110625uniba qtlsm genome 3 - ku leuven · 2011-12-27 · davey, mw 2 madav – uniba june 2011 kul...

Davey, MW

1

Madav – UNIBA June 2011

Mark W. Davey, Lab Fruit Breeding & Biotechnol, Dept. Biosystems,

KU Leuven

[email protected]


Leuven


Overview

1. Research at Lab Fruit Breeding and Biotechnology

2. Gene Discovery in Biotic Stress Responses

3. Fruit trait breeding: vitamin C

4. Reference genomes: what do they offer?

5. Sequencing, SNPs and markers

6. HTP Genotyping


Lab Fruit Breeding & Biotechnol


Tree architecture•production efficiencies,

•yelds and yield predication

•correlative effects

Fruit quality• antioxidants• texture

• quality traits (taste,

acidity..)

Development•flowering

•pollination

•fruit set

Resistance•abiotic stress

•biotic stress (Venturia

inaequalis, storage..)

Research Activities

HIGH QUALITY, SUSTAINABLE FRUIT PRODUCTION


Genetics•Genetic control (breeding)

•Application of molecular

markers

•Intra- and inter-species

(bio)diversity

•Inter-species Breeding barriers

Molecular Genetics•Gene expression

•Cloning and transformation

•Differential gene expression

•DNA sequencing (3 x 72)

•Genetic maps, QTL’s,

•Genetic fingerprinting

Biochemistry•(A)biotic stress

•Antioxidant Metabolism

•Proteomics

•Metabolite profiling

•…

Whole Plant Physiology•Fruit quality measurements

(NIR, etc.)

•Plant growth and

development

•Fruit storage

•…

Expertises

Davey, MW

2


KUL - Fruit Quality Improvement

Need for development of new apple cv’s to ensure renewal,

changing consumer preferences, climate change etc..

Bottle Necks to Breeding

• Long juvenile period,

• High degree of heterozygosity in apple,

• Quality traits are polygenic

• Complex biology (no easy phenotype to score)

Solutions

• Introgression of new genetic material (biodiversity)

• Molecular markers

• MAPS and MASS

• Gene Pyramiding

• Tools for improved breeding efficiency


Research at KULeuven

Projects:

1. Proteomics of Malus - Venturia interactions

2. Pear-scab – Venturia pirina

3. Fruit quality traits: molecular marker development

4. Carotenoid (vitamin A) metabolism and diversity in Musa

5. Genetic control of tree architecture

6. Induced resistance and cross-tolerance to Botrytis in Malus

7. Polyploidisation as a means to manipulate crops stress tolerance

Themes:

1. The plant stress adaptive responses

» Role of antioxidant metabolism

2. Molecular breeding;

» Tools, development and mapping


Genetic Diversity

Genomic resources

Genes and interactions for target traits

Validated molecular markers

Assays & methodologies

Breeding and Selection

Field Testing

Multiplication and Distribution

Neutral Markers

Functional Markers

Accelerated

Breeding Cycles

Gene Stacking

(Molecular) Crop Breeding



2D-PAGE - Proteomics


Apple Scab Phenotyping

days after infection

susceptible

polygenic

resistance

monogenic

resistance

% in

fect

ion

•Proteomics for resistance gene discovery

Davey, MW

3


Proteomics, 2D-PAGE

3 plants

3 leaves/plant

Image processing

Scanning

Image processing

Scanning

Image processing

Scanning


RESULTS: Image analysis

differential spots

Comparing treatments


Differential protein expression profiles

days after infection days after infection

days after infectiondays after infection

Scab-specific protein induction


Apple leaf proteome

pI

Mw

/kd

al

14

20

37

25

50

75

100

150

pH3 pH10

‘Gala’ apple leaf proteome, pI 3 � 10


2. Postharvest Phytopathogens & Plant defence

• Botrytis (grey mould) is a nectrotrophic pathogen & a major cause of post-harvest losses for stone and pome fruit.

• Need to develop new, low-input and sustainable methods for control of post-harvest infection

• Apple cultivars and show large variation in capacity for post-harvest storage and phytopathogen resistance

» Is it possible to exploit the plants’ natural defence systems?

» What mechanisms are involved?

» How are these defence systems regulated?

» How can we induce these defences?

Kn

ow

led

ge

Ga

p!


What do we know?

Necrotrophs kill host cells and utilise dead plant tissue for growth.

- production of H2O2 by sugar oxidases (phytopathogen)

- In B. cinerea, H2O2-detoxifying enzymes (SOD) are a pathogenesis factor

Plant response involves H2O2 production by NADPH oxidases

- prevents phytopathogen growth and colonisation (lignification)

- Stress signalling and defence gene induction

- Programmed cell death

Plant (a)biotic stress adaptation

- Upregulation AOX defence

- Improved H2O2 detoxification

- ..

Davey, MW

4


Induced Resistance and Cross-Tolerance

Antioxidants and vitamin C up-regulated and accumulate in response to abiotic

stress e.g. high light, ozone, altitude, UV, drought, etc.

Therefore conditions that lead to upregulation of AOX metabolism

could result in improved resistance to phytopathogens

0

10

20

30

40

50

60

70

80

90

100

3 6 9

Weeks Post-Infection

Infe

cti

on

Sco

re

Golden Delicious R

Golden Delicious G

Davey et al 2007, J Agr Food ChemDavey et al 2004, Plant Cell Environ

« Induced Resistance & Cross Tolerance »

Resistance to B. cinerea, red vs green


Experimental Design: AOX Profiling

1. Control

2. Mock Infection3. Infection, BH-105

Protein contents•Bradford assay

AOX Enzymes•CAT, SOD, APx

•POX, DHAR,

•MDHAR, GR

AOX Metabolites

•ORAC

•Vit C

•Phenolics

•sugars

•Red peel

•Red flesh

•Green peel

•Green flesh

Infection scoreGas Exchange•CO2

•ETH

stressREDGREEN

• Golden Delicious • Braeburn

t = 0 dpi, 5 dpi, 14 dpi


STRESS

WOUNDINGINFECTION

O2.- H2O2

H2O + ½O2

AsA

MDHA+

H2O DHA

GSH

GSSG

Flavonoid

Flavonoid.

+ H2O

APx MDHAR DHAR GR

POX

CAT

SOD

H2O2 and AOX Profiling

SOD: Superoxide dismutase

Apx: ascorbate peroxidase

CAT: catalase

POX: Peroxidase

MDHAR: Monodehydroascorbate reductase

DHAR: Dehydroascorbate reductase

GR: Glutathione reductase


RESULTS: disease symptoms

0.0

10.0

20.0

30.0

40.0

50.0

60.0

70.0

80.0

90.0

0 5 14

Infe

ctio

n S

en

siti

vit

y

Days Post Infection

GD red

GD green

Br Red

Br Green

GD

GD

Br

Br

•Braeburn > susceptible than Golden Delicious

•Red (stressed) > Resistance than green side of fruit.

•Genetic component to fruit resistance

•Stress adaptation associated with greater resistance

Br =Braeburn

GD = Golden Delicious


RESULTS: Profiling protein contents

FLESH

PEEL

Control vs Mock vs Infection:

•Braeburn: Infection results in loss of protein content.. Mock (wound stress) has no

effect.

•Golden: In flesh, infection results in lower protein content. No significant difference

in peel

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0 5 10 15

mg

pro

tein

/gfw

dpi

Br ControlBr InfectedBr Mock

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0 5 10 15

mg

pro

tein

/g

fw

dpi

G Control

G Infected

G Mock

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0 5 10 15

mg

pro

tein

/gfw

Days

Br ControlBr InfectedBr Mock

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0 5 10 15

mg

pro

tein

/gfw

Days

GD ControlGD InfectedGD Mock

Braeburn Golden


RESULTS: Profiling protein contents

FLESH

PEEL

14 DPI: Control vs Mock vs Infection (Healthy) vs Infection (Diseased):

•Braeburn: Red, infected healthy sites maintain protein contents. In green

infected sites there is a pathogen-associated loss of protein content

BEFORE diseases symptoms are visible!

•Red tissue is more resistant to biotic stress!

0.00

0.10

0.20

0.30

0.40

0.50

Control Mock Healthy

Infected

Diseased

Infected

Red

Green

0.00

0.10

0.20

0.30

0.40

0.50


Infected

Diseased

Infected

Red

Green

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70


Inf

Diseased

Inf

Red

Green

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70


Infected

Diseased

Infected

Red

Green

Braeburn Golden

Davey, MW

5


0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40


Infected

Diseased

Infected

Tit

le

Title

red

green

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80


Infected

Diseased

Infected

Red

Green

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40


Infected

Diseased

Infected

Red

Green

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80


Infected

Diseased

Infected

Red

Green

Profiling Apx activities

FLESH

PEEL

14 DPI: Control vs Mock vs Infection (Healthy) vs Infection (Diseased):

•Braeburn: Induction of Apx activity to deal with stress of infection

•Red induction >> Green inductioncontents.

•In Golden little induction! Pax activities also lower

Braeburn Golden


Metabolite profiling: Total phenolics

Total Phenolics (flesh):• Infection results in loss of total phenolics

• No impact of wounding (mock infection)• No difference between red and green

Braeburn Golden Delicious

0.0

5.0

10.0

15.0

20.0

25.0

30.0

0 5 10 15

mg

pro

tein

/gfw

dpi

Br Control

Br Infected

Br Mock

0.0

5.0

10.0

15.0

20.0

25.0

30.0

0 5 10 15

Tit

le

dpi

GD Control

GD Infected

GD Mock


Metabolite profiling: vit C

vit. C flesh:• Peel >> Flesh

• Red >> Green• GD: constant

• Vit. C: Br >> GD In Schil: rode zijde > groene zijde

Braeburn – Red Flesh Braeburn – Green Flesh

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0 5 10 15

Nm

ol/

gfw

dpi

Br Control Red

Br Infected Red

Br Mock Red

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0 5 10 15

nm

ol/

gfw

dpi

Br Control Green

Br Infected Green

Br Mock Green


RESULTS: Braeburn 2011:

0.0

50.0

100.0

150.0

200.0

250.0

300.0

350.0

0 1 3 6 8 10

Ne

cro

sis

DPI

Red Peel

Green Peel

RED GREEN

Braeburn 4 dpi

Braeburn 4 dpi

IF-R

IF-G


3. Fruit Trait Breeding: vit C – getting to the genes and developing markers


Why vit C?

� Roles in plant development, hormone and redox signalling, cell

wall loosening during fruit ripening...........

� Marker of fruit quality

� Stress tolerance in commercial crops

� Link to post-harvest fruit quality

� Storage disorders

� Antibrowning agent..

� …

What are the genetics underlying vit C accumulation?

Davey, MW

6


Vit C mutants

Plant vit C knockouts lethal

Minimum levels of ~25% WT required

- developmentally retarded,

- altered (a)biotic stress resistance profiles

Pavet V. et.al. Plant Physiol. 2011:139:1291-1303


0

200

400

600

800

1000

1200

1400

1600

1800

Sunris

e

Gra

vens

tein

Retin

a

Prima

Del

bare

Estival

Jam

es G

rieve

Alk

men

eArle

tG

ala

Elsta

r

Liber

ty

Mer

lijn

Prisci

lla

HL248

Ango

ld

Gold

en

Kanzi

Cox

Del

bare

Jubile

Mic

rom

alus

Gol

drush

Florin

a

Idar

ed

Rome

Beauty

Glo

ster

Green

star

Jona

gold

Fuji x

NEG

Ontario

x P

riscill

a

Bra

eburn

Pink

Lady

Variety

me

an

L-A

A i

n n

mo

l/g

fw

Harvest

Shelf-life

3-months

tot AsA contents: harvest v 10days shelf-life v 3-months cold storage

Davey et al 2004, JSciFoodChem

Vit C contents in Apple & Impact of Storage


Gene Discovery:

Traits, Linkage Maps and Quantitative Trait Loci


Complex Trait Inheritance

• Most crop traits such as yield, quality are controlled by multiple genes.

• These are known as ‘quantitative’, ‘polygenic,’ ‘multifactorial’ or

‘complex’ traits.

−Contrasts with ‘qualitative’, ‘monogenic’ traits e.g. dominant

resistance

• Genomic regions that contain genes associated with a particular

quantitative trait are known as quantitative trait loci (QTLs).

−Complex inheritance patterns

−How to combine the required alleles?

−No simple screening method


Quantitative Trait Loci (QTL)

With 30 – 60,000 genes/genome – how to find the genes regulating

quantitative trait expression??

QTL analysis simplifies the search for genes;

• A QTL is a section of the genome linked to a phenotypic trait (e.g. vitamin C)

• detect associations in a population between the phenotype of an individual

and its (molecular) marker genotype (‘profile’).

• If significant differences found between groups of individuals containing a

particular marker (set), then the marker is linked to a genomic region or

QTL, controlling the trait


Molecular Markers

DNA (molecular) markers = sites of DNA variation (polymorphisms).

• highly abundant

• DNA mutations e.g. substitution mutations (point mutations),

rearrangements (insertions or deletions) or errors in replication of

tandemly repeated DNA

• selectively neutral because they often located in non-coding regions

of DNA.

• ~unlimited in number and unaffected by environmental factors

and/or the developmental.

Apart from the use in MAS, & the construction of linkage maps, markers

also used to determine genetic diversity and cultivar identity

Davey, MW

7


RFLP

Restriction Fragment Length Polymorphisms

RAPD

Random Amplified Polymorphic DNA

AFLP

Amplified Fragment Length Polymorphisms

SSR

Simple Sequence Repeats

“Microsatellites”

SCAR / CAPS

Sequence Characterized Amplified Region

Cleaved Amplified Polymorphic Sequence

No sequence info

required

Sequence info

required

Types of Molecular Markers

Polymorphic Nucleotide Sequences


Cross-over and Recombination

E

E

F

F

f

f

e

e

G

G

H

H

g

g

h

h

P1

P2

P1

P2

% F1

G1

G2

G3

G4

P

R

P

R

45

5

5

45

E f

e F

e f

E F

G1

G2

G3

G4

P

R

P

R

30

20

20

30

G f

g H

g h

G F

% F1

parents

tight-linkage

loose-linkage

gametes(meiosis)

Non-Mendelian inheritance patterns

Map distances expressed as frequency of recombination


Crossover and Recombination

By analysing the segregation of markers in progeny, the order and

distances between markers can be determined.

i.e.the frequency of recombinant genotypes in the mapping population

can be used to calculate recombination fractions and the relative genetic

distance between markers.

The lower the frequency of recombination between two markers, the

closer they are situated on a chromosome.


Linkage Map Construction

mapping program

DNA extractions & PCR

Mapping Population

Marker Scoring/genotype

Linkage Map Construction


A genetic map is a linear map of the relative positions of markers/genes along each chromosome of a certain species.

Genetic Linkage Maps

• Genetic map (based on recombination frequencies) in cM

• Physical map: real distances between the markers/genes, in kb


Linkage Maps & QTL Mapping

Genotype F1 Progeny

(segregating molecular markers)

Groups A and B are significantly

different, and Marker is linked to a QTL

Phenotypic data (e.g. height, vit C,..)

Davey, MW

8


F1-Mapping Population • Telamon x Braeburn

• 257 individuals,

• >300 markers

• AFLPs, SSRs, SCARs,.

• Fruit quality, architecture,

vit C...

KUL Segregating F1-Population

Kenis & Keulemans 2005, Mol Breed, 15, p205-219Kenis et al 2008, TreeGenGen

Madav – UNIBA June 2011Davey et al 2006, Plant Physiol 142, p343

Linkage Group 10

Log

ari

thm

of

Od

ds

Vit C QTL’s, KUL

>95% probability

QTL flesh total AA

28%

•QTLs defined by the most closely linked

markers as bars on linkage maps

A.

Linkage Group 10

B.


TraitBraeburn 2006 Telamon 2006

QTL LG LOD cM %Variation Marker QTL LG LOD cM %Variation Marker

L-AA Flesh

1 11 3.70 32.1 22.3 EACMCAT122 1 17 3.22 15.9 13.8 EAGGMCCG73

2 17 2.85 11.2 8.9 Hi02f12 2 11 2.56 6.2 9.5 CH04g07

3 16 2.69 21.0 8.7 EAAGMCAC192 3 16 2.58 10.7 8.1 EACCMCGG94

39.9 31.4

DHA Flesh

1 11 3.33 19.4 28.6 EAGCMCAT122 1 16 3.19 15.2 31.1 EACAMCCA59

- - - - - - 2 11 2.93 10.0 13.9 ECACMCCT64

- - - - - - 3 15 2.66 5.1 12.0 CH02c09

28.6 57.0

Tot L-AA Flesh

1 11 4.65 31.1 27.1 EAGCMCAT122 1 11 4.78 18.2 15.2 Ch04G07

2 16 3.01 9.1 10.4 ECAAMCGA174 2 16 4.94 29.9 13.8 EAACMCGG94

3 17 2.47 5.3 7.3 Hi02f12 3 10 3.08 8.9 8.4 ECAAMCGA385

44.8 37.4

% DHA flesh

1 16 4.46 9.4 31.8 ECATMCAT283 1 17 4.09 10.8 20.4 ECAAMCG123

2 7 3.99 22.0 15.5 EAGAMCCG85 - - - - - -

3 14 2.87 9.7 11.4 EACGNCCG109 - - - - - -

58.7 20.4

VITAMIN C: QTLs


What next?

Compare results with other QTL studies:• Depends on presence of common markers (SSRs)

• Common phenotyping methodologies..

Map Candidate Genes:• Develop markers

• Genotype population

• colocalise with QTLs?

• Map-based cloning

• ..

Limitations:• Time and expense!

• Bias – model CG’s may not represent diversity of crop species!

• Biological assumptions..


4. Reference genomes:

What do they offer us?

Madav – UNIBA June 2011Feuillet et al 2011, Cell,

Catalogue:

• List of genes and regulatory elements

• Genome structure and evolution

Translational Research:

• structural and/or functional orthologues of known genes

• Identify genes underlying species-specific traits. e.g. apple pome fruit, etc.

• CG’s of model organisms cannot explain all species differences.

• More complex gene regulation in polyploid species

Sequences for crop improvement:• Mine the genomes to discover genes underlying agricultural traits of

importance.

Plant genome sequences

Davey, MW

9


Exploiting sequence data

Plant Genomes (2010):• 25 genomes from 19 plant species publically available

• 15 additional projects underway.

• BUT only A. thaliana and Oryza sativa, « finished »

Comparison of the apple genome to other sequenced plant genomes

Speciestot no.

genes/densitytransposable

elementstranscription

factorsmiRNAs

resistance genes

biosynthetic genes

Apple 57,386/0.78 42.4 4,021 178 992 (58, 27) 1,246

Cucumber 26,682/0.73 14.8 ND ND (171) 61 (ND) ND

Soybean 46,430/0.42 50.3 5,671 41 (85) 392 (61, 32) 958

Poplar 45,654/0.94 35 2,758 174 (234) 402 (59, 20) 1,034

Arabidopsis 27,228/2.2 18.5 2,437 89 (199) 178 (32, 52) 719

Grape 33,514/0.66 21.5 2,080 130 (137) 341 (57, 11) 1,121

Rice 40,577/0.97 39.5 2,798 140 (447) 535 (89, 0) 910

Brachypodium 25,532/0.94 28.1 2,187 62 (129) 238 (89, 0) 390

Sorghum 34,496/0.47 62 2,312 116 (148) 245 (75, 0) 555

Maize 32,540/0.15 84.2 5,246 153 (170) 129 (74, 0) 457

As of March 2010, 19,956 human protein-encoding genes had

been positively identified….

(Velasco et al 2010, Nature Biotechnol.)


Apple genome

Velasco et al 2010, Nature Biotechnol

• Provides a ~complete catalogue of genes and regulatory elements for a

species

• Genome structure and variation

• Understand gene function for exploitation of genetic diversity


Structural Genomics• Align genetic and maps with genome sequence to link maps and QTL data in

absence of common markers (marker order)

• Impact of structural variations such as copy number variation, indels,

present-absent variants.

High-thoughput marker development:• Generation of high density markers (SNPs, SSRs, indels..)

• Greatly accelerated map-based cloning of genes underlying QTLs.

• Exploration and exploitation of naturally occurring alleleic variation at CG’s

controlling traits (e.g. vit C)

Applications of plant genome sequences

Feuillet et al 2011, Cell,


Recycling

L-galactose

Uronic acids

Plant AsA Metabolism

D-Man-1-P D-Man-6-PGDP-D-Man

GDP-L-Gal

L-Ascorbate

L-Gal

L-Gal-1-P

GDP-L-Gulose

L-Gulose

L-Gulose-1-P

L-GuLL-GaL

UDP-GalUA

D-GalUA-1-P D-GalUA L-GalA

MeGalUA

GDP-L-Fuc

Polysaccharides/

N-Glycosylation

myo-Inositol

D-GlcUAL-GulA D-GlcUA-1-P

UDP-GlcUA

MDHA

oxalate

2GSH

GSSG

polysaccharides

D-Glc-6-P

NADPHthreonate

DHA

NADP

tartrate2,3 DKG

CO2 + H2O2AO

DHAR

MIPS

VTC1

APx

GPx

2H2O

H2O2


• In silico search of genes involved in synthesis, transport,

degradation and recycling of vitamin C underlying the QTLs,

using the GD apple genome sequence (Velasco et al 2010)

• Gene-specific primers developed and the genes mapped.

• Candidate genes for vit C metablism found within QTL intervals!

• 4 CGs belong to the recycling pathway, only 2 from biosynthetic

pathways(!)

• Several genes related to texture within QTLs for vit C (MdEXPA,

MdERF, MdPME, MdXET)

RESULTS: Candidate Gene mapping for vit C


Alignment to Golden Delicious genome (NZ)

� GMP/vtc1 ☺ (biosynthesis)

� DHAR ☺ (recycling)

� GPX ☺ (recycling)

(cM) (cM)(Mbp)

392 genes!

Davey, MW

10


Alignment to Golden Delicious genome

� MIPS (alternative

biosynthetic pathway)

(cM) (cM)(Mbp) 2010 data

2008 data

555 genes!


5. We need more markers!! - NGS


SSRs vs SNP Markers

SSRs

• Codominant, useful for map alignment

• Transferable between population and multiallelic

SNPs

• Very frequent, ~80% of all polymorphisms

• Occur in both coding and non-coding regions

• SNPs in coding regions may influence protein functionality

• Usually biallellic, therefore lower transferability than SSRs

• Mutationally stable, useful for LD association studies

high-throughput SNP analysis means it is possible to carry out

whole-genome molecular diversity studies with thousands of

markers in order to localize favorable genes and alleles through

linkage disequilibrium (LD).


NGS Resequencing & SNP Discovery

$75 MUS (2000) �� ~$1000 USD

“Next Generation” Sequencing (NGS) now affordable for labs -

therefore, instead of cloning individual CGs, directly resequence the

whole genome/transcriptome of individual cultivars.

HTP-SNP Identification

SNPs & Genetic Association Mapping

• Test whether individuals with different alleles (haplotypes) at a

locus, differ in a specific phenotype.

• whole genome scan (WGS)


Next Generation Sequencing (GAII)

Sequencing By

Synthesis:

Each synthesis

cycle, 1

nucelotide is

added and a

picture taken.

Each base has a

different

fluorescent label

• 76 cycles

• 76 images

• 76 bases /

cluster


Next Generation Sequencing (GAII)

The 76 bp sequence from each cDNA cluster (cDNA) is read as the colour changes in

consecutive images (76 cycli) at the same position.

300 million clusters are analysed in a single experiment!

Davey, MW

11


reads (76 bp)

de novo assembly of sequences

By overlapping all the short (76 bp) reads, a continuous sequence (contig) can

be assembled.

overlap

contig (400-1000 bp)


Reads assembly

GD Reference Gene

Assembled Gene/Transcript

Individual reads

Paired reads


Read mapping and SNP-calling

GD Reference Gene

SNPs

Sequencing errors


SNP-Polymorphisms & Haplotypes

15

Ap

ple

ge

no

typ

es


5. HTP-Genotyping


WGS & SNP chips!

International Apple SNP Chip Consortium:

• develop a 9K commercial apple SNP chip to run on the “Illumina Infinium”

system.

• SNPs chosen to be evenly distributed over the genetic region of the

genome.

SNP Identification and Chip development:

• the SNP Consortium has already carried out gDNA resequencing of an

additional 30 apple cultivars outside of the Golden Delicious reference

genome.

• KULeuven carrying out transcriptome sequencing, higher chance for

functional impact

• HTP-whole genome scanning

Davey, MW

12


RosBRE EDSNP _SNP_CT_115045_Lg2_328024_MAF50_328024_exon1

RosBRE EDSNP _SNP_CT_115936_Lg2_328024__328024_exon4

RosBRE EDSNP _SNP_AC _115951_Lg2_328024_MA F50_328024_exon4

0. 1

RosBRE EDSNP _SNP_TC_1219423_Lg2_00348_MAF20_1649423_exon1




1. 2

GD snp00348

RosBRE EDSNP _SNP_GA _1260672_Lg2_01134_MA F40_1677893_exon1

RosBRE EDSNP _SNP_TG_1270705_Lg2_01134_MAF10_484985_exon2


GD snp01134RosBRE EDSNP _SNP_GA _1278998_Lg2_01134_MA F30_MDP0000233214_exon4


1. 3

RosBRE EDSNP _SNP_AC _1552587_Lg2_snpCO 903605_M AF30_1674520_exon1

RosBRE EDSNP _SNP_AG _1557630_Lg2_snpCO 903605_M AF40_MD P0000631295_exon3

RosBRE EDSNP _SNP_TC_1576685_Lg2_snpCO903605_M AF20_MDP 0000404835_exon2

snpCO903605

RosBRE EDSNP _SNP_TC_1588425_Lg2_snpCO903605_M AF30_1630651_exon1

RosBRE EDSNP _SNP_GA _1590717_Lg2_snpCO 903605_M AF50_26379_exon3RosBRE EDSNP _SNP_TC_1597267_Lg2_snpCO903605_M AF50_MDP 0000303518_exon2

RosBRE EDSNP _SNP_CA _1599366_Lg2_snpCO 903605_M AF40_MD P0000303518_exon5

RosBRE EDSNP _SNP_CT_1606574_Lg2_snpCO903605_M AF10_99551_exon1

1. 6

RosBRE EDSNP _SNP_AG _1869486_Lg2_01735_MA F20_477197_exon1

RosBRE EDSNP _SNP_AC _1873474_Lg2_01735_MA F20_MDP0000289720_exon10

RosBRE EDSNP _SNP_GT_1877053_Lg2_01735_MAF40_554134_exon1

RosBRE EDSNP _SNP_TC_1879153_Lg2_01735_MAF30_M DP0000516949_exon1

RosBRE EDSNP _SNP_TG_1904567_Lg2_01735_MAF30_710770_exon1GD snp01735





RosBRE EDSNP _SNP_AG _1939660_Lg2_AA T1_M AF40_MD P0000145727_exon4

1. 9

RosBRE EDSNP _SNP_GA _1952049_Lg2_AA T1_M AF20_1688633_exon1

RosBRE EDSNP _SNP_GA _1958621_Lg2_AA T1_M AF20_1677156_exon1RosBRE EDSNP _SNP_CA _1966785_Lg2_AA T1_M AF30_262653_exon1

RosBRE EDSNP _SNP_GA _1979331_Lg2_AA T1_M AF50_MD P0000307573_exon4

RosBRE EDSNP _SNP_GA _2024247_Lg2_AA T1_M AF50_1670831_exon1

2. 0




RosBRE EDSNP _SNP_GA _2408882_Lg2_01565_MA F40_MDP0000189794_exon1

RosBRE EDSNP _SNP_GA _2411996_Lg2_01565_MA F10_622363_exon1RosBRE EDSNP _SNP_CT_2425858_Lg2_01565_MAF50_1673213_exon1

RosBRE EDSNP _SNP_CT_2430550_Lg2_01565_MAF10_M DP0000303326_exon1

GD snp01565

2. 4


RosBRE EDSNP _SNP_CA _2484201_Lg2_00959_MA F10_452824_exon1



RosBRE EDSNP _SNP_AC _2495581_Lg2_00959_MA F50_766824_exon1RosBRE EDSNP _SNP_GA _2504650_Lg2_00959_MA F30_MDP0000305192_exon3

GD snp00959



2. 5

RosBRE EDSNP _SNP_CT_2607533_Lg2_226032_MAF30_226032_exon12. 6

RosBRE EDSNP _SNP_AG _2909242_Lg2_RosCO S2955_MAF40_609985_exon1

RosBRE EDSNP _SNP_GA _2912144_Lg2_RosCO S2955_MAF50_M DP0000933335_exon2

RosBRE EDSNP _SNP_CT_2916981_Lg2_RosCO S2955_MAF50_M DP0000565228_exon1

2. 9

RosBRE EDSNP _SNP_CA _2951030_Lg2_RosCO S2955_MAF10_940098_exon1


RosBRE EDSNP _SNP_TG_2987146_Lg2_RosCO S2955_MAF20_1632390_exon5

RosBRE EDSNP _SNP_GA _2995367_Lg2_RosCO S2955_MAF20_1629016_exon2

3. 0

RosBRE EDSNP _SNP_AG _3243976_Lg2_RosCO S1998_MAF20_M DP0000162833_exon1

RosBRE EDSNP _SNP_TC_3246218_Lg2_RosCO S1998_MAF10_476703_exon4

3. 2

RosBRE EDSNP _SNP_GT_3252639_Lg2_RosCO S1998_MAF10_445039_exon1

RosBRE EDSNP _SNP_AG _3257068_Lg2_RosCO S1998_MAF20_110688_exon1RosBRE EDSNP _SNP_CT_3273690_Lg2_RosCO S1998_MAF30_67740_exon1






3. 3


RosBRE EDSNP _SNP_CT_3420282_Lg2_01641_MAF40_1669340_exon1RosBRE EDSNP _SNP_AG _3425722_Lg2_01641_MA F20_1660502_exon2




3. 4

GD snp01641

RosBRE EDSNP _SNP_AG _3463154_Lg2_01641_MA F30_MDP0000943030_exon1



3. 5


RosBRE EDSNP _SNP_AG _3582428_Lg2_127453_MA F40_127453_exon13. 6



RosBRE EDSNP _SNP_CT_3753597_Lg2_127385__127385_exon23. 8



RosBRE EDSNP _SNP_GA _4023123_Lg2_01476_MA F20_512064_exon1RosBRE EDSNP _SNP_AG _4025888_Lg2_01476_MA F10_203524_exon1




4. 0

GD snp01476

RosBRE EDSNP _SNP_CA _4085993_Lg2_01476_MA F10_MDP0000283614_exon4

4. 1




GD snp00203





4. 2

RosBRE EDSNP _SNP_CT_4326366_Lg2_01945_MAF50_1633451_exon1RosBRE EDSNP _SNP_CT_4328900_Lg2_01945_MAF30_M DP0000137471_exon4



RosBRE EDSNP _SNP_GT_4340866_Lg2_01945_MAF20_M DP0000457988_exon1


4. 3



GD snp01945RosBRE EDSNP _SNP_GA _4373183_Lg2_01945_MA F10_1634079_exon4



RosBRE EDSNP _SNP_CT_4403250_Lg2_RosCO S2816_MAF30_1637704_exon1





4. 4


4. 5 RosBRE EDSNP _SNP_GA _4554201_Lg2_M DP0000519575_MAF20_M DP0000519575_exon1

RosBRE EDSNP _SNP_AG _4554235_Lg2_M DP0000519575_MAF20_M DP0000519575_exon1

RosBRE EDSNP _SNP_GA _4554250_Lg2_M DP0000519575_MAF40_M DP0000519575_exon1

RosBRE EDSNP _SNP_GA _4554251_Lg2_M DP0000519575_MAF30_M DP0000519575_exon1

4. 6



4. 8

RosBRE EDSNP _SNP_AC _4851487_Lg2_RosCO S3565_MAF20_1640666_exon1

RosBRE EDSNP _SNP_GA _4895867_Lg2_RosCO S3565_MAF20_M DP0000203071_exon11RosBRE EDSNP _SNP_AG _4898009_Lg2_RosCO S3565_MAF30_1685164_exon4



4. 9




5. 0


RosBRE EDSNP _SNP_TC_5068386_Lg2_00077_MAF20_1634690_exon18RosBRE EDSNP _SNP_GA _5074647_Lg2_00077_MA F40_1649337_exon1

GD snp00077



5. 1




RosBRE EDSNP _SNP_AC _5318639_Lg2_00158_MA F50_1632963_exon1RosBRE EDSNP _SNP_TG_5322830_Lg2_00158_MAF10_711170_exon1




GD snp00158

5. 3

RosBRE EDSNP _SNP_TC_5370279_Lg2_00158_MAF10_M DP0000276264_exon15. 4


RosBRE EDSNP _SNP_CT_5859464_Lg2_01663_MAF40_1659846_exon2RosBRE EDSNP _SNP_CT_5864957_Lg2_01663_MAF20_M DP0000321546_exon2


RosBRE EDSNP _SNP_TG_5875405_Lg2_01663_MAF50_M DP0000137803_exon1

GD snp01663




5. 9

RosBRE EDSNP _SNP_CT_6261234_Lg2_00308_MAF40_M DP0000292425_exon4RosBRE EDSNP _SNP_CT_6266265_Lg2_00308_MAF40_1675094_exon1




GD snp00308



RosBRE EDSNP _SNP_AG _6321450_Lg2_00308_MA F50_1632382_exon1RosBRE EDSNP _SNP_TC_6332531_Lg2_00308_MAF10_11785_exon1

6. 3

RosBRE EDSNP _SNP_AG _6411601_Lg2_M DP0000290496_MAF40_M DP0000290496_exon16. 4







GD snp01162


6. 5





RosBRE EDSNP _SNP_TC_6597883_Lg2_00333_MAF10_1627535_exon2RosBRE EDSNP _SNP_AG _6616886_Lg2_00333_MA F50_1688429_exon1

GD snp00333


6. 6





RosBRE EDSNP _SNP_TC_6735528_Lg2_01549_MAF50_1636434_exon2RosBRE EDSNP _SNP_CT_6742332_Lg2_01549_MAF30_553488_exon3

6. 7


GD snp01549




6. 8

RosBRE EDSNP _SNP_TC_6958617_Lg2_RosCO S1581_MAF50_M DP0000284715_exon2

RosBRE EDSNP _SNP_GA _6960685_Lg2_RosCO S1581_MAF20_M DP0000284715_exon3RosBRE EDSNP _SNP_TC_6963343_Lg2_RosCO S1581_MAF20_816797_exon1







7. 0

RosBRE EDSNP _SNP_GA _7211402_Lg2_00505_MA F40_1655266_exon1RosBRE EDSNP _SNP_CA _7244943_Lg2_00505_MA F40_1671066_exon1

GD snp005057. 2




RosBRE EDSNP _SNP_AG _7300476_Lg2_RosCO S718_MAF 10_522878_exon3


7. 3

RosBRE EDSNP _SNP_GT_7724567_Lg2_MD P0000843352_MAF40_MD P0000843352_exon1RosBRE EDSNP _SNP_TC_7724576_Lg2_MD P0000843352_MAF50_MD P0000843352_exon17. 7


RosBRE EDSNP _SNP_TG_8127145_Lg2_173545_MAF50_173545_exon28. 1





GD snp00407RosBRE EDSNP _SNP_AG _8936738_Lg2_00407_MA F50_483435_exon1


8. 9

RosBRE EDSNP _SNP_GT_8977648_Lg2_00407_MAF50_1662497_exon29. 0

RosBRE EDSNP _SNP_CA _9337414_Lg2_167070_MA F10_167070_exon19. 3

GD snp0099110. 1







GD snp01223


10. 7







GD snp00159


11. 4


RosBRE EDSNP _SNP_GT_11464936_Lg2_00159_MAF10_M DP0000150757_exon1RosBRE EDSNP _SNP_TC_11503103_Lg2_01005_MAF40_254568_exon1








11. 5

GD snp01005




GD snp00614



RosBRE EDSNP _SNP_GT_11799850_Lg2_00614_MAF50_M DP0000175404_exon2RosBRE EDSNP _SNP_AG _11806852_Lg2_00614_MA F50_175518_exon1

11. 8







RosBRE EDSNP _SNP_AC _11996518_Lg2_RosCO S2709_MAF30_1663531_exon1RosBRE EDSNP _SNP_TG_11998839_Lg2_RosCO S2709_MAF50_1680670_exon1

12. 0


GD snp00174

RosBRE EDSNP _SNP_GA _12590482_Lg2_00174_MA F10_1653396_exon112. 6




RosBRE EDSNP _SNP_CT_12901428_Lg2_01552_MAF30_525812_exon2RosBRE EDSNP _SNP_CT_12903929_Lg2_01552_MAF30_1660471_exon1


GD snp01552



12. 9




13. 1




13. 6





RosBRE EDSNP _SNP_CT_13676580_Lg2_00214_MAF30_356820_exon1RosBRE EDSNP _SNP_GT_13683046_Lg2_00214_MAF10_76634_exon1

GD snp00214

13. 7

RosBRE EDSNP _SNP_CA _13921344_Lg2_248148__248148_exon113. 9





RosBRE EDSNP _SNP_CT_14489605_Lg2_00002_MAF30_187689_exon1RosBRE EDSNP _SNP_CT_14500796_Lg2_00002_MAF50_1621685_exon5



GD snp00002


14. 5



RosBRE EDSNP _SNP_AG _14573434_Lg2_00987_MA F40_1674211_exon1RosBRE EDSNP _SNP_CT_14581355_Lg2_00987_MAF50_517545_exon1


GD snp00987




14. 6


RosBRE EDSNP _SNP_GA _15184323_Lg2_00222_MA F30_MDP0000298218_exon2RosBRE EDSNP _SNP_GT_15206981_Lg2_00222_MAF20_18442_exon1





GD snp00222


15. 2

RosBRE EDSNP _SNP_TC_15273312_Lg2_00222_MAF50_82445_exon115. 3 RosBRE EDSNP _SNP_TC_16128155_Lg2_02686_MAF20_407655_exon1

16. 1 RosBRE EDSNP _SNP_TG_16158221_Lg2_02686_MAF30_M DP0000292769_exon3


GD snp02686




GD snp01309

16. 2


RosBRE EDSNP _SNP_TC_16257853_Lg2_01309_MAF10_M DP0000449067_exon116. 3






RosBRE EDSNP _SNP_GT_16842827_Lg2_RosCO S836_MAF40_M DP0000677244_exon2RosBRE EDSNP _SNP_CT_16845711_Lg2_RosCO S836_MAF40_M DP0000677244_exon1

16. 8

RosBRE EDSNP _SNP_TC_16893667_Lg2_326357__326357_exon216. 9





17. 2


RosBRE EDSNP _SNP_CT_18004558_Lg2_72623_MAF40_72623_exon1RosBRE EDSNP _SNP_GA _18005006_Lg2_325713_MA F20_325713_exon1


18. 0


RosBRE EDSNP _SNP_CT_18425455_Lg2_RosCO S906_MAF20_384122_exon118. 4



18. 7

GD snp02076

RosBRE EDSNP _SNP_GA _18771603_Lg2_02076_MA F30_1624620_exon1RosBRE EDSNP _SNP_AG _18785188_Lg2_02076_MA F10_MDP0000141906_exon1







18. 8


RosBRE EDSNP _SNP_GA _18882549_Lg2_02651_MA F50_MDP0000535127_exon1GD snp02651


18. 9

RosBRE EDSNP _SNP_CT_18978999_Lg2_MD P0000488361_M AF30_MD P0000488361_exon5




19. 2


RosBRE EDSNP _SNP_TG_19261463_Lg2_00934_MAF20_1667145_exon5RosBRE EDSNP _SNP_AG _19287810_Lg2_00934_MA F10_1630326_exon2

GD snp00934




19. 3

RosBRE EDSNP _SNP_TC_19428938_Lg2_217573_MAF30_217573_exon119. 4

RosBRE EDSNP _SNP_CT_19548750_Lg2_01840_MAF20_M DP0000736846_exon219. 5

RosBRE EDSNP _SNP_AC _19551567_Lg2_01840_MA F20_MDP0000234805_exon1RosBRE EDSNP _SNP_AG _19557571_Lg2_01840_MA F30_1661441_exon2

GD snp01840



19. 6


RosBRE EDSNP _SNP_GT_20578860_Lg2_MD P0000139073_M AF30_MD P0000139073_exon1220. 6


RosBRE EDSNP _SNP_TG_20660924_Lg2_RosCO S358_MAF50_1681238_exon2RosBRE EDSNP _SNP_TC_20667705_Lg2_RosCO S358_MAF50_M DP0000185281_exon1




RosBRE EDSNP _SNP_AC _20707414_Lg2_RosCO S358_MAF20_385922_exon1


RosBRE EDSNP _SNP_TG_20724858_Lg2_RosCO S358_MAF10_M DP0000629544_exon2

RosBRE EDSNP _SNP_GT_20728787_Lg2_RosCO S358_MAF40_M DP0000271022_exon1

20. 7



RosBRE EDSNP _SNP_AC _23074147_Lg2_RosCO S292_MAF20_M DP0000590787_exon1

RosBRE EDSNP _SNP_AG _23078001_Lg2_RosCO S292_MAF50_M DP0000407787_exon1




RosBRE EDSNP _SNP_AG _23111804_Lg2_RosCO S292_MAF10_10216_exon1RosBRE EDSNP _SNP_TG_23127933_Lg2_RosCO S292_MAF40_M DP0000175275_exon3

23. 1







RosBRE EDSNP _SNP_TC_23529831_Lg2_02155_MAF30_1642317_exon3RosBRE EDSNP _SNP_TC_23537758_Lg2_02155_MAF10_M DP0000250217_exon1

GD snp02155

23. 5


RosBRE EDSNP _SNP_AG _23924101_Lg2_327954__327954_exon1

RosBRE EDSNP _SNP_AG _23927850_Lg2_M DP0000314765__MDP 0000314765_exon123. 9


RosBRE EDSNP _SNP_GT_24105532_Lg2_MD P0000136940_M AF30_MD P0000136940_exon2

24. 1

RosBRE EDSNP _SNP_CA _24744626_Lg2_00833_MA F50_MDP0000263007_exon1RosBRE EDSNP _SNP_CA _24747820_Lg2_00833_MA F30_45322_exon124. 7





GD snp00833



24. 8




GD snp01935


25. 7


GD snp00092

RosBRE EDSNP _SNP_AG _26386122_Lg2_00092_MA F20_221224_exon1RosBRE EDSNP _SNP_GA _26390694_Lg2_00092_MA F30_MDP0000236703_exon5



26. 4




26. 5


RosBRE EDSNP _SNP_AG _27286399_Lg2_02271_MA F50_MDP0000291692_exon7RosBRE EDSNP _SNP_AG _27292845_Lg2_02271_MA F20_1632994_exon4



GD snp02271



27. 3


RosBRE EDSNP _SNP_CT_27618488_Lg2_02376_MAF20_M DP0000520193_exon3RosBRE EDSNP _SNP_GA _27638999_Lg2_02376_MA F10_326188_exon1

GD snp0237627. 6


RosBRE EDSNP _SNP_TG_29128375_Lg2_226032__226032_exon229. 1

RosBRE EDSNP _SNP_TG_29827721_Lg2_MD P0000556302_M AF30_MD P0000556302_exon1




29. 8





GD snp01251

30. 3




30. 4

RosBRE EDSNP _SNP_GA _30846147_Lg2_261916__261916_exon2


RosBRE EDSNP _SNP_TC_30846189_Lg2_263337__263337_exon2


RosBRE EDSNP _SNP_CT_30846581_Lg2_263337__263337_exon1


30. 8




31. 5





32. 1


GD snp00022

RosBRE EDSNP _SNP_GA _32168123_Lg2_00022_MA F30_1687463_exon3RosBRE EDSNP _SNP_CA _32171222_Lg2_00022_MA F40_980613_exon1



32. 2





32. 4

RosBRE EDSNP _SNP_AC _32854243_Lg2_M DP0000185319_MAF20_M DP0000185319_exon1RosBRE EDSNP _SNP_CT_32854273_Lg2_MD P0000185319_M AF20_MD P0000185319_exon132. 9





GD snp02223


RosBRE EDSNP _SNP_GA _33002490_Lg2_02223_MA F40_1642591_exon3RosBRE EDSNP _SNP_GA _33013805_Lg2_02223_MA F40_MDP0000310234_exon6




33. 0




RosBRE EDSNP _SNP_TC_33275489_Lg2_00629_MAF20_M DP0000126888_exon2RosBRE EDSNP _SNP_AC _33281719_Lg2_00629_MA F10_MDP0000164964_exon1


GD snp00629


33. 3





33. 5

RosBRE EDSNP _SNP_TC_33578382_Lg2_MD P0000233590_M AF30_MD P0000233590_exon233. 6





GD snp01349



33. 9


RosBRE EDSNP _SNP_AC _34035401_Lg2_RosCO S1019_MAF20_M DP0000184243_exon234. 0


RosBRE EDSNP _SNP_CT_34097516_Lg2_RosCO S1019_MAF30_M DP0000273734_exon134. 1




RosBRE EDSNP _SNP_AC _34180511_Lg2_RosCO S2050_MAF30_342651_exon3RosBRE EDSNP _SNP_CT_34184988_Lg2_RosCO S2050_MAF20_M DP0000295657_exon1






34. 2

GD snp00624

RosBRE EDSNP _SNP_AG _34276352_Lg2_00624_MA F50_299184_exon1RosBRE EDSNP _SNP_CT_34282261_Lg2_00624_MAF30_82386_exon134. 3

RosBRE EDSNP _SNP_TC_35144180_Lg2_86472__86472_exon2

RosBRE EDSNP _SNP_GA _35144224_Lg2_86472__86472_exon2



35. 1

RosBRE EDSNP _SNP_TC_35446282_Lg2_155393_MAF10_155393_exon235. 4


RosBRE EDSNP _SNP_GA _35461013_Lg2_00267_MA F20_MDP0000301641_exon1RosBRE EDSNP _SNP_AC _35485026_Lg2_00267_MA F30_MDP0000163550_exon4





GD snp00267


35. 5





GD snp00914


36. 2


RosBRE EDSNP _SNP_TG_36331759_Lg2_01322_MAF20_M DP0000707672_exon2RosBRE EDSNP _SNP_GT_36335353_Lg2_01322_MAF30_M DP0000707672_exon3


36. 3




GD snp01322


RosBRE EDSNP _SNP_CT_36421423_Lg2_01322_MAF10_M DP0000758646_exon1GD snp00669


36. 4






RosBRE EDSNP _SNP_CT_36478711_Lg2_00669_MAF10_M DP0000164775_exon2RosBRE EDSNP _SNP_AG _36489224_Lg2_00669_MA F10_12262_exon1


36. 5






RosBRE EDSNP _SNP_AC _38016824_Lg2_10007_MA F50_MDP0000780001_exon1GD snp10007

38. 0




RosBRE EDSNP _SNP_TC_38151718_Lg2_MD P0000020317_M AF20_MD P0000020317_exon638. 2



RosBRE EDSNP _SNP_TG_38924310_Lg2_00995_MAF20_M DP0000568968_exon3RosBRE EDSNP _SNP_CT_38935589_Lg2_00995_MAF30_M DP0000211904_exon5

38. 9


GD snp00995





39. 0


RosBRE EDSNP _SNP_GA _39231189_Lg2_01938_MA F20_MDP0000277119_exon2GD snp01938


39. 2

RosBRE EDSNP _SNP_CT_39271679_Lg2_01938_MAF20_M DP0000241144_exon139. 3





RosBRE EDSNP _SNP_GA _39526012_Lg2_00167_MA F50_1641137_exon4GD snp00167


39. 5





39. 6


RosBRE EDSNP _SNP_TC_40082868_Lg2_02535_MAF20_M DP0000320988_exon27RosBRE EDSNP _SNP_CA _40085225_Lg2_02535_MA F40_MDP0000320988_exon20

GD snp02535



40. 1

chr.2

GDsnp003480. 0

GDsnp011341. 2

snpCO9036052. 4

GDsnp017353. 7

GDsnp015654. 3

GDsnp009595. 0

GDsnp016417. 8

GDsnp014768. 5

GDsnp002039. 3

GDsnp0194510. 6

GDsnp0007713. 7

GDsnp0015814. 5

GDsnp0166316. 4

GDsnp0030817. 4

GDsnp0116218. 0

GDsnp0033320. 6

GDsnp0154923. 9

GDsnp0050527. 4

GDsnp0040728. 5

GDsnp0122329. 6

GDsnp0099130. 7

GDsnp0015931. 8

GDsnp0100532. 6

GDsnp0061435. 0

GDsnp0155238. 9

GDsnp0021439. 9

GDsnp0017441. 7

GDsnp0000242. 4

GDsnp0098743. 7

GDsnp0022244. 5

GDsnp0268645. 2

GDsnp0130947. 0

GDsnp0265151. 7

GDsnp0093453. 8

GDsnp0184054. 2

GDsnp0207655. 9

GDsnp0083358. 7

GDsnp0215560. 3

GDsnp0193561. 3

GDsnp0009263. 2

GDsnp0237664. 2

GDsnp0227165. 3

GDsnp0125166. 2

GDsnp0002266. 7

GDsnp0222368. 6

GDsnp0062970. 4

GDsnp0134973. 3

GDsnp0026776. 6

GDsnp0062477. 1

GDsnp1000778. 3

GDsnp0066979. 6

GDsnp0132280. 0

GDsnp0091481. 0

GDsnp0099582. 6

GDsnp0193883. 9

GDsnp0016784. 4

GDsnp0253585. 2

LG2

Apple 9k SNP Chip v1 (dec 2010)

• Mixture of CG SNP’s – located in exon

regions for functionality, and max 4 SNPs

per CG.

• 5613 evenly spread SNPs (in focal points)

• 906 Candidate gene based SNPs = 393

CGs

• 8898 SNPs in total

• Markers cover 1307 cM genetic distance

(average <1 SNP / 1.5 cM).

SNPs on Apple LG-2

Chagne 2011, PFR


RosBREEDSNP_SNP_CT_11771410_Lg2_00614_MAF30_1675314_exon1GDsnp00614RosBREEDSNP_SNP_AG_11777704_Lg2_00614_MAF40_1665749_exon5RosBREEDSNP_SNP_TC_11779814_Lg2_00614_MAF20_830296_exon1RosBREEDSNP_SNP_GT_11799850_Lg2_00614_MAF50_MDP0000175404_exon2RosBREEDSNP_SNP_AG_11806852_Lg2_00614_MAF50_175518_exon1

11.8

RosBREEDSNP_SNP_GA_11950668_Lg2_RosCOS2709_MAF40_1639624_exon2RosBREEDSNP_SNP_CT_11954759_Lg2_RosCOS2709_MAF50_MDP0000266474_exon10RosBREEDSNP_SNP_GA_11965366_Lg2_RosCOS2709_MAF20_MDP0000266475_exon2RosBREEDSNP_SNP_GT_11969851_Lg2_RosCOS2709_MAF30_1618610_exon1RosBREEDSNP_SNP_TC_11972340_Lg2_RosCOS2709_MAF40_889572_exon1RosBREEDSNP_SNP_TG_11993525_Lg2_RosCOS2709_MAF10_163123_exon1RosBREEDSNP_SNP_AC_11996518_Lg2_RosCOS2709_MAF30_1663531_exon1RosBREEDSNP_SNP_TG_11998839_Lg2_RosCOS2709_MAF50_1680670_exon1

12.0

RosBREEDSNP_SNP_CT_12512364_Lg2_00174_MAF30_141353_exon112.5GDsnp00174RosBREEDSNP_SNP_GA_12590482_Lg2_00174_MAF10_1653396_exon112.6

RosBREEDSNP_SNP_CT_12888634_Lg2_01552_MAF40_1644276_exon3RosBREEDSNP_SNP_CA_12895209_Lg2_01552_MAF20_1626835_exon1RosBREEDSNP_SNP_CT_12897345_Lg2_01552_MAF20_1626835_exon2RosBREEDSNP_SNP_CT_12901428_Lg2_01552_MAF30_525812_exon2RosBREEDSNP_SNP_CT_12903929_Lg2_01552_MAF30_1660471_exon1RosBREEDSNP_SNP_GA_12926120_Lg2_01552_MAF50_683506_exon1GDsnp01552RosBREEDSNP_SNP_CT_12933833_Lg2_01552_MAF40_1644477_exon4RosBREEDSNP_SNP_AG_12942637_Lg2_01552_MAF50_MDP0000683486_exon1

12.9

RosBREEDSNP_SNP_TC_13055105_Lg2_324795_MAF20_324795_exon2RosBREEDSNP_SNP_CT_13055225_Lg2_324795_MAF40_324795_exon2RosBREEDSNP_SNP_AG_13055342_Lg2_324795_MAF40_324795_exon2

13.1

RosBREEDSNP_SNP_CT_13641108_Lg2_00214_MAF40_MDP0000281231_exon6RosBREEDSNP_SNP_TC_13643738_Lg2_00214_MAF40_848655_exon1RosBREEDSNP_SNP_CT_13646169_Lg2_00214_MAF50_1635069_exon1

13.6

RosBREEDSNP_SNP_CT_13651288_Lg2_00214_MAF50_MDP0000131675_exon2RosBREEDSNP_SNP_GA_13656632_Lg2_00214_MAF20_MDP0000282278_exon1RosBREEDSNP_SNP_CA_13659348_Lg2_00214_MAF20_453677_exon1RosBREEDSNP_SNP_TC_13673501_Lg2_00214_MAF30_MDP0000235958_exon9RosBREEDSNP_SNP_CT_13676580_Lg2_00214_MAF30_356820_exon1RosBREEDSNP_SNP_GT_13683046_Lg2_00214_MAF10_76634_exon1GDsnp00214

13.7

RosBREEDSNP_SNP_CA_13921344_Lg2_248148__248148_exon113.9RosBREEDSNP_SNP_GA_14478242_Lg2_00002_MAF40_MDP0000805105_exon1RosBREEDSNP_SNP_GA_14480369_Lg2_00002_MAF10_1680403_exon1RosBREEDSNP_SNP_CT_14484409_Lg2_00002_MAF40_219048_exon1RosBREEDSNP_SNP_AG_14486643_Lg2_00002_MAF30_1630136_exon2RosBREEDSNP_SNP_CT_14489605_Lg2_00002_MAF30_187689_exon1RosBREEDSNP_SNP_CT_14500796_Lg2_00002_MAF50_1621685_exon5RosBREEDSNP_SNP_TG_14503620_Lg2_00002_MAF50_180022_exon1RosBREEDSNP_SNP_CA_14512918_Lg2_00002_MAF20_577821_exon1GDsnp00002RosBREEDSNP_SNP_CA_14539156_Lg2_00002_MAF10_279971_exon1

14.5

RosBREEDSNP_SNP_CT_14557542_Lg2_00987_MAF30_27239_exon1RosBREEDSNP_SNP_TC_14571102_Lg2_00987_MAF50_85433_exon1RosBREEDSNP_SNP_AG_14573434_Lg2_00987_MAF40_1674211_exon1RosBREEDSNP_SNP_CT_14581355_Lg2_00987_MAF50_517545_exon1RosBREEDSNP_SNP_GA_14588942_Lg2_00987_MAF30_1674484_exon1GDsnp00987RosBREEDSNP_SNP_AG_14599407_Lg2_00987_MAF40_375341_exon1RosBREEDSNP_SNP_CT_14609304_Lg2_00987_MAF20_MDP0000712295_exon1RosBREEDSNP_SNP_GA_14643636_Lg2_00987_MAF10_MDP0000733437_exon1

14.6

RosBREEDSNP_SNP_GT_15181769_Lg2_00222_MAF30_MDP0000849116_exon1RosBREEDSNP_SNP_GA_15184323_Lg2_00222_MAF30_MDP0000298218_exon2RosBREEDSNP_SNP_GT_15206981_Lg2_00222_MAF20_18442_exon1RosBREEDSNP_SNP_CA_15211202_Lg2_00222_MAF10_MDP0000236750_exon9RosBREEDSNP_SNP_GA_15214773_Lg2_00222_MAF40_54312_exon1RosBREEDSNP_SNP_GA_15218231_Lg2_00222_MAF20_MDP0000120828_exon2RosBREEDSNP_SNP_TC_15220265_Lg2_00222_MAF10_MDP0000250157_exon5GDsnp00222RosBREEDSNP_SNP_GA_15230080_Lg2_00222_MAF40_1630459_exon1

15.2

RosBREEDSNP_SNP_TC_15273312_Lg2_00222_MAF50_82445_exon115.3RosBREEDSNP_SNP_TC_16128155_Lg2_02686_MAF20_407655_exon116.1RosBREEDSNP_SNP_TG_16158221_Lg2_02686_MAF30_MDP0000292769_exon3RosBREEDSNP_SNP_AG_16171503_Lg2_02686_MAF40_MDP0000663783_exon1GDsnp02686RosBREEDSNP_SNP_GA_16177297_Lg2_01309_MAF50_330377_exon1RosBREEDSNP_SNP_TC_16203479_Lg2_01309_MAF20_1648449_exon1RosBREEDSNP_SNP_TC_16214893_Lg2_01309_MAF30_MDP0000282472_exon1GDsnp01309

16.2

RosBREEDSNP_SNP_AG_16252110_Lg2_01309_MAF20_80152_exon2RosBREEDSNP_SNP_TC_16257853_Lg2_01309_MAF10_MDP0000449067_exon116.3

RosBREEDSNP_SNP_AG_16760171_Lg2_RosCOS836_MAF20_950549_exon1RosBREEDSNP_SNP_GA_16792135_Lg2_RosCOS836_MAF10_1640965_exon2RosBREEDSNP_SNP_GA_16799144_Lg2_RosCOS836_MAF30_1666037_exon2RosBREEDSNP_SNP_AG_16803165_Lg2_RosCOS836_MAF10_406840_exon1RosBREEDSNP_SNP_CT_16830671_Lg2_RosCOS836_MAF30_MDP0000573608_exon1RosBREEDSNP_SNP_GT_16842827_Lg2_RosCOS836_MAF40_MDP0000677244_exon2RosBREEDSNP_SNP_CT_16845711_Lg2_RosCOS836_MAF40_MDP0000677244_exon1

16.8

RosBREEDSNP_SNP_TC_16893667_Lg2_326357__326357_exon216.9RosBREEDSNP_SNP_GA_17179364_Lg2_327287_MAF40_327287_exon1RosBREEDSNP_SNP_AG_17179555_Lg2_327287_MAF30_327287_exon1RosBREEDSNP_SNP_GA_17179731_Lg2_327287_MAF30_327287_exon1RosBREEDSNP_SNP_AG_17180168_Lg2_327287_MAF30_327287_exon1

17.2

RosBREEDSNP_SNP_CT_18003967_Lg2_325713_MAF20_325713_exon3RosBREEDSNP_SNP_CT_18004558_Lg2_72623_MAF40_72623_exon1RosBREEDSNP_SNP_GA_18005006_Lg2_325713_MAF20_325713_exon1RosBREEDSNP_SNP_TC_18005035_Lg2_325713_MAF40_325713_exon1

18.0

RosBREEDSNP_SNP_CT_18390503_Lg2_RosCOS906_MAF40_1630085_exon1RosBREEDSNP_SNP_CT_18425455_Lg2_RosCOS906_MAF20_384122_exon118.4

RosBREEDSNP_SNP_AG_18717999_Lg2_02076_MAF50_22779_exon1RosBREEDSNP_SNP_GT_18746181_Lg2_02076_MAF20_MDP0000178428_exon118.7

GDsnp02076RosBREEDSNP_SNP_GA_18771603_Lg2_02076_MAF30_1624620_exon1

GDsnp01223GDsnp0099130.7

GDsnp0015931.8

GDsnp0100532.6

GDsnp0061435.0

GDsnp0155238.9

GDsnp0021439.9

GDsnp0017441.7

GDsnp0000242.4

GDsnp0098743.7

GDsnp0022244.5

GDsnp0268645.2

GDsnp0130947.0

GDsnp0265151.7

GDsnp0093453.8

GDsnp0184054.2

GDsnp0207655.9

GDsnp0083358.7

GDsnp0215560.3

GDsnp0193561.3

GDsnp0009263.2

GDsnp0237664.2

Apple 9k SNP Chip v1

Future = 25K apple chip in 12 – 24 months!

SNPs on Apple LG-2

Chagne 2011, PFR


Acknowledgements

Plant and Food Research, NZ

David Chagné, Sue Gardiner

Ross Crowhurst

Lab. Fruit Breeding and Biotechnol, KU

Leuven, BE

Ifigeneia Mellidou

Stijn Vanderzande

Bruno Daniels

Tuyet-An

Wannes Keulemans

Mark Davey

Cameron Peace (WSU) Amy Iezzoni (MSU)

Nahla Bassil (OSU)

IASMA:

Michela Troggio, Ricardo Velasco


Thanks!

Onderzoek gefinancierd door:IWT – Instituut voor de Aanmoediging van Innovatie door Wetenschap en Technologie in Vlaanderen

Veiling Haspengouw, Veiling Brava, Better3fruit NV

110625uniba qtlsm genome 3 - ku leuven · 2011-12-27 · davey, mw 2 madav – uniba june 2011 kul...

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