

MouseMouse 2.6 x 102.6 x 1099 ~34,000~34,000

Fruit flyFruit fly 1.8 x 101.8 x 1088 ~14,000~14,000

WormWorm 1.2 x 101.2 x 1088 ~20,000~20,000

YeastYeast 1.2 x 101.2 x 1077 ~6,000~6,000

How Much is 1 Billion bp?How Much is 1 Billion bp?

300 volumes of 300 volumes of “Methods in “Methods in EnzymologyEnzymology””

300 volumes of 300 volumes of “Methods in “Methods in EnzymologyEnzymology””

Genome Mapping ToolsGenome Mapping Tools

Single Nucleotide Polymorphism (SNP) Single Nucleotide Polymorphism (SNP) mapping panelsmapping panels

• coverage, density, economy/automationcoverage, density, economy/automation

Single Nucleotide Polymorphism (SNP)

ATT GGA CAG AAC CGG - QATT GGA CAC AAC CGG – H *

1 million SNPs

Complete Genome Complete Genome SequencesSequences

SpeciesSpecies Genome SeqGenome Seq SNPs submittedSNPs submitted

HumanHuman Assembly v36Assembly v36 11.9 million11.9 million

ChimpanzeeChimpanzee Assembly v2Assembly v2 1.5 million1.5 million

MacaqueMacaque Assembly v1Assembly v1 780780

CowCow Assembly v4Assembly v4 2.2 million2.2 million

PigPig In prepIn prep 8,4008,400

ChickenChicken Assembly v2Assembly v2 3.2 million3.2 million

DogDog Assembly v2Assembly v2 3.3 million3.3 million

Cat Cat In prepIn prep 327,000327,000

Mouse Mouse Assembly v37Assembly v37 14.4 million14.4 million

RatRat Assembly v3Assembly v3 44,00044,000

SNPsSNPs

• Find the SNPs…. 1/1000 in humans = 3 million between individuals

• Find the ‘causative’ SNPs… a single SNP in some cases

A Home-grown ExampleA Home-grown Example

NS mink rancher imports NS mink rancher imports black male(s) with ‘silky’ furblack male(s) with ‘silky’ fur

Silky males bred to NS black Silky males bred to NS black females for a number of yearsfemales for a number of years

Eventually litters containing Eventually litters containing black and ‘marbled’ pups black and ‘marbled’ pups appearappear

Himalayan minkHimalayan mink

HM: IFEQWLRRHHPLQEVYPEANHM: IFEQWLRRHHPLQEVYPEAN WT: IFEQWLRRHHPLQEVYPEANWT: IFEQWLRRHHPLQEVYPEAN HM: APIGHM: APIGQQNRESYMVPFIPLYRNNRESYMVPFIPLYRN WT: APIGWT: APIGHHNRESYMVPFIPLYRNNRESYMVPFIPLYRN HM: GDFFISSRDLGYDYSNLQESHM: GDFFISSRDLGYDYSNLQES WT: GDFFISSRDLGYDYSNLQESWT: GDFFISSRDLGYDYSNLQES

SNP in exon 4 of tyrosinase SNP in exon 4 of tyrosinase gene… gene… one nucleotide out of 2.5 one nucleotide out of 2.5 billionbillion

Simple vs Complex TraitsSimple vs Complex Traits

SimpleSimple = most of genetic variation in = most of genetic variation in trait due to a single genetrait due to a single gene

ComplexComplex = trait controlled by a = trait controlled by a number of genes each… major and number of genes each… major and minor genesminor genes

Distribution TailsDistribution Tails

High versus low performersHigh versus low performers• Size, color, behaviour, etcSize, color, behaviour, etc

Human2001$1 billion

Mouse2002$200 million

Cow2005$50 million

2010$100,000

2015$10,000

Cost of Sequencing a Complex GenomeCost of Sequencing a Complex Genome

Next Generation SequencingNext Generation Sequencing

Massively parallelMassively parallel• SolexaSolexa• SolidSolid

Single molecule Single molecule • HelicosHelicos• MobiusMobius

Archon X-prize = $10 millionArchon X-prize = $10 million• 10 human genomes for < $10K per genome10 human genomes for < $10K per genome

Toward DNA-based Selection in Toward DNA-based Selection in MinkMink

Mink genome sequencingMink genome sequencing• Reference genome assemblyReference genome assembly

Re-sequencing on divergent minkRe-sequencing on divergent mink• SNP marker discoverySNP marker discovery

SNP panels (whole genome/targeted)SNP panels (whole genome/targeted)• Primary tools for association studiesPrimary tools for association studies

DNA Tests: Beef CattleDNA Tests: Beef Cattle Company Test Name Trait Date of validation

Igenity      www.igenity.com 

Profile® Fat Thickness 12/2008

Profile® Marbling Score 12/2008

Profile® Quality Grade  (% ≥ Choice) 12/2008

Profile® Rib Eye Area 12/2008

Profile® Yield Grade 12/2008

Profile® Average Daily Gain 12/2008

Profile® Tenderness 12/2007

Profile® Residual Feed Intake (RFI)           (for Bos indicus influenced cattle)

12/2007

Profile® Residual Feed Intake (RFI)           (for Bos taurus cattle)

6/2008

Profile® Dry matter intake (DMI)               (for Bos indicus influenced cattle)

12/2007

Profile® Heifer Pregnancy Rate  

Profile® Stayability (longevity)  

Profile® Maternal Calving Ease  

Profile® Docility  

Pfizer Animal Genetics (Bovigen) www.bovigen.com

GeneSTAR® Tenderness Tenderness 2/2009

GeneSTAR® Marbling % IMF (Feedlot cattle) 2/2009

GeneSTAR®  Feed Efficiency

Net Feed Intake (NFI)2/2009

MMI genomics www.metamorphixinc.com

 

Tru-Marbling™ Marbling Score and Quality Grade  

Tru-Tenderness™ Tenderness  

Genomic evaluations have arrived for Holsteins!Genomic evaluations have arrived for Holsteins!

Canadian Dairy Network (CDN) has released the August 2009 genetic Canadian Dairy Network (CDN) has released the August 2009 genetic evaluations for all breeds that can be easily accessed by clicking on evaluations for all breeds that can be easily accessed by clicking on the Genetic Evaluation link and selecting the preformatted pdf files for the Genetic Evaluation link and selecting the preformatted pdf files for printing reports, top lists, etc. or by going further and clicking on Data printing reports, top lists, etc. or by going further and clicking on Data Files to choose files to download to your computer.Files to choose files to download to your computer.

For genotyped Holsteins, a new Genomic Evaluation Details page is For genotyped Holsteins, a new Genomic Evaluation Details page is linked to their Genetic Evaluation Summary and all genomic linked to their Genetic Evaluation Summary and all genomic evaluations are labelled with a “G” prefix to the proof type label of PA, evaluations are labelled with a “G” prefix to the proof type label of PA, EBV or MACE.EBV or MACE.

CDN is pleased to provide the information accessible on this web site CDN is pleased to provide the information accessible on this web site as part of its continued commitment to providing valuable genetic as part of its continued commitment to providing valuable genetic evaluation and selection information.evaluation and selection information.

Applications in MinkApplications in Mink

Breed improvement in minkBreed improvement in mink• Disease resistanceDisease resistance

e.g. Aleutian Diseasee.g. Aleutian Disease

• Coat qualityCoat quality Hair density, length, colorHair density, length, color

• ReproductionReproduction• Feed efficiencyFeed efficiency

Budget & Time LinesBudget & Time Lines

NGS sequencing for prototype genome sequence developmentNGS sequencing for prototype genome sequence development• Library construction: 3 paired-end libraries each with a different Library construction: 3 paired-end libraries each with a different

fragment size at $1,200 per library = $3,600fragment size at $1,200 per library = $3,600• NGS sequencing: 5 slides x 7 lanes/slide = 35 lanes at $2,250/lane = NGS sequencing: 5 slides x 7 lanes/slide = 35 lanes at $2,250/lane =

$78,750$78,750 Sequence assembly for prototype genome sequence Sequence assembly for prototype genome sequence

developmentdevelopment• Bioinformatics, sequence assembly = $25,000 Bioinformatics, sequence assembly = $25,000

NGS sequencing for SNP discoveryNGS sequencing for SNP discovery• Library construction: 4 libraries at $1,100 each = $4,400Library construction: 4 libraries at $1,100 each = $4,400• NGS sequencing: 20 lanes at $1,200 each = $24,000NGS sequencing: 20 lanes at $1,200 each = $24,000

SNP discovery SNP discovery • Bioinformatics, SNP discovery = $10,000 Bioinformatics, SNP discovery = $10,000

Total budget: approximately $175,000 CDN over 18 to 24 Total budget: approximately $175,000 CDN over 18 to 24 months with 20% from NS Dept of Agriculture; 40% from the months with 20% from NS Dept of Agriculture; 40% from the mink industry and 40% from Canadian granting agency, mink industry and 40% from Canadian granting agency, NSERCNSERC

CollaboratorsCollaborators

NSAC (Bernhard Benkel)NSAC (Bernhard Benkel)

NIH/Laboratory of Genomic NIH/Laboratory of Genomic Diversity (Stephen O’Brien)Diversity (Stephen O’Brien)

Université de Montréal (Bruce Université de Montréal (Bruce Murphy)Murphy)

Your RoleYour Role

Six months down the road... Six months down the road... provide financial support provide financial support

Immediately… start collecting Immediately… start collecting phenotypes and samplesphenotypes and samples

FollowupFollowup Whole genome association in livestockWhole genome association in livestock

• How does it work, what does it cost, why is How does it work, what does it cost, why is it popular?it popular?

• (www.semex.com/downloads/(www.semex.com/downloads/Genomaxbrocure_ART_LR.pdf)Genomaxbrocure_ART_LR.pdf)

Genome sequencingGenome sequencing• Implications for medicine of the $1000 Implications for medicine of the $1000

genome sequence?genome sequence?• Complex traits and prediction of phenotype Complex traits and prediction of phenotype

from genome sequence infofrom genome sequence info

Applications Applications

SpeciesSpecies SNP SNP Markers Markers (validated)(validated)

SNP Map SNP Map Panel Panel

(comm)(comm)

HumanHuman 6.2 million6.2 million 10,00010,000

100,000100,000

500,000500,000

MouseMouse 6.5 million6.5 million 1,5001,500

5,0005,000

9,000**9,000**

CattleCattle 14,50014,500 10,00010,000

25,00025,000

50,00050,000

ChickenChicken 3.2 million3.2 million 50,000*50,000*

MinkMink handfulhandful NANA

Whole Genome Scan to Whole Genome Scan to identify genes controlling identify genes controlling important traits important traits

coronary artery disease in humanscoronary artery disease in humans type 2 diabetes in humanstype 2 diabetes in humans feed efficiency in cattlefeed efficiency in cattle

Whole Genome SelectionWhole Genome Selection black box approachblack box approach marker assisted selectionmarker assisted selection

Gene Order ValidationGene Order Validation

Using Genomic Info for Breed Using Genomic Info for Breed ImprovementImprovement

Discover genetic variation by sequencingDiscover genetic variation by sequencing• Single nucleotide polymorphisms (SNPs)Single nucleotide polymorphisms (SNPs)

1/1000 between individuals (human)1/1000 between individuals (human)

Develop SNP panels for:Develop SNP panels for:• Whole genome association studiesWhole genome association studies

Shotgun or black box approachShotgun or black box approach

• Functional candidate gene approachFunctional candidate gene approach Surgical strike - do you feel lucky?Surgical strike - do you feel lucky?