Download - MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main
MSU
Amy Iezzoni (PD)Jim Hancock
Dechun WangCholani Weebadde
WSUCameron Peace
Dorrie MainKate Evans
Karina Gallardo Raymond Jussaume
Vicki McCracken Nnadozie Oraguzie
Mykel 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
Outline of Presentation
RosBREED
The RosBREED Project
Resource Development
MAB Enablement
International Context
The RosBREED
Project
RosBREED
• 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
• Centered on breeders & breeding programsThe RosBREED Project
Project Director,Amy Iezzoni
-breeder (tart cherry)-geneticist-genomicist-leader
We will create a dynamic, sustained program in research, infrastructure establishment, training, and outreach for developing and applying marker-assisted breeding based on improved knowledge of industry value and consumer preferences to accelerate and increase the efficiency of rosaceous cultivar release and successful cultivar adoption.
RosBREED
The RosBREED Project
Mission
RosBREED
1) Enhance new cultivar adoption, enlarge market potential, increase consumption= socio-economics knowledge of trait values
2) Establish sustainable infrastructure for MAB in Rosaceae= genome scanning capability, new QTLs (“jewels”)
3) Integrate socio-econ and genomics resources into breeding= pedigree-based breeding information management system
4) Conduct MAB in demo breeding programs, fruit quality focus= MAB implementation
5) Enhance sustainability of cultivar development= tech transfer to more breeders & engage other stakeholders
RosBREED’s Objectives
QTL discovery(looks promising...)
MAB Pipelining(polishing...)
Breeding(assembling into masterpieces)
RosBREED
“Jewels in the Genome”- discovering, polishing, applying
Project Assistant
Extension Team Leader: Cholani Weebadde
Genomics Team Leader: Dorrie Main
Genotyping Team Leader: Nahla Bassil
BIMS Team Leader: Gennaro Fazio
Socio- Economics Team
Leader: Chengyan Yue
MAB Pipeline Team Leader
Cameron Peace
Pedigree- Based Analysis Team Leader: Eric van de Weg
Breeding Team LeaderJim Luby
Apple· Jim Luby· Susan Brown· Kate Evans
Strawberry· Chad Finn· Jim Hancock· Tom Davis
Peach· Ksenija Gasic· John Clark· Dave Byrne· Tom Gradziel
Cherry· Amy Iezzoni· Nnadozie Oraguzie
Executive CommitteeCameron Peace Nahla BassilGennaro FazioJim Luby Dorrie MainJim McFersonEric van de WegCholani WeebaddeChengyan Yue
Project DirectorAmy Iezzoni
RosBREED’s Management
WSU
U Minn
Cornell U
UC Davis
Clemson U
U Arkansas
Texas A&M
MSU
UNHUSDA-ARS
Corvallis
WSU MSU
Rosaceae
Demonstration Breeding Programs
Demonstration Breeding Programs
RosBREED
Resource Development
RosBREEDTrait Values
Breeder survey 2010
Producer survey Fall 2011-
Winter 2012
Market Intermediary survey Fall 2010-
Winter 2011
Household data analysis
2010;consumer survey 2012
What trait is my next breeding
target?
We like disease resistant apple
trees!
I like tasty strawberries!
We like firm tart cherries that pit well!
Processors
RosBREEDAroma
PhytonutrientShape
TartnessJuiciness
SizeOther fruit quality attributes
Storage lifeDisease resistance
No storage disordersExternal appearance
Sugar/acid balanceSweetness/soluble solids
Shelf life at retailFruit firmnessExterior colorFruit crispness
Fruit flavor
0 20 40 60 80 100
2
2
27
9676
1543
33
5
13
335
2610
23
54
777
7
2341
Socio-Economics Surveys (example for apple)
Breeders Market Intermediaries
Michigan Producers
Washington Producers
% of respondents
MOST
important
traits
LEAST
important
traits
SNP Genome Scans
RosBREED
Illumina Infinium® II SNP arrays:developed 2010, used 2011
9K 8K
+1K
6K
Verde et al. 2012 PLoS One, accepted
Chagne et al. 2012 PLoS One 7(2):e31745
Peace et al. manuscript in prep.
SNP Genome Scans
RosBREED
9K 8K 6K
40-60 kb
intervals
sweet cherry
P. avium genome
sour cherry
SNP
SNP
SNP100-200 kb
intervals
SNP
SNP
SNP
SNPSNPSNP
SNPSNPSNP
SNP
Avg 446 kb/clusterAvg 72% SNPs polymorphicAvg 94% clusters polymorphicR
ES
ULT
SS
TRAT
EG
Y
P. fruticosa genome
Avg 27 kb/SNPAvg 84% SNPs
polymorphic
every 4th-5th detected SNP chosen, so spacing varies over genome
Avg 38 kb/SNPAvg SNPs polymorphic =
32% (sweet), 36% (sour)
RosBREED
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
WeisW int
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
PCFW 2-134
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
Reference Germplasm
CROP REFERENCE
SETn=480
BREEDING PEDIGREE SETS
Any breeder’s additional germplasm with data
RosBREED
Reference GermplasmMinnesota
BP Set(n=160)
Washington BP Set
(n=160)
New York BP Set(n=160)
CROP REFERENCE
SETn=480
RosBREED
Standardized Phenotyping• Reference Germplasm Sets
Public: 480 individualsAdditional: +480 individuals
• Standardized phenotypingat multiple locations,esp. for fruit quality (www.rosbreed.org)
• Evaluations 2010 & 2011(2012 next)
• Available at Genome Database for Rosaceae (www.rosaceae.org/breeders_toolbox)
FlexQTLTM
for QTLdiscovery, validation, characterization
RosBREED
RallsJan Delicious Winesap RomBeauty Jonathan M_PRI668-100 GoldenDel F2_26829-2-2
Fuji Crandall PRI14-126
PRI668-100
X-2771
X-3143
X-3318
Fruit firmness in apple (HiDRAS data)
Pedigree-Based Analysis
Flow of a specific linkage block
Pedimap for visualizing pedigrees
(with alleles, traits,Identity-By-Descent)
Jewel Discovery
SNPgenome scans
RosBREED
Standardized phenotypic data
Pedigree-Based Analysis
QTL discovery
MAB Enablement
PBA: crop-wide
PBA: breeding program
Breeding markersScre
ening
servi
ces
Marker
priori
ties
Crossin
g
sche
me
Trial
MASS
Socio-economics information
DNA information
Efficient, precise, creative breeding
Systematic QTL Validation– The MAB Pipeline
Seedli
ng
selec
tion
sche
mesupported by RosBREED’s in-developmentBreeding Information Management System
RosBREED
“Cross Assist”
“Seedling Select”
New
gen
erat
ions
enr
iche
d fo
r fav
orab
le a
llele
s
MAB Successes So Far
MAPS
MASS
marker-assisted parent selection
marker-assisted seedling selection
Two jewels polished in RosBREED, put to routine use in demo breeding
programs
RosBREED
“Cross Assist”
“Seedling Select”
MAB Successes So Far
RosBREED
Routine Use of QTLs in Breeding
allele 1 carriers
allele 2carriers
Use of QTLs: does not predict definitive differences, but enriches for favorable alleles. Brave breeders!
frequ
ency
trait level
Predicted to belarge-fruited (& self-
fertile)
Thousands of inferior seedlings culled- est. $180K saved!
Improved efficiency in seedling evaluationsince fall 2010 in RosBREED breeding programs
Routine MAB with QTLs
(WSU’s apple and sweet cherry breeding programs)
RosBREED
Tables of functional genotypes
(www.rosbreed.org/breeding/jewel-use)
peach fruit texture type
“How To” for Rosaceae Breeders
Example here is for
RosBREED
“How To” for Rosaceae Breeders
Peach fruit texture type
RosBREED
Apple fruit storability
“How To” for Rosaceae Breeders
RosBREED
Cherry fruit size
“How To” for Rosaceae Breeders
RosBREED: Filling the Treasure Chest for Rosaceae Breeders
International Context
RosBREED
The International Rosaceae Genomics, Genetics, & Breeding Community
Plant Research International, NetherlandsEast Malling Research, UKCRA-FRU, Rome, ItalyIASMA, Trento, ItalyINRA (Bordeaux, Avignon, Angers), France
Andres Bello University, Chile Plant & Food Research, New Zealand
ARC, South Africa
RosBREED participant
location
Critical International Partnerships
+ 2 Scientific Advisory Panel members (Spain, New Zealand)
Future Funding...
-crops?-traits?-approaches?-resources?-partners?
RosBREED
We are seeking funding beyond Aug 2013
Proposalsubmission= Jan 2013
Must be newobjectives
Ideas are coalescing now
Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture
Questions?
www.rosbreed.org