Transcript Slide 1

QTL and QTL allele
validation in peach
Ksenija Gasic
25 July 2013
ASHS Palm Desert, CA
Outline of Presentation
 Choosing the trait and QTL
 QTL validation – G4Mat maturity
 QTL allele validation – G4Mat maturity
Choosing the trait and QTL
Choosing the trait and QTL
- 4 breeding programs
- Fresh market and processing peach
Choosing the trait and QTL
- SE results for fresh market peaches
Fruit size
Fruit shape
23.3%
Fruit skin color
Fruit flavor
40%
Fruit firmness
Sweetness/soluble solids
6.7%
Disease resistance
Productivity
6.7%
Production consistency
Other fruit quality attribute
3.3%
10%
10%
Some of the known loci in the Prunus genome
G1
G2
Sugars
Mi
G3
Flwg date
G4
G5
Ripe date
G6
D
Xap
Acidity
Ripe date
Sugars
Sugars
Skin blush
D
Xap
Y
Skin blush
sharka Bruising
Mealiness
Pcp
Fc
Acidity
Xap
Flwg date
Ripe date
Sugars
Lb
Xap
Sc
Gr
Sk
G
Sf
E
Sugars
Acidity
Acidity
Br
Dl
F-M
Mealiness
Bleeding
Peach, Nectarine
Flwg date
Flwg date
S
Sugars
B
Xap
Ripe date
Sugars
Evg
G8
Nl Fruit size
Acidity
Ripe
Dw date Ma
Sugars
Ps Skin blush
Browning
Ag
Pi
Flwg date
Cs
Bruising
Ripe date
Mealiness
G7
Bruising
Almond
Si Apricot
QTL Validation
- confirming the G4Mat QTL really exists
in peach breeding germplasm
Peach Material
• ~980 individuals
(cultivars, ancestors,
founders, breeding lines,
selections, and seedlings
McIntosh
Melba
W illiams
LivelRasp
F_Spartan
Jolana
Spartan
PRI14-126
Starr
OR38T610
Delicious
KidsOrRed
NJ53
F_W illiams
PRI14-226
PRI14-644
Cox
Sonora
Gala
PRI612-1
F1_9433-2-2
RomBeauty
NJ8
W inesap
GoldenDel
NJ24
NJ67634
F1_9433-2-8
F_Ill_#2
Mflor821
P21R4A30
F2_26829-2-2
Jonathan
NY65707-19
Keepsake
Ill_#2
F_P21R4A30
M_MN1764
Prima
NJ123249
Frostbite
F_Honeycrisp
NJ27
NJ110037
NorthSpy
Melrose
Honeycrisp
Sonya
JerseyBla
PRI668-100
Julyred
Macoun
F_Gingergold
sibLiberty
NY752
PRI54-12
F_JamesGr
Liberty
W ealthy
Jerseymac
MN1691
GingerGold
NY913
F_IngMarie
Jam esGr
Tetofsky
NJ130o
F_Delfloki
NJ37848
Florina
PRI47-147
YelTransp
IngMarie
NJ117637
Longfield
NJ88
NJ31
DuchOlden
PRI610-2
Raritan
NJ12
Monroe
Rubin
F_PattenGr
Mantet
Edgewood
W orcPearm
RallsJan
Mavis
BenDavis
Elstar
Vanda
PRI1661-1
PRI855-102
Oriole
Sharon
NY88
Nicola
StateFair
Chinook
W SU2
Fireside
PattenGr
Gravenstein
F_Goodland
Close
M_MolliesDel
PRI643-11
NJ14
PRI1661-2
NY241
PRI1018-101
PacQueen
Goodland
PacRose
AurGoldGa
NJ440249
Jongrimes
W agener
NJ19237
Zestar
BC-8S-27-2
Crandall
M2439
Coop-17
BC-8S-31-56
Redfree
NJ35437
BC-SPA493
FrancRus
LadyW ill
CrownPR
PCFW 2-134
Lambourne
P7R25A27
NJ136055
BlushiGol
Clivia
F_Undine
Splendour
Indo
NJ15
Suncrisp
PRI669-205
Braeburn
PRI2482-100
Grifer
NJ303955
Malinda
Ambrosia
Glockenapfel
Zari
Cameo
MolliesDel
DrOldenbu
Fuji
Bellida
PRI1235-100
F_Helios
Enterprise
NJ35934
XIIA277
Civni
• Genotyped genome-wide
with SNP markers
F_EdGoulGol
F_NJ15
F_Sandow
KAZ95-17-14
Ecolette
Cortland
A28/39
Coop-15
NJ109
Lundbytrop
Milwa
F_MolliesDel
KAZ95-18-07
A849-5
PRI1469-100
BeautBath
Delcorf
Kanzi
VKrakers
KAZ96-05-04
Idared
Nicoter
Rubinola
Goldrush
NZ_RGxBB
Ariane
Pilot
BelHerm
Maigold
Priscilla
LaFlam
PRI2059-101
Akane
Rubinstep
Pinova
F_Brina
Nevson
Sundowner
Scarlet
CrippsPink
Senshu
Sansa
Rucla
Coop-10
NJ381049
Delblush
StarkEarl
Scifresh
Undine
PitmPine
Linda
X4598
Delfloki
Scilate
Orin
Topaz
MN1764
Shizuka
W SU24
X3174
Toko
AnanasRei
MN1702
W SU37
Camuzat
F_MN1764
AutGold
BaumanRei
BernRos
GMAL4591
Haralson
W SU17
Monark
Telam on
GMAL4593
W SU36
M_Sunrise
Boskoop
Delorina
Honeygold
GMAL4595
BrixPlatt
Calamari
Calvilla
PCF-3-120
Hatsuaki
Sunrise
CIVG198
Jonagold
CrimsSnow
M_NY632
Croncels
Gloster
W SU38
Jonafree
Pop_BBxPR
Arlet
Dalitron
Ped-PinxCam
NY632
DallaRosa
PRI69-52
ShinGold
4-27-0019
• Phenotyped in 2010-12 for
fruit quality and other
high-impact traits
Pop_GaxC15
EarlyGold
Alkmene
Fiesta
W SU34
Edelb
5-87-0019
Helios
Fiamma
52-05-26
Apollo
5-90-0019
Empire
GelEdel
Gewurz
Zonga
Pop_HCxCP
Akagi
Ped-HCxPit(692)
Hampshire
EdGoulGol
HarbRei
PRI1956-6
Limoncini
Ped-SonxNY241
25-120-9928
Freedom
6-73-0019
Piros
Ped_HCx1764
MN1914
Santana
Fortune
Sandow
MPop_HCx1702
4A-100-0013
Magre
SchonNord
Shinsekai
MN1628
MPop_HCxMon
Ped-HCxZest
4A-38-0013
GranSmith
Napoleone
Silken
Delgollune
GoldenOr
Dolgo
Summerfree
Ped-GoldrxNY913
Ontario
PermainDor
RedFiled
Angold
RenCanada
Ariwa
Merlijn
Pristine
Pop_AurxHC
NY75414-1
Sabina
Tunda
RenChamp
CrimsCrisp
Discovery
W SU46
Robusta5
W SU35
Belgica
W SU22
RosBian
Rafzubin
B_TxBB
4-159-9926
RosdiCal
GoldPink
RosDop
Nicogreen
Pop_ArlxCP
Brina
Ped_HCxJonf
W SU30
RotStett
SanLugano
Pop_GDxSc
Sila
Creston
Stayman
Delearly
N_PxF
Delcoros
E_FxGD
Snowsweet
NJ90
E_FxGlo
TavBian
Ligol
Kerr
TirSpitz
Dalinette
W eisW int
Murray
Saturn
Galmac
Crop Reference Sets
•
478 individuals (cultivars, ancestors, founders, breeding lines, selections,
and seedlings)
Peach related: P. davidiana, P. mira
Almond related: P. argentea, P. scoparia
33
72 9%
5%
20
4%
88
18%
27 5%
352 82%
362 75%
Peach
Almond
Seedlings
Peach related
Almond related
Advanced selections/germplasm
Cultivars
G4Mat – Maturity Date
TX
56% PVE
(phenotypic
variance explained)
SC
64% PVE
AR
77% PVE
CA
73% PVE
QTL Allele Validation
- detecting and valuing G4Mat alleles
in peach breeding germplasm
G4Mat – Maturity Date
APR
MAY
JUN
JUL
AUG
SEP
• 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...
G4Mat – Maturity Date
40 days!
AR Pop1
x

182
200 207
222
±6
±6
±7
±8
G4Mat – Maturity Date
SC Pop0823 
TX Pop3 
CA Pop8-3 
164
192 194
210
±0
±5 ±4
±5
140
150 152
191
±2
±8 ±9
±7
192 211
212
233
±11
±7
±5
±5
G4Mat – Maturity Date
TX
All Locations
SC
VE
E
M
L
AR
VL1
VL2
XL
alm
CA
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
APR
- G4Mat – maturity date
- G4Mat – SSC
- G3Bl – blush
- G1Xap & G6Xap - bacterial spot resistance
MAY
JUN
JUL
AUG
SEP
Loci of interest on Prunus genome
G1
G2
Sugars
Mi
G3
Flwg date
G4
G5
Ripe date
G6
D
Xap
Acidity
Ripe date
Sugars
Sugars
Skin blush
D
Xap
Y
Skin blush
sharka Bruising
Mealiness
Pcp
Fc
Acidity
Xap
Flwg date
Ripe date
Sugars
Lb
Xap
Sc
Gr
Sk
G
Sf
E
Sugars
Acidity
Acidity
Br
Dl
F-M
Mealiness
Bleeding
Peach, Nectarine
Flwg date
Flwg date
S
Sugars
B
Xap
Ripe date
Sugars
Evg
G8
Nl Fruit size
Acidity
Ripe
Dw date Ma
Sugars
Ps Skin blush
Browning
Ag
Pi
Flwg date
Cs
Bruising
Ripe date
Mealiness
G7
Bruising
Almond
Si Apricot
G4Mat – SSC
oBrix
13.8
14.4
AR Pop1
13.9
16.4
11.9
10.6
22%
PVE
TX all pops
11.3
14.0
15%
PVE
AR=38%, CA=21%, SC=28%
APR
MAY
JUN
JUL
AUG
SEP
G4Mat
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
Red color in apple, cherry and peach
Apple
L9
Cherry
G3
Peach
G3
Cs locus
MYB1/10
Fruit skin &
flesh color
MYB1/10
Fruit skin &
flesh color
(red color around stone)
& QTL for flesh
bleeding
MYB1/10
Fruit skin color
Allele distribution for G3Bl
250
RosBREED CRS
Frequency
200
blbl
27%
150
Blbl
19%
100
blbl
50
Blbl
BlBl
0
SC
AR
CA
Breeding Program
TX
BlBl
54%
CAPS markers for G3Bl
A
BlBl
B
Blbl
blbl
Fruit texture type
Peach fruit
texture type
Tables of functional genotypes
(www.rosbreed.org/
breeding/jewel-use)
Example here is for
peach fruit
texture type
Springold, Lovell, LateCrawford
e
f
O’Henry, Blazeprince, Flordaprince,
SU
c
RE
R
JH Hale, Mayfire, RioOsoGem
Resistance
Moderate
m
b/d
al
Contender, Elberta, Early Crawford,
Georgia Belle, Loring, Redhaven,
Tropic Beauty, Winblo
Susceptibility
?
a
M
UFGold, Candor, Bailey, Arrington
M
alm
M
alm
Almond
Chinese cling
Yang et al. 2012 TGG
?
R
R
SU
RE
Clayton, Westbrook, WhiteCounty,
WhiteRiver,
SU
RE
• G1XapF & G6XapF Bacterial spot resistance
Allele distribution for G1XapF
400
CRS
350
1%
300
6%
3%
13%
SU|SU
SU|RE
14%
250
SU|R
SU|M
200
24%
3%
SU|?
RE|RE
150
RE|R
RE|M
100
24%
RE|alm
12%
50
0
AR
CA
SC
TX
SU|SU
SU|RE
SU|R
SU|M
SU|?
RE|RE
RE|R
RE|M
RE|alm
M|RE
M|R
M|M
M|alm
R|R
M|RE
Allele distribution for G6XapF
400
350
CRS
3% 1%
300
7%
250
15%
200
1%
150
44%
5%
100
24%
50
0
AR
CA
SC
TX
SU|SU
SU|RE
SU|R
SU|M
SU|?
RE|RE
RE|R
RE|M
RE|alm
M|RE
M|R
M|M
M|alm
R|R
SU|SU
SU|RE
SU|R
SU|M
SU|?
RE|RE
RE|R
RE|M
RE|alm
M|RE
M|R
M|M
M|alm
Acknowledgements
This project is supported by the Specialty
Crop Research Initiative of USDA’s
National Institute of Food and Agriculture
MSU
Amy Iezzoni (PD)
Jim Hancock
Dechun Wang
Cholani Weebadde
Univ. of Arkansas
John Clark
WSU
Cameron Peace
Dorrie Main
Kate Evans
Univ. of Minnesota
Karina Gallardo
Jim Luby
Vicki McCracken
Chengyan Yue
Nnadozie Oraguzie
Former WSU
Oregon State Univ.
Raymond Jussaume
Alexandra Stone
Mykel Taylor
Cornell
Susan Brown
Kenong Xu
Clemson
Ksenija Gasic
Gregory Reighard
Texas A&M
Dave Byrne
USDA-ARS
Nahla Bassil
Gennaro Fazio Univ. of CA-Davis
Chad Finn
Tom Gradziel
Carlos Crisosto
Plant Research Intl,
Netherlands
Univ. of New Hamp.
Eric van de Weg
Tom Davis
Marco Bink