Transcript Slide 1

RosBREED’s
Breeding Germplasm Used
for Validation of Promising Trait Loci
Jim Luby
Ksenija Gasic
Chad Finn
Nnadozie Oraguzie
Susan Brown
David Byrne
John Clark
Amy Iezzoni
Tom Davis
Kate Evans
Tom Gradziel
Jim Hancock
Phil Stewart
Vance Whitaker
Cameron Peace
Nahla Bassil
Dorrie Main
Cholani Kumari
Eric van de Weg
Marco Bink
Outline of Presentation
 RosBREED Demonstration Breeding
Programs
 Reference Germplasm Sets
 Genotyping
 Phenotyping
 Data Sets as Community Resources
 Marker-Locus-Trait Associations
RosBREED Demonstration
Breeding Programs
Demonstration Breeding Programs
• Represent all major growing regions and
germplasm in US for RosBREED crops
Demonstration Breeding Programs
• Breeding Trainees in each breeding
program
•
RosBREED’s
Collaborated with other RosBREED
Realto Miners!
investigators
develop genotype
and phenotype information
Photo by Wayne Ranney
RosBREED Reference
Germplasm Sets
Crop Reference Set
•
McIntosh
~480 individuals (cultivars, ancestors, founders, breeding
lines, selections, and seedlings)
Melba
LivelRasp
F_Spartan
W illiams
Jolana
Spartan
PRI14-126
Starr
OR38T610
NJ53
F_W illiams
PRI14-226
Delicious
KidsOrRed
PRI14-644
Cox
Sonora
Gala
NJ8
W inesap
GoldenDel
PRI612-1
F1_9433-2-2
RomBeauty
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
NJ110037
NJ27
NorthSpy
Melrose
•
Honeycrisp
Sonya
JerseyBla
PRI668-100
Julyred
Macoun
F_Gingergold
Relevant Germplasm for community of breeders and other
researchers
sibLiberty
NY752
PRI54-12
F_JamesGr
Liberty
W ealthy
Jerseymac
MN1691
GingerGold
NY913
F_IngMarie
Jam esGr
F_Delfloki
Tetofsky
Florina
NJ37848
NJ130o
PRI47-147
YelTransp
Longfield
IngMarie
NJ117637
NJ88
NJ31
DuchOlden
Mantet
Edgewood
W orcPearm
RallsJan
Mavis
PRI610-2
Raritan
NJ12
Monroe
F_PattenGr
Rubin
Elstar
PRI1661-1
Vanda
PRI855-102
Oriole
Sharon
NY88
Nicola
StateFair
Chinook
W SU2
Fireside
BenDavis
PattenGr
Gravenstein
F_Goodland
PRI1661-2
NY241
PRI1018-101
PacQueen
Goodland
Close
PRI643-11
PacRose
M_MolliesDel
NJ14
AurGoldGa
NJ440249
Jongrimes
W agener
NJ19237
Crandall
M2439
BC-8S-31-56
NJ35437
BC-SPA493
FrancRus
LadyW ill
CrownPR
BlushiGol
F_Undine
Splendour
Indo
NJ15
Suncrisp
PRI2482-100
NJ303955
Ambrosia
Glockenapfel
Zari
Cameo
MolliesDel
DrOldenbu
•
Fuji
Bellida
F_Helios
NJ35934
F_EdGoulGol
XIIA277
Genotyped genomewide with SNP markers
Civni
F_NJ15
F_Sandow
KAZ95-17-14
Ecolette
Cortland
Lundbytrop
A28/39
A849-5
Milwa
F_MolliesDel
KAZ95-18-07
PRI1469-100
Kanzi
BeautBath
VKrakers
BelHerm
Delcorf
KAZ96-05-04
Idared
Nicoter
NZ_RGxBB
Pilot
Maigold
LaFlam
PRI2059-101
Akane
F_Brina
Pinova
Nevson
Sundowner
Scarlet
CrippsPink
NJ381049
Senshu
Sansa
Delblush
StarkEarl
Scifresh
Undine
PitmPine
Linda
X4598
Scilate
Orin
Grifer
PRI1235-100
Enterprise
Coop-15
NJ109
Rubinola
Goldrush
Ariane
Priscilla
Rubinstep
Rucla
Coop-10
Delfloki
Topaz
MN1764
Shizuka
W SU24
X3174
Toko
AnanasRei
CROP
REFERENCE
SET
Redfree
P7R25A27
PRI669-205
Braeburn
Malinda
Coop-17
PCFW 2-134
Lambourne
NJ136055
Clivia
Zestar
BC-8S-27-2
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
Dalitron
Ped-PinxCam
NY632
DallaRosa
PRI69-52
ShinGold
n=480
4-27-0019
Pop_GaxC15
EarlyGold
Alkmene
Fiesta
W SU34
Edelb
•
5-87-0019
Helios
Fiamma
52-05-26
Empire
GelEdel
Gewurz
Zonga
HarbRei
Limoncini
Magre
EdGoulGol
5-90-0019
Pop_HCxCP
Akagi
Ped-HCxPit(692)
Hampshire
Ped-SonxNY241
25-120-9928
Phenotyped in 2010-12
for fruit quality traits and
other high-impact traits
Apollo
Freedom
W SU38
Jonafree
Pop_BBxPR
Arlet
6-73-0019
Piros
Ped_HCx1764
MN1914
PRI1956-6
Santana
Fortune
Sandow
MPop_HCx1702
4A-100-0013
SchonNord
Shinsekai
MN1628
MPop_HCxMon
GranSmith
Napoleone
Ontario
PermainDor
RedFiled
Ped-HCxZest
4A-38-0013
Silken
Delgollune
GoldenOr
Dolgo
Summerfree
Ped-GoldrxNY913
Merlijn
Angold
Pristine
Pop_AurxHC
NY75414-1
Sabina
RenCanada
Ariwa
Tunda
RenChamp
CrimsCrisp
Discovery
W SU46
Robusta5
W SU35
Belgica
RosBian
Rafzubin
RosdiCal
W SU22
B_TxBB
4-159-9926
GoldPink
RosDop
Nicogreen
Pop_ArlxCP
Brina
RotStett
SanLugano
Sila
Stayman
Pop_GDxSc
Delearly
Snowsweet
NJ90
Ligol
Kerr
TirSpitz
Dalinette
Saturn
E_FxGD
E_FxGlo
TavBian
W eisW int
Murray
Ped_HCxJonf
W SU30
N_PxF
Delcoros
Creston
Galmac
Breeding Pedigree Sets
•
~100-300 extra individuals
proprietary to each
breeding program
•
Washington
State
BP Set
(n=160)
together with the Crop
Reference Set,
represent Important
Breeding Parents
Minnesota
BP Set
(n=160)
CROP
REFERENCE
SET
n=480
Cornell
BP Set
(n=160)
Any breeder’s
BREEDING
additional
PEDIGREE
germplasm
SETS
with data
Strategy for Assembling RosBREED
Reference Germplasm Sets
AE0109
AE0240
AE0215
Tetofsky
Mantet
Available
Ancestor
AE0226
AE0229
AE0230
McIntosh
AE0241
AE0308
Oriole
StateFair
MN1914
YelTransp
MN1925
MN2033
MN2041
LivelRasp
Fireside
MN1691
Zestar!Zestar
MN2044
MN2050
AE_HCxZest
AE0122
Unavailable
Ancestor
Longfield
MN1937
PattenGr
Goodland
MN1940
MN2016
DuchOlden
MN2046
AE0206
F_Goodland
F_PattenGr
Visualized with
Pedimap software
Important
Breeding
Parent:
Zestar!
AE0207
AE0219
AE0103
AE0242
Use pedigreelinked relatives
to represent
Available
Important
progeny
Breeding
Parents
Average Allele Representation Units
(AAR) for Important Breeding Parents
• Number of chances in a germplasm set for an allele at a
random locus of an IBP to be identical by descent to an
allele at that locus
• We chose 12.5 AAR units per IBP as minimum to
balance statistical power and available resources
• Equivalent to 25 F1 offspring
• 99.6% chance of ≥ six individuals carrying each allele
• Provides power of 0.8 to detect a mean difference
between allele effects > 1.8× the pooled standard
deviation
Genome Coverage (GC)
• Refinement of Average Allele Representation: some sets
of relatives unevenly represent the genome of an
Important Breeding Parent
• Example: F1 seedlings provide balanced Genome
Coverage as each is a random assortment of the IBP’s
genome
• Example: relatives through maternal lineage represent
skewed Genome Coverage as only the maternal half of
an IBP genome contributed by the mother, unless
complementary relatives are included
Allele Representation of Important Breeding
Parent Through Available Ancestors
Unavailable
Ancestor
Available
Ancestor
3 Balanced AAR Units through
self, parents, grandparents
Tetofsky
Mantet
0.125
McIntosh
0.125
YelTransp
LivelRasp
0.25
0.5
StateFair
Oriole
0.25
Fireside
0.25
0.125
0.0625
Longfield
PattenGr
0.5
Goodland
0.25
DuchOlden
Zestar
Zestar!
MN1691
F_Goodland
F_PattenGr
0.4375 Skewed AAR Units through
great- and great-great-grandparents
1.0
Include Progeny to Adequately Represent
Important Breeding Parent
12 progeny x
Goal = 12.5 AAR Units
Tetofsky
0.5
Mantet
McIntosh
YelTransp
LivelRasp
Longfield
Oriole
StateFair
Fireside
PattenGr
AE0206
MN1691
Zestar!
Zestar
Goodland
DuchOlden
F_Goodland
F_PattenGr
AE0242
25 progeny x
0.5
3.0 Units through self and balanced ancestors
0.4375 Units through skewed ancestors
18.5 Balanced AAR Units through 37 progeny
Zestar! = ~22 Ave Allele Representation Units
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
WSU2
NY02
BC8S-27-43
Clivia
Apple Crop
Reference Set
NY10
Nicola
Melrose
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
Pinova
BC-8S-27-2
Chinook
KidsOrRed
Gala
Braeburn
Splendour
Pop_AurxCP
Zestar
DuchOlden
CrippsPink
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
AE0251
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
CornellPop13
MN1915
NY543
MN1942
Suncrisp
Topaz
MN1702
Williams
NY14
Fiesta
Wijcik
F2_26829-2-2
WSU36
Hatsuaki
Jonagold
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
Regent
NY65707-19
MN1980
MN2016
MN1802
NY15
MN2036
MN1984
MN1627
Pop_EntxArl
Freedom
Monark
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
CoromandelRed
MN1839
YellNewtown
AE0118
AE0406
Pop_HCxCP
MN1760
GMAL4327
BeautBath
Cameo
AE0213
CornellPop07
Ambrosia
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Pop_HCxEnt
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
72
Important
Breeding
Parents
From
Univ of Minnesota
Wash St Univ
Cornell Univ
Peach Crop Reference Set
•
4 Breeding programs
•
Limited overlap of germplasm
between market types
JH_Hale
O'Henry
Fairhaven
Flordaprince
Halehaven
Frank
OP11
TropicBeauty
Redhaven
Pallas
Bolinha
P97-14
Candor
Clayton
P34-106
CAF4
Nemaguard
Saturn
Loring
ChineseCling
Greensboro
BY03P22388
Redskin
Everts
OP1
CAF2
Goldprince
TX2293-3
Y142-75
CAF3
Andross
A34-160
P.argentea
•
Hakuho
118 cultivars and selections
S-37OPxNemaguard
UFGold
White_County
Georgia_Belle
ArkC
Blazeprince
Rizzi
Winblo
Orange_Cling
Lola
TX-Pop2
2001,7-180
ZinDai
Springtime
Mayfire
•
BY01P6160
TXW1293-1
91,17-262
373 progeny in 23 crosses
F8,5-166
ArkB
Dr._Davis
BY00P6346-t
Jefferson
Peento
Contender
BY01P6245
TX2B136
China-Pearl
SC-POP_G
TX-Pop3
SC-Pop1
SC-POP22
Guardian
Dixon1
18,8-11
18,8-23
Lovell
•
Up to 11 generations
OP12
SC-Pop2
St_John
Nonpareil
Cumberland
Marigold
Diamante
Early_Crawford
SC-POP_Blush
Hiley
Mayflower
Springold
CA-Pop2
RioOsoGem
S-37
Admiral_Dewey
Springbrite
Okinawa
OP10
OP14
SC-POP09
Riegels
SC-Pop3
OP13
Crimsonbaby
Panamint
Slappey
Summercrest
CA-Pop1
Kakamas
AR-Pop1
OldmixonFree
Babcock
CA-Pop3
LeGrand
F10C,12-28
Sunfre
SC-POP23
TX-Pop1
Peach Crop Reference Set
NJ5107397
Panamint
TX2B136
FLAQ3033
PanaxJewel
Jewel
FLA2-13
Palomar
FLA15-85W
Candoka
JH_Hale
Sunhigh
Sunlite
Columbina
NJN21
FLA3-4N
Hermosillo
Sunfre
Kaygold
FLA4-65
FLA68-50
P42-81
Okinawa
P42-91
FV131-48
P97-14
Springbrite
Southland
Elberta
Early_Crawford
FLA5-5
TX2293-3
FLA8B27
Goldprince
ChineseCling
TXW 1293-1
OP43
OP36
FLA35-30
VP
Fairhaven
FLA10-48
EarlyCrawford
NJ53939
FLA2-7
OP19
P60-38
K61-48
Halehaven
TropicBeauty
Springtime
Sunrise
Southhaven
FLA16-61
Robin
NJ40CS
Carman
NJN55
VP
VP
Golden_Globe
Arp_Beauty
561483
NJ271
KimxJuly_Elberta
2000,2-18
Fireglow
Mayflower
BY01P6160
A34-160
StrawberryxPeento
FLA5-58
D2-46-143--
K519-47
104325
Cumberland
Crimson_Lady
602903
RR38-4-662001
OP10
Sunred
LeGrand
Maravilha
CA-Pop-9-33-341
113115
FLA28-48
FV317-97
Marigold
Admiral_Dewey
OP35
Goldfinch
OP13
Meredith
Mayfire
O'Henry
VP
Kim
JHHxQuetta
Lola
Dix,8
Red_Diamond
Valiant
2000,A-235
Merrill.Bon
Nectared7
NJ230
JHHxLippiatt
TardyxJordan
Quetta
Lippiatt
555036
P51-138
CA-Pop-6-1-3
FLA9-20C
2000,3-157
RR105-10--
2000,8-149
Hakuho
Loring
OP38
JHHxLevi
Babygold7
554367
OP24
125936
OP23
Jerseyland
NJ66325
5109028
E22-59
Georgia_Belle
TuscanxPaloro
Pallas
Crimsonbaby
Jungerman
Dix,6-6
NJN14
Stock3-17
5110301
562025
C1-25-177--
76925
Dix,5A-1
OP21
K173-9
Prarie_Dawn
(TxP)
13232xCherryred
2000,8-150
F8,5-156
2000,8-153
F8,5-161
2000,8-154
F8,5-162
2000,8-157
F8,5-164
2000,8-158
RR51-32--
F8,72-33
NJ196
CA-Pop-7-11-23
2000,16-93
5110007
90,10-91
58127
OP26
Loadel
RR71-322--
Da30-13
NJ257
OP12
Y150-13
CA-Pop-7-10-235
F8,5-179
F8,5-182
FLA92-2C
OP22
P30-122
CA-Pop-7-26-80
2000,A-241
562158
OP11
CA-Pop-6-1-33
2000,8-164
F8,5-165
F8,5-172
582990
C1-19-122--
OP2
OP28
F8,5-147
F8,5-171
5102896
DukeofGA
P107-78
2000,8-138
Early_Hale
Levi
F85-147
CA-Pop-7-25-178
FV9-46
554039
Armqueen
Nectared4
Hiley
P57-56
UFGold
F8,5-166
Frank
Dix,22A-5
OP4
OP44
CrimsonLady
NJF8
Sungrand
Saturn
Flordaprince
Luken'shoneyxJElberta
Peento
SprGoldxSunfre
FV15-48
R1T6
July_Elberta
Strawberry
D33-1
NJ291
P34-106
PalxSprtime
K6E121
St_John
OP29
Springold
SunGrand
FLA3-2
dummy2
Luken's_Honey
P87-147
P37-79
Springcrest
Armking
Slappey
P87-79
FV3-257
FV89-14
Babcock
Earligold
Y142-75
P83-48
G69-83N
FLA3-56
FLAR9T10
2001,18-215
2000,16-125
CA-Pop-8-35-81
5106543
OP32
Cherryred
OP41
Paloro
Lemon_Free
Dixon1
PI35201
Dixon2
Red_Grand
Summercrest
A130P
7-5
2000,16-110
Raritan_Rose
VP
90,10-92
Contender
P83-62
Hesse
89,10-44
OP48
FLAK5W 35
Dix,58-6
OP46
94727
Fortuna
89,10-55
KimxLeGrand
Early_Sun_Grand
89,10-60
PI101681
Dix,16-3
89,10-61
NonpareilBF
W olvamade
FLNCseedling
91,18-6
W algant
DukeofYork
VP
W oltemade
18,6-33
Goodwin
TachibanaW asa
5105965
VP
Dixon
2000,12-110
NC7366
2000,12-56
Pekin
NC64
VP
Transvaal-Cling
RR122-15
Ark_145N
Redskin
2000,8-37
98,4-177
F10C,20-51
S-37OPxNemaguard
P79-56
CA-Pop-8-17-71
Vilmos
88,2-77
E22-59N
2000,16-202
BY81P2840
Kalhaven
OrangeClingSdlg
Orange_Cling
CA-Pop-7-2-167
2000,16-199
98,9-7
96,9-292
OP25
Lovell
CA-Pop-9-34-69
Riegels
F10C,12-28
FLA84-18C
AustralianMuir
99,4-123
NCA2679
88,2-75
Hann_Almond
Mexican_Honey
CA-Pop-7-9-28
W hite_County
NJLA3
Everts
OP47
CA-Pop-7-3-47
96,1-171
91,17-195
54P455
Greensboro
Reina_Elena
China-Pearl
BY00P6346-t
Dr._Davis
F8,76-45
OP31
Ark_433N
DrDavis
6128
A270N
OP39
VP
98838
TardyNonpareil
OP45
BY01P6245
Candor
FLA8-11
Bolivian
CA-Pop-8-55-50
NCA2219
NJ156
38026
Ark_392
OP40
Splendid
BY96P3240
SC-POP22
89,10-59
Honeydew_Hale
CAF2
2000,2-15
89,10-53
OP37
PI91459
P48-57
CA-Pop-8-42-50
13232
2000,16-177
2000,8-69
Blazeprince
2000,8-71
Redhaven
GoodmansChoice
CA-Pop-8-19-90
18,9-41
96,9-171
Alameda
87,13-13
RoundTuscan
2005,10-10-90
92,10-119
87,12-31
2000,A-151
Ark_224
D25-9E
Nonpareil
Y140-77
NC7130
Jordanolo
90,9-116
2000,2-8
GoldenGlory
90,9-134
2000,2-9
Bonanza
Lilliland
G40-5E
CA-Pop-8-27-128
CA-Pop-5-4-228
93,1-75
93,3-108
97,2-19
W inblo
93,3-225
92,10-125
ArkC
CA-Pop-7-4-176
CA-Pop-9-34-301
93,3-22
Lilleland
OP7
2000,16-207
Clayton
Andross
Hakuto
Denjuro
TX-Pop3
91,17-262
90,10-120
93,5-50
Leader_sdlg
Diamante
CAF3
2000,A-219
2000,A-220
93,5-26
91,9-161
P91-23
CA-Pop-8-25-99
F8,1-121
GH2-48
93,5-24
OP17
E7-35
dummy1
89,9-82
CA-Pop-5-1-78
93,5-220
2000,8-44
92,14-73
CA-Pop-8-30-54
CA-Pop-5-5-248
Y142-194
93,3-247
2000,16-159
OP15
Fla.86-28C
Yellow_Alberge
Norman
CA-Pop-5-9-248
2000,16-209
93,5-80
97,5-270
90,1-4
OP16
Oro_A
OP30
2000,16-92
2001,7-126
CA-Pop-5-9-76
PI,292557
93,3-159
93,4-166
ArkB
93,4-185
18,8-11
VP
96,9-8
HoneydewHale
OP5
96,4-49
CA-Pop-9-1-198
CA-Pop-10-3-5
96,4-55
Ross
A419-P
96,5-11
CA-Pop-7-13-72
CA-Pop-7-11-108
CA-Pop-7-11-24
CA-Pop-6-4-234
CA-Pop-7-6-82
2000,1-234
CA-Pop-9-22-229
F8,1-42
Padre_al
2001,19-6
2000,B-219
CA-Pop-9-34-253
F8,1-96
Bolinha3
2000,3-159
CA-Pop-7-5-207
E,1-16
CA-Pop-5-17-24
CA-Pop-9-14-48
Kakamas
CA-Pop-8-15-77
CA-Pop-7-13-63
CA-Pop-7-26-67
97,9-200
89,6-103
98,8-188
CA-Pop-5-19-79
CA-Pop-7-1-1
2000,15-116
OP6
2000,15-119
D62-193
2000,15-122
OP1
2000,15-126
Halford
2000,15-127
CA-Pop-5-17-192
CA-Pop-9-5-82
91,12-4
CA-Pop-9-7-274
91,13-26
CA-Pop-5-20-139
91,13-7
CA-Pop-7-13-245
CA-Pop-9-31-182
CA-Pop-9-7-91
Ogawa
2000,15-73
CA-Pop-9-4-49
2000,15-88
CA-Pop-9-7-244
S-37OP
2001,1-185
CA-Pop-7-23-78
CA-Pop-7-19-20
CA-Pop-5-18-246
2003,1-329
CA-Pop-9-14-25
2000,3-205
Da,30-13
2001,7-180
CA-Pop-7-27-1
2001,2-84
2001,3-303
OldmixonFree
2005,11-56
CA-Pop-5-10-61
2005,12-231
CA-Pop-10-1-7
D6-15W
CA-Pop-5-18-181
CA-Pop-8-4-99
CA-Pop-9-36-29
CA-Pop-7-10-3
CA-Pop-5-8-229
2000,B-202
2002,9-8
18,9-8
Nickels
89,15-309
CA-Pop-10-1-11
CA-Pop-9-23-55
CA-Pop-7-2-209
91,12-54
2001,9-215
2000,11-58
CA-Pop-7-16-218
2004,2-142
SC-POP09
CA-Pop-10-1-3
Hansen2
2004,2-148
CA-Pop-5-17-147
VP
2000,8-64
KimxJelberta
CA-Pop-5-12-88
98,2-132
2001,9-275
OP20
2002,3-124
F8,5-55
CA-Pop-8-3-157
2004,2-150
Ross*R,1-1
PP904
CA-Pop-5-16-146
2001,9-305
CA-Pop-7-12-126
CA-Pop-5-14-124
SC-POP23
2001,9-6
CA-Pop-5-16-209
CA-Pop-9-20-301
2000,6-38
FLA4695
CA-Pop-8-28-264
2002,3-128
F8,72-22
CA-Pop-9-1-150
dummy95
OP42
SC-Pop3
SC-Pop2
2000,11-157
2002,3-236
dummy96
OP34
CA-Pop-9-20-126
CA-Pop-9-30-298
99,15-99
CA-Pop-5-1-223
dummy99
OP33
CA-Pop-10-2-6
2001,9-65
CA-Pop-7-17-1
2001,7-256
Hansen1
Merrill_Prince
SC-POP_Blush
2001,9-130
2000,11-177
92,7-25
LateCrawford
CA-Pop-5-11-227
2005,12-51
CA-Pop-7-10-198
Brights
OldmixonCling
CA-Pop-8-20-64
CA-Pop-10-1-9
CA-Pop-8-52-11
Klampt
9,20-C
CA-Pop-8-27-83
CA-Pop-7-13-254
CA-Pop-9-22-282
CA-Pop-9-17-197
dummy91
2005,12-256
CA-Pop-8-33-7
CA-Pop-8-47-55
2000,15-241
2002,9-76
Yumyeong
CA-Pop-5-12-199
CA-Pop-5-7-168
RioOsoGem
99,19-23
CA-Pop-8-38-106
CA-Pop-8-42-67
CA-Pop-7-2-73
CA-Pop-5-9-231
CA-Pop-10-2-8
2001,2-93
S-37
CA-Pop-9-34-105
2005,10-236
97,5-152
93,5-19
98,4-24
18,8-23
OP18
2005,10-223
2005,10-228
2001,2-4
P55-454
Dix22A-5
2002,6-283
CA-Pop-9-33-66
CA-Pop-5-18-11
VP
2000,3-217
Nemaguard
F8,5-104-146
CA-Pop-9-31-99
CA-Pop-8-18-11
CA-Pop-9-32-253
Klamt
F8,1-71
dummy97
CA-Pop-8-4-112
CA-Pop-7-9-218
StHelena
dummy98
CarolynG
CAF4
CA-Pop-9-30-233
CA-Pop-8-13-154
CA-Pop2
CA-Pop-9-31-301
CA-Pop-9-28-284
CA-Pop-7-19-164
96,1-149
P.argentea
persicaXdavidiana
CA-Pop-9-23-25
CA-Pop-9-9-250
BY03P22388
96,1-148
CA-Pop-8-9-165
19,1-40
TX86606
CA-Pop-8-41-92
CA-Pop-5-2-200
99,16-131
CA-Pop-6-4-51
CA-Pop-7-17-29
OP14
dummy90
CA-Pop-9-23-152
97,9-273
CA-Pop-9-20-1
CA-Pop-9-20-174
Jing
dummy89
TX-Pop2
CA-Pop-7-17-214
CA-Pop-9-12-102
CA-Pop-5-19-168
RedGold
P.mira#19
P78-49
CA-Pop-10-2-10
CA-Pop-7-13-130
F10E,1-16
CA-Pop-9-1-265
CA-Pop-7-8-68
2000,16-133
OP3
SC-Pop1
2005,23-6
Guardian
Bolinha6
Bolinha7
2005,22-166
RR_53-194
P.scoparia
P7-34
CA-Pop-5-22-204
Jefferson
2W _68W
CA-Pop-5-5-86
CA-Pop-9-5-273
CA-Pop-6-5-95
dummy93
Ark_154N
CA-Pop-9-34-227
99,12-155
2000,B-218
CA-Pop-7-18-192
VP
Bolinha
H_523
CA-Pop-8-33-208
2002,15-255
2000,1-228
2000,B-217
D,62-193
LateRoss
OP9
dummy92
H,6-55
96,7-165
VP
OP8
CA-Pop-7-7-146
CA-Pop-5-21-145
93,3-189
2000,1-222
Carson
OP27
ZinDai
dummy94
CA-Pop-8-61-26
93,3-175
CA-Pop-8-5-100
2000,1-215
Leader
PI134401
F85-166
CA-Pop1
Rizzi
94,4-223
CA-Pop-7-3-204
R1-1
VP
2002,1-79
2000,10-223
96,4-51
R3-53
Tuscan
Fla.79-20C
CA-Pop-7-3-157
CA-Pop-10-1-5
Erly-Red-Fre
SC-POP_G
2002,1-50
CA-Pop-5-9-33
CA-Pop3
CA-Pop-9-24-286
AR-Pop1
99,15-145
2002,13-152
TX-Pop1
Strawberry Crop Reference Set
• 26 generations
• High pedigree connectedness due to history of
strawberry breeding
• Multiple distinct germplasm groups
- CA, PNW, Eastern US, Europe, Wild
• 209 cultivars and selections
• 78 wild strawberries
- F. virginiana, F. chiloensis or F. virginiana x chiloensis
• 618 seedlings in 44 crosses
Strawberry Crop Reference Set
Hudson_Bay
dummy13
White_Carolina
OSC_346
OSC_1765
Sparkle
Northwest
Brightmore
Juspa
Keens_Seedling
Puget_Beauty
dummy15
Totem
Korona
Methven_Scarlet
Nanaimo
ORUS_850-4
OSC_3746
dummy14
OSC_2732
Charles_Downing
Hovey
dummy10
Tamella
Wilson
Independence
ORUS_750-1
OSC_2414
Narcissa
Keens_Imperial
OSC_2975
ORUS_850-48
Gorella
dummy7
Neunan
dummy17
Linn
F.chiloensis(Chile)
Induka
OSC_3845
OSC_2931
F.virg'Native_Iowa'
ORUS_1076-124
Puget_Summer
OSC_2012
F.chiloensis(Ecuador)
OSC_456
dummy6
OSC_2136
NJ_1051
Downer's_Prolific
dummy5
Cal_52.16-13
Crescent
ORUS_2781-1
Molalla
OSC_2242
F.chiloensis(PatPoint)
Ross_Phoenix
ORUS_746-4
OSC_3727
Puget_Reliance
Cal_52.16-15
Royal_Sovereign
dummy11
US_3763
OSC_1509
OSC_4727
NC__1768
F.chiloensis(Peru)
WA_87010-7
Siletz
King_of_the_Earlies
N.J.Scarlet(F.virg)
F.chiloensis
F.chiloensis(Rockaway#3)
Redgauntlet
Belmont
Vale
ORUS_1069-3
WSU_1945
OSC_1757
Benton
Haverland
ORUS_2016-1
F.chiloensis(ScottsCreek)
F.vesca
F.chiloensis10-B
Sharpless
NC_1767
Talisman
Hoffman
Goliath
Jucunda
Wiltguard
Cal_5649-1
NC_1759
US_543
OSC_1816
MDUS_3082
Green_Prolific
Cal_64.57-108
OSC_2467
Douglas
NW_90049-19
OSC_4681
NC_1768
US_634
NW_90054-36
dummy2
Excelsior
Marshall
US_3374
US_4127
FRA_1075
BC_77-2-72
Muir
Anaheim
Cal_70.3-117
Jessie
Cal_51.51-1
Howard_17
FRA_1100
ORUS_2493-2
Lassenxself
MDUS_430
Miner
Likely_Chesapeake
Cal_39.117-4
MDUS_1972
Dorsett
FRA_1092
Cal_611.4
Surecrop
Fairland
Laxton's_Noble
Ettersburg_121
Laguna
OSC_4682
FRA_1088
F_Marshal
Likely_Lake_Stevens
Cal_829.9
MDUS_3184
Ruby
OP
F.virginiana-M_Marshall
Temple
Sierra
Lassen
Redcrest
WSU_1985
Aberdeen
Selva
Irvine
ORUS_984-49
OSC_4357
Fairfax
Cal_161.1
FRA_1104
WSU_1697
Missionary
Valley_Red
OSC_2234
OSC_1490
William_Belt
Cal_103.22
Cumberland_Triumph
FRA_1108
Cal_42.8-16
dummy1
Portia
FRA_1267
Chesapeake
OSC_1491
OSC_2100
OSC_305
Cal_A.08
Cal_69.62-103
Bountiful
OSC_2315
OSC_154
Sequoia
FRA_1691
Seascape
Cal_168.1
Cheam
OSC_3628
Tillamook
dummy9
BC_41-14R-5
Parry
Noble
FRA_1692
TD8
Cal_168.3
OSC_821
Cal_186.1
Fairpeake
Cal_177.19
Redstar
Cal_177.21
MDUS_683
Cal_474.2
Cal_588.1
ORUS_767-4
FRA_24
Cal_65.65-601
OSC_2981
UnserFritz
NJ_selection
Konig.von.Sachsen
F_Konig.von.Sachsen
FRA_34
(SharplessxParry)F3
Oregon
Sieger
Tenn_Beauty
OSC_3551
USEB_18
Cuesta
Cal_39.96-18
OSC_4445
ORUS_1267-236
Albritton
dummy16
FRA_357
Clyde
NC_2967
Fendall
Cal_54.124-2
FRA_368
Blakemore
Scot_BK-46
US_4152
ORUS_1267-250
OSC_3577
Tufts
Tioga
Cal_58.45-11
Cal_71.98-604
ORUS_2180-1
Earlibelle
ORUS_869-13
FRA_372
Souvenir_de_Charles_Machiroux
Cal_39.82-19
Fern
OSC_3554
Bubach
Captain_Jack
ORUS_3304
Tribute
Suwannee
Seedling#4Howard
Markee
Cal_83.25-2
Cal_65.63-601
OSC_3624
Huachi(Ambato_NAH)
Cal_468.4
Jersey_Queen
Fendalcino
Cal_63.7-101
FRA_42
F_Fendall
Cal_21.9
Nich_Ohmer
Cal_71.98-605
Cal_159.1
WSU_685
OSC_7
Parker
MDUS_2611
Middlefield
ORUS_3305
NW_90005-1
FRA_48
Pinnacle
dummy8
Cal_86.6
Sunrise
NC__1053
US_3328
Columbia
F.virg.glauca.Wasatch
Cal_BH_14_(Mixed_Cross)
FRA_743
ORUS_923-316
Midland
MAR1A
Claribel
OSC_1629
WA_80053-17
Cal_53.10-2
Cal_59.41-1
WSU_1623
Rainier
MDUS_2101
ORUS_2427-1
OSC_3653
US_836
OSC_2475
FRA_796
WA_7531-22
WSU_1149
Cal_370.14
Cal_43.1-36
EarliglowxChandler
MDUS_3364
FRA_688
Shuksan
ORUS_1723-3
Cal_59.41-14
Cyclone(Old)
Cal_60.19-2
OSC_812
Stelemaster
ORUS_2161-1
Evita
MDUS_4258
Rose_Ettersburg
Cal_85.92-602
US_253_OP
Yaquina_B
Rockhill_Derivative
Cal_752.23
WSU_157
dummy4
F.virginiana
Del_Norte
BRA1A
OSC_2769
Redgem
OSC_2950
ORUS_1722-2
Cal_37.20-45
WSU_1574
Laxtons_Noble
Senga_Sengana
Seedling#1Howard
ORUS_1009-1
Cal_752.31
Cal_7.20
ORUS_3321
F1_hybrid
Olympus
F.chil.Cape.Mendicino
Streamliner
Cal_7.9a
Early_Jersey_Giant
WSU_175
Eurisko
ORUS_2427-4
Cal_46.5-1
OSC_3596
OSC_6058
Dunlap
S0_20-2
Yellow_Wonder
Firecracker
Cal_564.6
Pawtuckaway
Fred9xLH50-4
ORUS_2075-1
RH30xMR10
Oberschlesien
Cal_403.8
Van_Deman
Cal_86.5
Cal_564.7
Cal_68.24
Cal_337.2
Cal_68.25
Cal_337.3
Oso_Grande
Cal_72.361-105
Cal_720
Sarian
Montana_Missionary
MN_1181
OSC_4319
Earliglow
Cal_35.102-5
Elsanta
OSC_2853
Cal_55.32-1
US_3358
Joe
Shasta
OSC_767
Bemidji_Chief
B144
Tyee
Alpine(F.vesca)
ORUS_1735-1
Glendale
MSU_56
OSC_4863
Cal_460.11
Ark_5063
ORUS_1027-1
OSC_3044
WA_88097-47
MDUS_5132
Auchincruive_Climax
NY_113
S.65122
ORUS_1376-16
Solana
Gandy
ORUS_3324
FL_83-418
Cal_77.3-603
Cal_135.18
FL_84-1389
Delite
Cal_249.5
Cal_59.51-11
Kaiser_Samling
Clark
NY_844
OSC_3991
Fort_Laramie
OSC_4275
FL_84-3163
Camarosa
US_253
B753
FL_83-1452
Cal_179.15
Cal_222.11
Cal_179.2
Cal_222.4
K87-5
((MFruherxSSengana)xGeorgSolt)
F.virginiana(AL)
Harvester
Pajaro
MDUS_2713
B754
OSC_2066
Cardinal
Aiko
Formans_Excelsior
F.virginiana(MS)
RH30xLH50-4
Chandler
SCXMAR1A
Pocomoke
Cal_67.5
WSU_1532
Geneva
ORUS_1384-3
Honeoye
Capitola
Donner
K86-19
FL_87-418
Ark_5431
F.virginiana(SC)
Cal_Z_11
MN_2374
NY_4626
OSC_18
Cal_10.21
Pan_American
Redheart
Earlidawn
SCxFRA24
Brighton
ORUS_3325
Jewel
OSC_2122
FL_87-200
OSC_3040
OSC_2338
FRA_110
NJ_8713-8
LA_59-2012
CF1116
Kent
Klondike
F.virginiana(NC)
Early_Ozark
Cal_75.121-101
(Providence_self)
K72-9
NAHxBRA1A
Cabot
NC__1065
FRA_1435
Redglow
LA_59-138
Macherauchs_Marieva
OSC_2261
Cavendish
ORUS_1091-1
Darselect
Cal_Z_9
FRA_1455
FL_80-456
((KlonmxMidl)x(TennShipxMidl))
Massey
F.moschata
Cassandra
Southland
T._de_Leopold
FRA_1694
K79-5
(GorellaxMDUS3184)
Tenn_Shipper
MR10xRH23
OSC_1815
SCxNAH
WIUS_8008
K68-58
Glooscap
Tiogax(Redgauntx(WiltgxGorel))
Raritan
Providence
Reiko
OSC_59
Marlate
FRA_1695
MSU_9-13
Cal_145.38a
Vanguard
WSU_828
MDUS_4377
OSC_1776
NJ_821-5
Everest
OSC_2371
Princesse_Dagmar
Kurume103
MDUS_4463
NY_254
FRA_1466
FRA_1696
Joliette
MDUS_2188
ArKing
HM1xNAH
Prinz_Julius_Ernst
NJ_459
Hummi_Gento
MDUS_4380
ORUS_3277
FavourxNY844
K74-5
Holiday
FRA_1697
K79-4
ORUS_1391-1
WSU_438
(Tenn_Shipper_x_Midland)
Tangi
Pathfinder
Uberreich
FRA_1698
MR10xN8688
Bounty
WSU_450
Dixieland
Strawberry_Festival
MDUS_4386
Dana
NJ_357
MSU_49
Micmac
MSU_9-2
Sel.Salvi_N.15
FRA_1699
Cal_145.52
Mesabi
Pocahontas
US_542
Cal_144.2
Florida_90
Sitkahybrid
FRA_1700
(WiltguardxGorella)
K61-87
FVC_18-1
WSU_14
MDUS_2650
Governor_Simcoe
Annapolis
Cal_144.21
46-4J
Jerseybelle
Cal_66.96-101
BelrubixMacherauchs_Marieva
OSC_3965
Scott
FRA_1701
Ottawa485
Capron
Lulu
FVC_11-1
Hogyoku
J.23
FVC_18-18
FRA_1702
Deutsch_Evern
Macherauchs_Fruhernte
Cal_32.50
ORUS_1083-135
PocahontasXRegina
MSU_9-6
WA_94023-1
SJ85189
(Klonmore_x_Midland)
Beaver
Gariguette
Progressive
FRA_1703
Cal_32.63
Regina
ORUS_3278
Berri_Supreme
ORUS_1827-2
(MachFruherntexSengana)
F.chiloensis-M_Sitka
F.cuneifolius
MDUS_2359
FVC_11-2
FRA_338
(Redgauntx(WiltgxGorella))
MDUS_3700
Cal_66.2
F_Sitka
FRA_58
SYS_3672-179
Belrubi
Benizuru
Corvallis
NY_1221
US_4144
FVC_30-1
Red_Giant
NY_E58
Lion's_Head_3
Guardsman
WSU_2833
Dover
Guardian
Red_Rich
FVC_30-2
MS_34-12
RedgauntletxKorona
FL_69-1302
K88-4
Sumas
NYUS_119
Harunoka
Favour
Redchief
(Sitkahybridx46-4J)
Redrich
ORUS_1407-76
MS_34-4
Vibrant
Etna
MDUS_2386
ORUS_3323
OSC_4867
MSU_9-11
FVC_11-4
The_Sun
FVC_30-3
B6.117
NW_90055-35
Hood
J._Riffaud
Miyazaki
ORUS_3307
BC_91-14-31
NY_316
Valentine
Rockhill
FVC_11-3
F_ORUS_1407-76
MDUS_4616
WIUS_8002
FRA_982
F.virginiana_ovalis
F_JH_101-1
Madame_Lebreton
Aptos
Redcoat
Duluth
Sable_Beach_8
Sweet_Charlie
Midway
OSC_913
Hapil
ORUS_3279
MSU_9-15
Cal_43.2
Sitka
Lateglow
y32b
MNUS_99
Georg_Soltwedel?
D5.23
FVC_30-4
OSC_1366
FVC_11-5
MDUS_2966
FL_71-189
Ostara
G7
ORUS_2262-2
ORUS_2361-1
G8
General_Chanzy
Lupton
US_3919
ORUS_1769-1
MDUS_3816
Ettersburg_80
NJ_953
L1
MDUS_2927
MSU_9-16
FVC_30-5
Rabunda
Hansa
BC6
Macherauchs_Dauerernte
FVC_11-6
Rosa_Linda
H4
Glenheart
MSU_9-14
NJ_925
(Miyazaki_x_The_Sun)
Hummi_GentoxOstara
Palmyre
Ettersburg_20
Repita
Chilean
Ville_de_Paris
Yellow_WonderXPawtuckaway
Cal_604.4
Cal_814.6
WSU_1651
Whonnock
ORUS_986-129
Stolo
ORUS_1754-1
Cal_491.1
Klonmore
ORUS_3314
British_Queen
ORUS_2490-1
MDUS_2992
Cal_87.112-6
MDUS_3694
FVC_8-1
Crown
Veestar
Cal_134.31
Cal_88.270-1
NETHBIN
((GorellaxMDUS3184)xTioga)
MSU_9-7
ORUS_2240-1
MDUS_2321
Rotkappchen
E-30324
Florida_Belle
Cal_94.16-1
MDUS_2905
FL_82-1556P
Joe_Reiter
FVC_8-2
((Sitkahybridx46-4J)xOttawa485)
Cal_213.4
Rockhill_selfed
FVC_33-1
ORUS_1963-5
US_4419
US_2506
Cal_470.9
FRA_1557
MDUS_4587
MNUS_52
MSU_9-17
LA_2556
Cal_378.16
LA_883
US_2267
Washington
General_de_Castelnau
FVC_8-3
ORUS_2676-1
Atlas
Cal_490.9
ORUS_973-1
Gem
ORUS_3308
Cal_42.17-18
LB48
OSC_4474
St._Joseph
Cheyenne3
L'Acadie
MSU_9-12
NC_2839
Ada_Herzberg
ORUS_2159-2
Lucie_Boiselet
NC_2665
JH_101-1
Everglade
FRA_1408
FVC_8-4
FRA_1414
FVC_8-5
ORUS_3319
ORUS_3315
Pickerproof
Twentieth_Century
ORUS_3306
(MidlandxCheyenne2)
J92D12
Duc_de_Malakoff
NC_1729
FVC_10-1
Cal_648.2
OSC_4816
Shuswap
MSU_9-9
Fukuba
BCPink
Easypicker
(RockhillxCheyenne3)
ORUS_3326
British_Sovereign
Protem
MSU_9-4
(FairfaxXF.ovalis)
Cal_794.19
Cal_45.5-1
Diamante
MSU_9-1
FVC_10-2
ORUS_2742-1
Cal_37.2-11
Cheyenne2
Cal_543.14
Allstar
OSC_4916
Mara_des_Bois
Cal_800.13
Trumpeter
LB48xH4
ORUS_3320
Cal_74.3
Frel
FRA_1620
Revada
ORUS_3318
Cal_638.45
ORUS_2369-1
Burgundy
FVC_17-20
Apollo
FRENCHBIN
LA_8311
MSU_9-5
ORUS_740-7
Aromas
dummy3
Hecker
MSU_9-10
Docteur_Morere
ORUS_3322
Hawaii4
BxD
NC_3140
Cyclone
Idea
Cal_544.3
Heidi
FVC_28-1
Cal_143.32
Madame_Raymond_Poincare
MSU_9-8
Ourown
Robinson
Rapella
MDUS_3413
MDUS_2787
Liberation_d'Orleans
FRA_1580
FVC_16-1
ORUS_1947-2
ORUS_1239R-21
Marmolada(Onebor)
Pelican
Marajox
Koro103
Ozark_Beauty
Crimson_King
Beaversweet
MSU_9-3
Winona
Nyohou
Ooishi-shikinari2
Delmarvel
Evie-2
SARGENTOCTOPLOID
Beaverbelle
SARGENTDIPLOIDBIN
St._Claude
UNK
Florence
L'Authentique_Orleans
MDUS_2856
Albion
Hummi_Ferma
Lake_Stevens
ORUS_3317
Bismarck
Commander
dummy12
dummy18
E-30397
OSC_4817
ORUS_3316
Sans_Rivale
Ogallala
Evangeline
Genotyping:
SNP Detection Panels
Genome Scans
Identity Validation
Detection Panel for Single Nucleotide
Polymorphisms (SNPs)
NY59333-006
Empire
McIntosh
Delicious
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
EsopSpitz
NY10
Nicola
Melrose
WSU2
NY02
BC8S-27-43
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
Arlet
MN1628
Clivia
Pinova
KidsOrRed
Gala
Braeburn
Splendour
BC-8S-27-2
Chinook
Pop_AurxCP
Zestar
DuchOlden
CrippsPink
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
AE0251
NY06
WSU30
NY01
• Individuals for genome
sequencing to identify SNPs
distributed along genome
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
CornellPop13
MN1942
Suncrisp
Topaz
MN1702
Williams
NY14
Fiesta
MN1915
NY543
F2_26829-2-2
WSU36
Hatsuaki
Jonagold
Wijcik
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
MN1980
MN2016
MN1802
Regent
NY65707-19
MN1627
Freedom
NY15
MN2036
MN1984
Monark
Pop_EntxArl
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
• 20 to 30 individuals from Crop
Reference Set
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
CoromandelRed
MN1839
BeautBath
AE0213
YellNewtown
AE0118
AE0406
Pop_HCxCP
MN1760
GMAL4327
Cameo
CornellPop07
Ambrosia
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Pop_HCxEnt
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
• Includes diverse key founders or
intermediate ancestors
Apple SNP Panel
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
NY10
Nicola
Melrose
WSU2
NY02
BC8S-27-43
Frostbite
Clivia
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
Pinova
Chinook
KidsOrRed
Gala
Braeburn
Splendour
Founders
BC-8S-27-2
Pop_AurxCP
Zestar
DuchOlden
CrippsPink
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
AE0251
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
CornellPop13
MN1915
Wijcik
NY543
MN1942
Suncrisp
Topaz
MN1702
Williams
NY14
Fiesta
Jonagold
F2_26829-2-2
WSU36
Hatsuaki
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
Regent
NY65707-19
MN1980
MN2016
MN1802
NY15
MN2036
MN1984
MN1627
Pop_EntxArl
Freedom
Monark
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
YellNewtown
AE0118
CoromandelRed
AE0406
MN1839
Pop_HCxCP
MN1760
GMAL4327
BeautBath
Cameo
AE0213
CornellPop07
Ambrosia
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Pop_HCxEnt
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
Delicious
Golden Delicious
McIntosh
Jonathan
Cox’s Orange Pippin
Rome Beauty
Northern Spy
Dolgo
Duchess of Oldenburg
Wagener
Intermediate
Ancestors
Cripp’s Pink
Fuji
Honeycrisp
Zestar!
Goldrush
CrimsonCrisp
Coop-15
F2 2689-2-2
Frostbite
Haralson
International RosBREED SNP Consortium
Apple 8K SNP Array v1
International Peach SNP Consortium
Peach SNP Array v1
RosBREED Cherry 6K SNP Array v1
Development and evaluation of a genome-wide 6K SNP
array for diploid sweet cherry and tetraploid sour cherry
Peace, C., Bassil, N., Main, D., Ficklin, S., Rosyara, U.R., Stegmeir, T., Sebolt,
A., Gilmore, B., Lawley, C., Mockler, T.C., Bryant, D.W., and Iezzoni, A.
PLoS ONE, submitted July 2012
RosBREED SNP Consortium Markers
in RosBREED Reference Germplasm
Crop
Apple
Peach
Total
SNPs
7867
8144
Polymorphic
SNPs
5554
6444
Sweet Cherry
Tart Cherry
5696
5696
1825
2058 resolved
1743 unresolved
~ 8.6 Million Data Points for Breeder’s Toolbox
Genotype Data Used to Validate Identity
Available
Ancestor
AE0109
AE0240
AE0215
Tetofsky
AE0226
Mantet
Pedigree
Correct
McIntosh
AE0229
AE0230
Crossing
error!
AE0241
AE0308
Oriole
StateFair
MN1914
YelTransp
MN1925
MN2033
MN2041
LivelRasp
Fireside
MN1691
Zestar!
Zestar
MN2044
MN2050
Available
progeny
AE_HCxZest
AE0122
Unavailable
Ancestor
Longfield
MN1937
PattenGr
DuchOlden
Imputed
Genotype
Goodland
Parentage
Correct
MN1940
MN2016
MN2046
AE0206
F_Goodland
AE0207
F_PattenGr
Important
Parent
AE0219
AE0103
AE0242
Parentage
Correct
Phenotyping:
Standardized Phenotyping
Protocols and Data Checking
Standardized Phenotyping Protocols
• Each crop team chose critical fruit quality traits
and other important traits
• Developed standardized phenotyping protocols
to enable data pooling across locations and
institutions
• Protocols available at www.RosBREED.org
Phenotypic Data Collection and Checking
and 2011
Seasons
•Phenotypic
Phenotyping Data
on all from
fruiting2010
individuals
in reference
Over
375,000
germplasm
setsObservations
in 2010-2012 for Breeder’s Toolbox
Crop
Locations
Traits
Strawberry
5
35
Peach
4
25
Apple
3
135
Sweet Cherry
1
23
Tart Cherry
1 and outliers35
• Data
checked for errors
• Formatted for upload to Breeder’s
Toolbox
Observations
130,700
41,600
171,600
13,800
17,500
RosBREED Data Sets
As Community Resources
What’s Available as
Community Resources?
• Crop Reference Sets
- Peach, Apple, Sweet Cherry, Tart Cherry,
Strawberry
• Information for each individual
- Pedigree
- Genotype for SNPs and other markers
- Phenotype for fruit quality traits and other
critical traits
Data Sets Available as Community Resources
Breeder’s
Toolbox
Tools
to Find Jewels
in a Pile of Rocks!
www.rosaceae.org
Data Overload - Tools to Handle RosBREED Ore!
Sook Jung presents the Breeder’s Toolbox later this morning
Data Sets Available as Community Resources
• Breeders Toolbox Output to Pedimap
JH_Hale
Roeland Voorips,
O'Henry
Fairhaven
Flordaprince
Halehaven
Frank
OP11
TropicBeauty
Redhaven
Pallas
Bolinha
P97-14
Candor
Clayton
Goldprince
TX2293-3
Y142-75
CAF3
P34-106
CAF4
Nemaguard
Saturn
Loring
ChineseCling
Greensboro
BY03P22388
Redskin
Everts
OP1
CAF2
Andross
A34-160
P.argentea
Hakuho
www.plantbreeding.wur.nl/UK/software_pedimap.html
S-37OPxNemaguard
UFGold
White_County
Georgia_Belle
ArkC
Blazeprince
Rizzi
Winblo
Orange_Cling
Lola
TX-Pop2
2001,7-180
ZinDai
Springtime
Mayfire
BY01P6160
TXW1293-1
91,17-262
F8,5-166
ArkB
Dr._Davis
BY00P6346-t
• Free software to visualize
Peento
Contender
BY01P6245
TX2B136
China-Pearl
SC-POP_G
TX-Pop3
SC-Pop1
SC-POP22
Jefferson
Guardian
Dixon1
18,8-11
18,8-23
Lovell
Nonpareil
OP12
SC-Pop2
St_John
Cumberland
Marigold
Diamante
Early_Crawford
SC-POP_Blush
Hiley
Mayflower
Springold
CA-Pop2
RioOsoGem
S-37
- Pedigree
- Phenotypic data
- Genotypic data
Admiral_Dewey
Springbrite
Okinawa
OP10
OP14
SC-POP09
Riegels
SC-Pop3
OP13
Crimsonbaby
Panamint
Slappey
Summercrest
CA-Pop1
Kakamas
AR-Pop1
OldmixonFree
Babcock
CA-Pop3
LeGrand
F10C,12-28
Sunfre
SC-POP23
TX-Pop1
Pedimap for Pedigree Visualization of
Phenotypic and Genotypic Data
Honeycrisp x Splendour
Genotype
SNPs in 2
regions of
apple linkage
group 16
Offspring Individuals
Courtesy of Sujeet Verma.
Visit Poster #375 – “Fresh Sensation” in Apple
Phenotype
Sensory Acidity
Marker-Locus-Trait
Associations
QTL Discovery
and Validation
• Pedigree-Based Analysis of phenotype and genotype data
to discover and validate QTL using FlexQTL software
LG1
WSU 2011 Fructose at Harvest in Apple
Bayes Factor (nQTL model): 7.3 (1/0); 3.7(2/1)
Courtesy of Yingzhu Guan
Visit Poster #376 – Sugars and Sweetness in Apple
Marker-Locus-Trait Associations
Oral Presentations Featuring RosBREED
Phenotype and Genotype Resources
• Fruit Breeding 1 -11:00am Wednesday
- Mathey et al. – Red Stele Root Rot in Strawberry
• Fruit Breeding 2 - 2:45pm Friday
- Bellamkanda et al.– Fruit Firmness in Cherry
- Zhao et al. – Fruit Retention Force in Cherry
- Frett et al.– Skin Color in peach
Jewels in the Making!
Posters Featuring RosBREED
Phenotype and Genotype Resources
• Fruit Breeding 1 -11:15pm Wednesday
- Clark et al. #373 – Apple Scab Resistance
- Schmitz et al. #374 – Apple Fruit Texture Traits
- Verma et al. #375 – “Fresh Sensation” in Apple
- Guan et al. #376 – Sugars and Sweetness in Apple
• Genetics & Germplasm 3 – 12:15pm Thursday
- Clark et al. #425 – Apple Fruit Size, Appearance,
Disorders
Marker-Locus-Trait Associations
Upcoming Presentations This Morning
• Functional Alleles: Jewels Available in
Apple, Peach, and Cherry
– Cameron Peace and Ksenija Gasic
Acknowledgements
This project is supported by the Specialty
Crop Research Initiative of USDA’s
National Institute of Food and Agriculture
Extra slides
Demonstration Breeding Programs
Clemson U
WSU
Texas A&M
UC Davis
U Minn
U Arkansas
Rosaceae
Cornell U
WSU
MSU
Driscolls
USDA-ARS
Corvallis
UNH U Florida
MSU
Marker-Locus-Trait Associations
“Jewels in the Genome”
- discovering, polishing, applying
QTL discovery
MAB Pipelining
Breeding
(looks promising...)
(polishing...)
(assembling into
masterpieces)
Apple Crop Reference Set
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
Goal:
Allele Representation
for Important
Breeding Parents in
Multiple Programs
NY10
Nicola
Melrose
WSU2
NY02
BC8S-27-43
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
Clivia
Pinova
KidsOrRed
Gala
BC-8S-27-2
Chinook
Pop_AurxCP
Zestar
DuchOlden
Braeburn
CrippsPink
Splendour
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
AE0251
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
CornellPop13
MN1915
Wijcik
NY543
MN1942
Suncrisp
Topaz
MN1702
Williams
NY14
Fiesta
Jonagold
F2_26829-2-2
WSU36
Hatsuaki
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
MN1980
MN2016
MN1802
Regent
NY65707-19
MN1627
Freedom
NY15
MN2036
MN1984
Monark
Pop_EntxArl
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
YellNewtown
AE0118
CoromandelRed
MN1839
BeautBath
AE0213
AE0406
Pop_HCxCP
MN1760
GMAL4327
Cameo
CornellPop07
Ambrosia
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Pop_HCxEnt
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
Apple Crop
Reference Set
NY10
Nicola
Melrose
WSU2
Clivia
Pinova
KidsOrRed
Gala
BC-8S-27-2
Chinook
Pop_AurxCP
Zestar
DuchOlden
Braeburn
CrippsPink
Splendour
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
AE0251
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
NY14
Fiesta
CornellPop13
MN1915
NY543
F2_26829-2-2
WSU36
Hatsuaki
Jonagold
Wijcik
MN1942
Suncrisp
Topaz
MN1702
Williams
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
Regent
NY65707-19
MN1980
MN2016
MN1802
NY15
MN2036
MN1984
MN1627
Pop_EntxArl
Freedom
Monark
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
CoromandelRed
MN1839
YellNewtown
AE0118
AE0406
Pop_HCxCP
MN1760
GMAL4327
BeautBath
Cameo
AE0213
CornellPop07
Ambrosia
Pop_HCxEnt
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
U of MN
NY02
BC8S-27-43
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
35
Important
Breeding
Parents
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
Apple Crop
Reference Set
NY10
Nicola
Melrose
WSU2
Clivia
Pinova
KidsOrRed
Gala
BC-8S-27-2
Chinook
Pop_AurxCP
Zestar
DuchOlden
Braeburn
CrippsPink
Splendour
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
AE0251
NY04
JamesGr
Sunrise
Melba
Coop-17
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
NY14
Fiesta
Jonagold
CornellPop13
MN1915
NY543
F2_26829-2-2
WSU36
Hatsuaki
Wijcik
MN1942
Suncrisp
Topaz
MN1702
Williams
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
MN1980
MN2016
MN1802
Regent
NY65707-19
NY15
MN2036
MN1984
MN1627
Pop_EntxArl
Freedom
Monark
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
YellNewtown
AE0118
CoromandelRed
AE0406
MN1839
Pop_HCxCP
MN1760
GMAL4327
BeautBath
Cameo
AE0213
CornellPop07
Ambrosia
Pop_HCxEnt
MN1914
MN1899
MN1925
NY12
MN1964
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Wash. State
NY02
BC8S-27-43
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
38
Important
Breeding
Parents
NY59333-006
Empire
McIntosh
Blackjon
669NJ5
NY70712-53
NY55158-002
RussianSeedling
NY88
Delicious
AutumnCrisp
Jonathan
Coop-18
Crandall
AurGoldGa
NorthSpy
Fuji
MN1708
RomBeauty
P14-126
Honeycrisp
PacQueen
Arlet
MN1628
EsopSpitz
WSU2
NY02
BC8S-27-43
Clivia
Apple Crop
Reference Set
NY10
Nicola
Melrose
Frostbite
GoldenDel
NY03
Monroe
Keepsake
Sweet16
NY752
PacRose
Pinova
BC-8S-27-2
Chinook
KidsOrRed
Gala
Braeburn
Splendour
Zestar
DuchOlden
CrippsPink
Enterprise
Pop_AurxEnt
Sansa
GranSmith
Pop_AurxArl
Cox
Sundowner
Rubin
Idared
LadyWill
NY08
Vanda
PRI1661-1
PRI1661-2
StateFair
Wagener
MN1691
Mantet
Akane
Pop_AurxHC
NY632
YelTransp
Empress
Burgundy
Malinda
WSU49
WSU50
Silken
Oriole
Wealthy
WSU52
Lambourne
Fireside
Jonamac
Sonya
Scifresh
WSU57
BenDavis
WSU24
Goodland
NY241
VistaBella
Montgomery
WSU37
WorcPearm
Honeygold
BlushiGol
Sunrise
Coop-17
NY04
NY05
AE0206
NY07
EarlyCortland
CornellPop08
Haralson
Linda
AE0251
JamesGr
Melba
NY06
WSU30
NY01
NY11
Cortland
WSU17
WSU46
NY92607-16
NY247
Lodi
Delorgue
Delblush
NY66305-289
CornellPop13
MN1915
NY543
MN1942
Suncrisp
Topaz
MN1702
Williams
NY14
Fiesta
Wijcik
F2_26829-2-2
WSU36
Hatsuaki
Jonagold
GingerGold
MN1955
MN2034
WSU35
Beacon
MN1789
Raritan
MN1965
MN2062
Macoun
Liberty
WSU48
MN1971
Hudson
Spartan
MN1764
Regent
NY65707-19
MN1980
MN2016
MN1802
NY15
MN2036
MN1984
MN1627
Pop_EntxArl
Freedom
Monark
MN2056
RedBaron
Jonafree
PitmPine
MN2057
Pop_HCxAr
MN2063
Goldrush
Snowsweet
WSU34
Prima
MN2000
Mflor821
Britemac
WSU65
GMAL4332
NY13
MN1706
MN1937
NJ90
CornellPop09
IngMarie
MN1988
Winesap
WintBanana
Dolgo
Fantazja
MN1940
Coop-15
MN2031
GMAL4329
WSU38
MN2042
AE_HCxJonf
NY76406-007
Fortune
CoromandelRed
MN1839
YellNewtown
AE0118
AE0406
Pop_HCxCP
MN1760
GMAL4327
BeautBath
Cameo
AE0213
CornellPop07
Ambrosia
MN1914
MN1899
MN1925
NY12
MN2033
Elstar
GMAL4328
MN1837
PRI14-126
MN2041
Kerr
CrimsCrisp
Pop_HCxEnt
MN1964
MN1888
Sundance
MN1836
MN2044
Sawa
Tsugaru
NY913
MN2050
Dayton
NJ53
NY09
WSU7
MN2046
PixieCrunch
Redfree
Discovery
WSU5
AE0210
Cornell
Pop_AurxCP
18
Important
Breeding
Parents
Abstract: Rosbreed's Breeding Germplasm
Used for Validation of Promising Trait Loci
•
The use of a comprehensive germplasm set representing materials that breeders use is
critical for efficiently enabling systematic and statistically robust validation and utility
assessment of jewels in the genome (high value marker–locus–trait (M-L-T) associations).
Therefore, at the onset of the RosBREED project, 12 demonstration breeding programs
compiled relevant germplasm to constitute a “Crop Reference Sets” (CR Sets) for
validation and utility assessment of M-L-T associations in each crop (apple, peach,
strawberry, sweet cherry, and tart cherry). All data for the CR Sets will be archived on the
Genome Database for Rosaceae and publicly available. In establishing each CR Set,
breeding programs identified important breeding parents and traced their pedigrees. To
efficiently represent the genomes of these key individuals, available progeny, intermediate
ancestors, and founders were included. In addition to the CR Sets, additional Breeding
Pedigree Sets (BP Sets) specific to each breeding program were established so that,
together with the CR Sets, there was full representation of further important breeding
parents. The CR and BP Sets have been phenotyped since 2010 for fruit quality traits and
other critical traits using standardized phenotyping protocols developed by the breeding
teams. SNP genome scans provided high-resolution genetic data that is being used to
validate known M-L-T associations and identify new ones. Genetic tests for several
reported M-L-T associations in each crop were fast-tracked through the validation and
utility assessment process to demonstrate the use of reference germplasm sets. The
visualization of pedigree, phenotypic, and genotypic data for these germplasm sets is
enabled for any fruit and nut crop with the publicly available software, Pedimap.
Amy’s suggested outline
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Talk #2. Jim Luby: RosBREED’s breeding germplasm used for validation of promising trait loci
Main deliverables to be communicated: CRS with pedigree data, phenotypic data, and genotypic data and how to access this data. Pedimap
RosBREED Demonstration Breeding Programs: who and where
Inclusive to represent all the major growing regions (& germplasm) for these crops in the US
Reference Germplasm Sets
Allelic and genomic representation, concept of CRS ( and supplemental BPS)
Cameron’s germplasm choice manuscript draft has a lot of nice background discussion
Point to make is that this germplasm is relevant for a wide community of researchers as by design it was put together to maximize information on the
entire range of functional alleles present in US apple, peach, cherry and strawberry germplasm
Mention that the genetic data generated was used to validate pedigrees.
GENOTYPING
SNP Detection Panels
How Panels chosen by breeding teams
Genome Scans
You can describe briefly with available slides in the publication portal dropbox
PHENOTYPING
Standardized Phenotyping Protocols
Discuss collecting and checking pheno data as activity of demo breeding programs but leave details of format and use in BIMS to Sook (yes)
Include some great examples of the detail of the phenotypic data obtained by mentioning some of the crop posters.
3 data sets: Pedigree, phenotypic, genotypic – spend some time showing examples of pedimap (Cho has some prior slides) as this is useful for
everyone
M-L-T associations
Mention the use of FlexQTL as it can handle this germplasm but no need to provide details
Identify that the pipeline aspects of validation and utility assessment were accomplished ( this will explain why we know the functional alleles and
provide a “hand off” to Cameron and Ksenija. )
Crop Reference Sets
•
Relevant Germplasm for community of breeders and
other researchers
•
~480 individuals (cultivars, ancestors, founders,
breeding lines, selections, and seedlings)
•
Genotyped genome-wide with SNP markers
•
Phenotyped in 2010-12 for fruit quality traits and other
high-impact traits
•
Enable efficient validation and utility assessment of M-LT associations
Breeding Pedigree Sets
•
Breeding Pedigree Sets
•
Resource for proprietary benefit of breeding program
benefit only
•
~100-300 extra individuals for each breeding program that,
together with the Crop Reference Sets, allow full
representation of founders of interest to that program
•
Information may remain with each breeding program; datasharing improves power
Reference Germplasm Sets
• Approach:
- Identify Important Breeding Parents (IBP) in breeding
programs
- Trace pedigrees to founders and identify available
founders and intermediate ancestors
- Identify progeny available in breeding programs
- Use PediMap™ to visualize pedigree relationships
- Identify a set of relatives for each IBP that provides
sufficient Average Allele Representation of IBP
- Use genotype information to validate pedigree and
identity of relatives