QTL and QTL allele validation in peach

Ksenija Gasic

25 July 2013ASHS Palm Desert, CA

Outline of Presentation

RosBREED

Choosing the trait and QTL

QTL validation – G4Mat maturity

QTL allele validation – G4Mat maturity

Choosing the trait and QTL

- 4 breeding programs- Fresh market and processing peach

Choosing the trait and QTL

40%

3.3%

10%

10%

6.7%

6.7%

23.3%

Fruit size

Fruit shape

Fruit skin color

Fruit flavor

Fruit firmness

Sweetness/soluble solids

Disease resistance

Productivity

Production consistency

Other fruit quality attribute

Choosing the trait and QTL

- SE results for fresh market peaches

Sweetness & acidity

Some of the known loci in the Prunus genome

Y

F-M

B

Evg

Mi Nl

D

Br

Dl

Pi Pcp

Cs

Ag

Fc

LbSk

G

D

ScGr

Ps

Ma

S

Sf

E

Si

Ripe date

Skin blush

Flwg date

Sugars

Skin blush

Ripe dateAcidity

Sugars

Sugars

Sugars

Ripe date

Acidity

AciditySugars

Flwg date

Ripe date

AciditySugars

Bruising

Bruising

Bruising

Flwg date

Flwg date

Fruit size

Ripe date

Skin blush

Sugars

Acidity

BleedingMealiness

Mealiness

Mealiness

Browning

Sugars

sharka

Dw

G6G5G4G3G2G1 G8G7

Peach, Nectarine

Almond

Apricot

Xap

Xap

Xap

Xap

Xap

Ripe date

Flwg date

QTL Validation- confirming the G4Mat QTL really exists

in peach breeding germplasm

McIntosh

LivelRasp

F_Spartan

Starr

Delicious

Cox

GoldenDel

RomBeauty

Mflor821

Jonathan

F_P21R4A30

Frostbite

NorthSpy

JerseyBla

F_Gingergold

F_JamesGr

Wealthy

F_IngMarie

Tetofsky

YelTransp

Longfield

DuchOlden

F_PattenGr

Edgewood

WorcPearm

RallsJan

Mavis

BenDavis

Gravenstein

Close

PRI643-11

Jongrimes

Wagener

FrancRus

LadyWill

BlushiGol

F_Undine

Indo

Malinda

Glockenapfel

DrOldenbu

F_Helios

F_EdGoulGol

F_Sandow

Lundbytrop

A28/39

A849-5

BeautBath

VKrakers

BelHerm

PRI2059-101

F_Brina

Scarlet

NJ381049

StarkEarl

Linda

X4598

X3174

AnanasRei

AutGold

BaumanRei

BernRos

Boskoop

BrixPlatt

Calamari

Calvilla

CrimsSnow

Croncels

DallaRosa

EarlyGold

Edelb

Fiamma

Freedom

GelEdel

Gewurz

Hampshire

HarbRei

Limoncini

Magre

MN1628

Napoleone

Ontario

PermainDor

RedFiled

RenCanada

RenChamp

Robusta5

RosBian

RosdiCal

RosDop

RotStett

SanLugano

Sila

Stayman

TavBian

TirSpitz

WeisWint

Melba

Spartan

OR38T610

KidsOrRed

Sonora

F1_9433-2-2

F1_9433-2-8

P21R4A30

Keepsake

M_MN1764

F_Honeycrisp

Melrose

Macoun

PRI54-12

GingerGold

JamesGr

NJ130o

IngMarie

NJ31

Monroe

Mantet

Oriole

Sharon

Fireside

PattenGr

F_Goodland

M_MolliesDel

NJ14

NJ19237

Crandall

NJ35437

CrownPR

Clivia

Splendour

Braeburn

Ambrosia

Cameo

Fuji

NJ35934

F_NJ15

Cortland

F_MolliesDel

PRI1469-100

Delcorf

Idared

Maigold

Akane

Sundowner

CrippsPink

Delblush

Undine

Orin

Shizuka

Toko

F_MN1764

Haralson

Telamon

M_Sunrise

PCF-3-120

Hatsuaki

Jonagold

M_NY632

Gloster

PRI69-52

Alkmene

Helios

Apollo

Empire

Akagi

EdGoulGol

PRI1956-6

Sandow

SchonNord

GranSmith

Delgollune

Dolgo

Angold

Ariwa

Discovery

Belgica

Rafzubin

GoldPink

Brina

Pop_GDxSc

Creston

Delearly

Ligol

Dalinette

Jolana

F_Williams

Gala

NJ67634

F2_26829-2-2

Prima

Honeycrisp

sibLiberty

Liberty

F_Delfloki

NJ117637

NJ12

Elstar

NY88

StateFair

Goodland

NJ440249

M2439

Lambourne

NJ15

NJ303955

MolliesDel

XIIA277

KAZ95-17-14

KAZ95-18-07

KAZ96-05-04

Pilot

Pinova

Senshu

PitmPine

MN1764

MN1702

Monark

Honeygold

Sunrise

Arlet

NY632

Fiesta

52-05-26

Zonga

Piros

Fortune

Shinsekai

GoldenOr

Summerfree

Sabina

WSU46

B_TxBB

Nicogreen

Delcoros

Snowsweet

Kerr

Williams

PRI14-126

PRI14-226

PRI14-644

Winesap

F_Ill_#2

NY65707-19

NJ123249

NJ27

Sonya

NY752

MN1691

NJ37848

PRI47-147

NJ88

Rubin

Vanda

Nicola

WSU2

Chinook

PacQueen

PacRose

AurGoldGa

BC-8S-27-2

BC-8S-31-56

BC-SPA493

NJ136055

Suncrisp

PRI2482-100

Zari

Bellida

Civni

Ecolette

Milwa

Kanzi

Nicoter

NZ_RGxBB

LaFlam

Nevson

Sansa

Scifresh

Scilate

WSU24

WSU37

GMAL4591

GMAL4593

GMAL4595

CIVG198

Dalitron

Ped-PinxCam

ShinGold

WSU34

25-120-9928

Pop_HCxCP

Ped-HCxPit(692)

Ped_HCx1764

MPop_HCx1702

MPop_HCxMon

Silken

Merlijn

NY75414-1

Tunda

WSU35

4-159-9926

Pop_ArlxCP

N_PxF

E_FxGD

E_FxGlo

Murray

NJ53

PRI612-1

Ill_#2

PRI668-100

NY913

PRI610-2

PRI855-102

NY241

Zestar

PCFW2-134

PRI669-205

PRI1235-100

NJ109

Rubinola

Rubinstep

Rucla

Topaz

WSU17

WSU36

Pop_BBxPR

4-27-0019

5-87-0019

5-90-0019

6-73-0019

4A-100-0013

4A-38-0013

Pop_AurxHC

WSU22

WSU30

NJ90

NJ8

NJ110037

Florina

PRI1661-1

PRI1661-2

Coop-17

Grifer

Coop-15

Priscilla

Coop-10

Camuzat

Jonafree

Ped-SonxNY241

MN1914

Ped-HCxZest

CrimsCrisp

Saturn

NJ24

Julyred

Raritan

PRI1018-101

P7R25A27

Enterprise

Goldrush

Delfloki

Delorina

Pop_GaxC15

Santana

Pristine

Ped_HCxJonf

Jerseymac

Redfree

Ariane

WSU38

Ped-GoldrxNY913

Galmac

RosBREED

Peach Material• ~980 individuals

(cultivars, ancestors, founders, breeding lines, selections, and seedlings

• Genotyped genome-wide with SNP markers

• Phenotyped in 2010-12 for fruit quality and other high-impact traits

Crop Reference Sets

RosBREED

• 478 individuals (cultivars, ancestors, founders, breeding lines, selections, and seedlings)

352

82%

72 9% 335%

204%

Peach Almond Peach relatedAlmond related

Peach related: P. davidiana, P. miraAlmond related: P. argentea, P. scoparia

362

75%

27 5%

8818%

SeedlingsAdvanced selections/germplasmCultivars

G4Mat – Maturity Date

CA

AR

TX

SC

73% PVE

77% PVE

56% PVE(phenotypic variance explained)

64% PVE

QTL Allele Validation- detecting and valuing G4Mat alleles

in peach breeding germplasm

G4Mat – Maturity DateAPR MAY JUN JUL AUG SEP

Maturity date

• 4 SNPs 8 haplotypes distinguished• Labeled VE (very early), E, M, L, VL1, VL2,

XL, alm• 36 possible genotypes (allelic combinations)• Uneven allele distribution in populations...

RosBREED

G4Mat – Maturity Date

AR Pop1

x

182±6

200±6

207±7

222±8

40 days!

RosBREED

G4Mat – Maturity Date

SC Pop0823 164±0

192±5

194±4

210±545 days

!

TX Pop3 140±2

150±8

152±9

191±750 days

!

CA Pop8-3 192±11

211±5

212±7

233±541 days

!

G4Mat – Maturity Date

CA

AR

TX

SCAll Locations VE

EMLVL1VL2XLalm

Other Jewels for Peach

Some Jewels To Tell You About

- D – acidity- G – fruit type (p/n)- Y – flesh color- F-M flesh texture & adhesion- G4Mat – maturity date- G4Mat – SSC- G3Bl – blush- G1Xap & G6Xap - bacterial spot resistance

APR MAY JUN JUL AUG SEP

Maturity date

Sweetness & acidity White vs.

yellow flesh Nectarine vs. peach

Fruit skin color

RosBREED

Fruit texture type

Fruit Xap resistance

Loci of interest on Prunus genome

Y

F-M

B

Evg

Mi Nl

D

Br

Dl

Pi Pcp

Cs

Ag

Fc

LbSk

G

D

ScGr

Ps

Ma

S

Sf

E

Si

Ripe date

Skin blush

Flwg date

Sugars

Skin blush

Ripe dateAcidity

Sugars

Sugars

Sugars

Ripe date

Acidity

AciditySugars

Flwg date

Ripe date

AciditySugars

Bruising

Bruising

Bruising

Flwg date

Flwg date

Fruit size

Ripe date

Skin blush

Sugars

Acidity

BleedingMealiness

Mealiness

Mealiness

Browning

Sugars

sharka

Dw

G6G5G4G3G2G1 G8G7

Peach, Nectarine

Almond

Apricot

Xap

Xap

Xap

Xap

Xap

Ripe date

Flwg date

AR Pop1

G4Mat – SSCSweetness

14.413.8 13.9

16.4

TX all pops11.9 10.6 11.3

14.0

oBrix

22% PVE

15% PVE

AR=38%, CA=21%, SC=28%

G4MatSweetness

VE-BBBA Arrington, Bradley, CAF2, Hesse, Westbrook, A672, Saturn, Tropic Beauty, Yumyeong, Zin Dai

E-ABBB A672, Saturn, Tropic Beauty

M-ABBA Elberta, JHHale, O'Henry, Dr Davis, Halford,White County, Winblo

L-BBAA Bolinha, A773

VL1-AAAA White County

VL2-AAAB Chinese Cling, Elberta, JHHale, O'Henry, 40A17, Peento, Vilmos, Yumyeong, Zin Dai

XL-BAAB Winblo

alm-BBBB all almonds, 2000,2-8, persicaxdavidiana

APR MAY JUN JUL AUG SEP

Maturity date

Red color in apple, cherry and peach

Cherry

G3

MYB1/10Fruit skin & flesh color

Peach

G3

Cs locus(red color around stone)

& QTL for flesh bleeding

Apple

L9

MYB1/10Fruit skin & flesh color

RosBREED

MYB1/10Fruit skin color

Allele distribution for G3Bl

RosBREEDPoster #

359SC AR CA TX

0

50

100

150

200

250

blblBlbl BlBl

Breeding Program

Freq

uenc

y

BlBl 54%

Blbl 19%

blbl26%

RosBREED CRS

CAPS markers for G3Bl

RosBREED

A

B

BlBl

Blbl

blbl

RosBREED

Fruit texture type

Peach fruit texture type

RosBREED

(www.rosbreed.org/breeding/jewel-use)

peach fruit texture type

Tables of functional genotypes

Example here is for

?

• G1XapF & G6XapF Bacterial spot resistance

SU

RE M almR

SU

RE M almR

RE R

SU

Clayton, Westbrook, WhiteCounty, WhiteRiver,

O’Henry, Blazeprince, Flordaprince,

Contender, Elberta, Early Crawford, Georgia Belle, Loring, Redhaven, Tropic Beauty, Winblo

UFGold, Candor, Bailey, Arrington

JH Hale, Mayfire, RioOsoGem

Springold, Lovell, LateCrawford Almond

Susceptibility

Resistance

Mal m

Moderate

RosBREEDYang et al. 2012 TGG

? Chinese cling

a

b/d

c

e

f

Allele distribution for G1XapF

RosBREED

13%

24%

12%24%

3%

14%

1%6%

3%CRS SU|SUSU|RESU|RSU|MSU|?RE|RERE|RRE|MRE|almM|REM|RM|MM|almR|R

AR CA SC TX0

50

100

150

200

250

300

350

400

SU|SU SU|RE SU|R SU|M SU|?RE|RE RE|R RE|M RE|alm M|REM|R M|M M|alm R|R

Allele distribution for G6XapF

RosBREED

44%

24%

5%1%

16%

7%

3% 1% CRS

SU|SUSU|RESU|RSU|MSU|?RE|RERE|RRE|MRE|almM|REM|RM|MM|almR|R

AR CA SC TX0

50

100

150

200

250

300

350

400

SU|SU SU|RE SU|R SU|M SU|?RE|RE RE|R RE|M RE|alm M|REM|R M|M M|alm R|R

Acknowledgements

This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

MSUAmy Iezzoni (PD)

Jim HancockDechun Wang

Cholani Weebadde

WSUCameron Peace

Dorrie MainKate Evans

Karina Gallardo Vicki McCracken

Nnadozie OraguzieFormer WSU

Raymond JussaumeMykel Taylor

CornellSusan BrownKenong Xu

Clemson Ksenija Gasic

Gregory Reighard

Texas A&MDave Byrne

Univ. of CA-DavisTom Gradziel

Carlos Crisosto 

Univ. of New Hamp.Tom Davis

Univ. of MinnesotaJim Luby

Chengyan Yue

Oregon State Univ.Alexandra Stone

Plant Research Intl, Netherlands

Eric van de WegMarco Bink

USDA-ARSNahla Bassil

Gennaro FazioChad Finn

Univ. of ArkansasJohn Clark