MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY

TARGETS VALUABLEFUNCTIONAL ALLELES

Cameron Peace, Washington State Universitywith: Nahla Bassil, Michael Coe, Gennaro Fazio, Karina Gallardo,

Ksenija Gasic, Jim Luby, Dorrie Main, Jim McFerson, Cholani Weebadde, Eric van de Weg, Chengyan Yue, & Amy Iezzoni

Outline of Presentation

The RosBREED Project

Available “Jewels in the Genome”

Jewels in Breeding Application

What’s Next? RosBREED 2

The RosBREED Project

• Goal: Enable MAB for U.S. Rosaceae crops

• PI: Amy Iezzoni, Michigan State University

• 4 years, Sep 2009 – Aug 2013

• Funded by SCRI(USDA-NIFA’s Specialty Crop Research Initiative)

• $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners)

• Collaboration U.S.-wide and international

The RosBREED Project

QTL discovery(looks promising...)

MAB Pipelining(polishing...)

Breeding(assembling into masterpieces)

“Jewels in the Genome”- discovering, polishing, using

Jewels= valuable genetic discoveries ready for breeding application= marker-locus-trait associations validated in a breeding program

Application of Genomics Knowledge

Known QTLs

DN

A in

form

atio

n

Linkage maps

Expression profiles

Whole genome

sequences

Genetic/allelic

diversity

GMO

Application in current cultivars

Application in breeding

Find trait-controlling genes

Application

Application of Genomics Knowledge

Known QTLs

DN

A in

form

atio

n

Linkage maps

Expression profiles

Whole genome

sequences

Genetic/allelic

diversity

GMO

Application in current cultivars

Application in breeding

Find trait-controlling genes P

ractical application

What DNA information is

available?

What is the practical

goal?

Various waysto get there

Application of Genomics Knowledge

Known QTLs

Application in breeding

Breeding markersDNA te

sting

serv

icesQTL

prior

ities

Cross

ing

sche

mes

Trial

MASS

Simple validation

Allele effects& distributions

Seedli

ng

selec

tion

sche

mes

Application of Genomics Knowledge

Known QTLs

Application in breeding

Breeding markersDNA te

sting

serv

icesQTL

prior

ities

Cross

ing

sche

mes

Trial

MASS

Simple validation

Allele effects& distributions

Seedli

ng

selec

tion

sche

mes

1.Tool utility = predictive power in germplasm

of a breeding program

Application in Breeding - Requirements

2.Tool itself = assay (DNA markers) usableby a breeding program

1.Tool utility = predictive power in germplasm

of a breeding program

Application in Breeding - Requirements

2.Tool itself = assay (DNA markers) usableby a breeding program

ready-to-use

marker-locus-trait associations

DNA tests for contrasting alleles at locifor valuable traits

1.Tool utility = predictive power in germplasm

of a breeding program

Application in Breeding - Requirements

2.Tool itself = assay (DNA markers) usableby a breeding program

ready-to-use

marker-locus-trait associations

DNA tests for contrasting alleles at locifor valuable traits

Idiosyncratic!One size does not fit all!

...all breeding-program-specific

Available“Jewels in the Genome”

Sweetness & acidity

Maturity date

Bitter pit susceptibility

Self-fertility

Fruit size

Ever-bearing

Fruit skin color

Fruit color

Fruit storability

Melting vs. Non-melting flesh

Freestone vs. clingstoneFruit size

Available “Jewels in the Genome”

Red stele resistance

Leaf spot resistance

Acidity

Sunburn susceptibility

Firmness

“Fresh sensation”(crispness, tartness, juiciness)

Fruit color

Strawberry: Red Stele Resistance

• Validation of marker by inoculations:- 75% match genotype-phenotype- 20% individuals have otherresistance sources

0 1 2 3 4 5

3.43 disease

threshold

Is presence of certain SSR allele associated with red stele resistance?

• Genotypic data also used to identifymany cases of incorrect parentage

Red stele resistance

Marker(s)? 1 SSR

Application? Parents: crossing Seedlings: culling Selections: advance

Apple: Skin Coloration

Cover amount over apple skin surface

Allele & Genotype frequencies in 192 cvs

rfRf rfrf

RfRf

Rfrf

1000 seedlings – how many with score >4?

Rfrf x RfRf ---> 647

RfRf x RfRf ---> 818

+26% efficiency!

prob

abilit

y

Marker(s)? 1-3 SNPs from 8K array genome scan

Application? Parents: crossing Selections: distinguish Rfrf / RfRf

Peach: Maturity Date

-40 -20 20 July

+20 +40 days

-40 -20 20 July

+20 +40 days

AA:AAGA:AA

AA:AG GA:AG 168:168 156:168

Three 2-SNP haplotypes (AA,GA,AG) in four combinations

Two SSR alleles(168,156) in two combinations

One trait locus,two ways of genotyping

Maturity date

Marker(s)? 2 SNPs from 9K array ...or ... 1 SSR

Application? Parents: crossing Seedlings: culling Selections: advance

Apple: Acidity

• Two lociMa – LG16“A” – LG8

Acidity

• Not quite additive – some epistasis

Use together Marker(s)? 2 SNPs from 8K array genome scan

Application? Parents: crossing Selections: distinguish low/med/high

“Fresh sensation”(crispness, tartness, juiciness)

Apple: Multiple Traits Around Ma Locus

Bitter pit susceptibilityMa

Fruit size

Mb0

2

4

6Maturity date

cM0

101520

5

2530

• Every individual has 2 haplotypesHoneycrisp Golden Del. Braeburn Gala Pink Lady

L E L L

Target B?

LL

Marker(s)? 1 SSR

Application? Parents: crossing Seedlings: culling Selections: advance

Target A?

LL

Cherry: G2 Fruit Size and Firmness– An Economic Trade-Off

Socio-economic value ($ per lb)

0.10

0

0.08

0.06

0.04

0.02

G2 locus haplotype

G2 locus diplotypeBL ALL

ECB

Hm

F

CE

BEAAAB

AEAD AC

BDAHAm AN BN Bm

AF

Population average

D

A

N O

SE value=

value of reaching threshold

xprobability of achieving it

Fruit sizeFirmness

Marker(s)? SSRs – 2 flanking the QTL

Application? Parents: crossing Seedlings: culling Selections: advance

Jewels in Breeding Application

Cost per initial seed

Marker-Assisted Seedling Selectionin the Washington Apple Breeding Program

Savings

DNA testing

$8

$4

$0

$6

$10

$2

Rearing & evaluating those kept

Early rearing

$62K2010

estimated projected resource savings

$38K2011

$60K2012

seedlings tested

seedlings culled

8000

5000

5417

2937

7452

4403

“Fresh sensation”(crispness, tartness, juiciness)

Fruit storability

What’s Next? RosBREED 2

A Planned New RosBREED Project

Socio-

economics

informatio

n

DNA

informatio

n

Innovative, superior,

risk-mitigating new cultivars

Efficient, accurate, creative breeding

Accessible natural diversity

PRODUCTIONPROCESSINGMARKETING

Post-breeding

Breeding

Pre-breeding

NATURAL DIVERSITY

CONSUMPTION

Seedling selectionParent selection

Cultivar commercialization

Germplasm development

Acknowledgements

This project is supported by the Specialty Crop Research Initiative of USDA’s

National Institute of Food and Agriculture

Questions?