Transcript Genomics-based tools for the American mink Bernhard Benkel Nova

Genomics-based tools for the
American mink
Bernhard Benkel
Nova Scotia Agricultural College
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
Breed Improvement
Breed Improvement
28 days
Broilers: days to market from 34 d in 1998 to 28 d in 2008
Breed Improvement
Milk production: from 7,500 kg per cow
in 1990 to 10,000 kg today
Traditional versus Genomicsassisted


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
Genomics
Source: DOE/HGMIS
DNA Sequence
Genome Information Content
Size (bp)
Genes
~35,000
Mouse
3.2 x 109
(Billion)
2.6 x 109
Fruit fly
1.8 x 108
~14,000
Worm
1.2 x 108
~20,000
Yeast
1.2 x 107
~6,000
Human
~34,000
How Much is 1 Billion bp?
300 volumes of
“Methods in
Enzymology”
Genome Mapping Tools

Single Nucleotide Polymorphism (SNP)
mapping panels
• coverage, density, economy/automation
Single Nucleotide
Polymorphism (SNP)
ATT GGA CAG AAC CGG - Q
ATT GGA CAC AAC CGG – H
*
1 million SNPs
Complete Genome
Sequences
Species
Genome Seq
SNPs submitted
Human
Assembly v36
11.9 million
Chimpanzee
Assembly v2
1.5 million
Macaque
Assembly v1
780
Cow
Assembly v4
2.2 million
Pig
In prep
8,400
Chicken
Assembly v2
3.2 million
Dog
Assembly v2
3.3 million
Cat
In prep
327,000
Mouse
Assembly v37
14.4 million
Rat
Assembly v3
44,000
SNPs
• Find the SNPs….
1/1000 in humans
= 3 million
between
individuals
• Find the
‘causative’
SNPs… a single
SNP in some
cases
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
Himalayan mink


HM: IFEQWLRRHHPLQEVYPEAN
WT: IFEQWLRRHHPLQEVYPEAN
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HM: APIGQNRESYMVPFIPLYRN
WT: APIGHNRESYMVPFIPLYRN
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HM: GDFFISSRDLGYDYSNLQES
WT: GDFFISSRDLGYDYSNLQES
SNP in exon 4 of tyrosinase
gene…
one nucleotide out of 2.5
billion
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
Distribution Tails

High versus low performers
• Size, color, behaviour, etc
Cost of Sequencing a Complex Genome
Human
2001
$1 billion
Mouse
2002
$200 million
Cow
2005
$50 million
2010
$100,000
2015
$10,000
Next Generation Sequencing

Massively parallel
• Solexa
• Solid

Single molecule
• Helicos
• Mobius

Archon X-prize = $10 million
• 10 human genomes for < $10K per genome
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
DNA Tests: Beef Cattle
Company
Igenity
www.igenity.com
Pfizer Animal Genetics
(Bovigen) www.bovigen.com
MMI genomics
Test Name
Trait
Date of validation
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)
indicus influenced cattle)
(for Bos
12/2007
Profile®
Residual Feed Intake (RFI)
taurus cattle)
(for Bos
6/2008
Profile®
Dry matter intake (DMI)
(for Bos
indicus influenced cattle)
Profile®
Heifer Pregnancy Rate
Profile®
Stayability (longevity)
Profile®
Maternal Calving Ease
Profile®
Docility
GeneSTAR® Tenderness
Tenderness
GeneSTAR® Marbling
% IMF (Feedlot cattle)
GeneSTAR® Feed
Efficiency
Net Feed Intake (NFI)
Tru-Marbling™
Marbling Score and Quality Grade
Tru-Tenderness™
Tenderness
www.metamorphixinc.com
12/2007
2/2009
2/2009
2/2009
Genomic evaluations have arrived for Holsteins!
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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.

Applications in Mink

Breed improvement in mink
• Disease resistance

e.g. Aleutian Disease
• Coat quality

Hair density, length, color
• Reproduction
• Feed efficiency
Budget & Time Lines
NGS sequencing for prototype genome sequence development

•
•
Sequence assembly for prototype genome sequence
development

•
Bioinformatics, sequence assembly = $25,000
NGS sequencing for SNP discovery
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•
•
Library construction: 4 libraries at $1,100 each = $4,400
NGS sequencing: 20 lanes at $1,200 each = $24,000
SNP discovery
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•
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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
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
Collaborators

NSAC (Bernhard Benkel)

NIH/Laboratory of Genomic
Diversity (Stephen O’Brien)

Université de Montréal (Bruce
Murphy)
Your Role


Six months down the road...
provide financial support
Immediately… start collecting
phenotypes and samples
Followup

Whole genome association in livestock
• How does it work, what does it cost, why is
it popular?
• (www.semex.com/downloads/Genomaxbroc
ure_ART_LR.pdf)

Genome sequencing
• Implications for medicine of the $1000
genome sequence?
• Complex traits and prediction of phenotype
from genome sequence info
Applications
Species
Human
SNP
Markers
(validated)
SNP Map
Panel
(comm)
6.2 million
10,000
100,000
500,000
Mouse
6.5 million
1,500
5,000
9,000**
Cattle
14,500
10,000
25,000
50,000
Chicken
3.2 million
50,000*
Mink
handful
NA
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
Gene Order Validation
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
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Shotgun or black box approach
• Functional candidate gene approach
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Surgical strike - do you feel lucky?