instant utilization - rosbreed...co-pis and participants of nri project “candidate genes for fruit...
TRANSCRIPT
Instant
Utilization
(DNA information not needed this time)
TAKE HOME MESSAGE
1. Think like a curator
2. Static collections
3. Descriptors
4. Phenotypes
To Facilitate Utilization of Tree Fruit Genebanks:
Think like a breeder
Segregating descendant populations
Comprehensive and standardized
performance information
Performance-predictive DNA information
Chair, Prunus CGC
Member, Apple CGC
Co-Project Director
MAB Pipeline Team Leader
Asst Prof
Tree Fruit Genetics
WHO IS THIS GUY?
ACKNOWLEDGEMENTSBreeders: Tom Gradziel, Amy Iezzoni, Jim Olmstead, Kate Evans,
Nnadozie Oraguzie, Jim Luby
Germplasm curators: Phil Forsline, Gennaro Fazio, Ed Stover, John
Preece
Germplasm DNA evaluators: Gayle Volk, Nahla Bassil, Malli Aradhya
Co-PIs and participants of NRI project “Candidate genes for fruit
softening in Prunus”
Co-PIs and participants of NRI project “Functional gene markers
for Rosaceae tree fruit texture”
Co-PIs and participants of SCRI project “RosBREED: Enabling
marker-assisted breeding in Rosaceae”
Outline of Presentation
Value of Genebanks to Crop Improvement
Think Like a Breeder
Segregating Descendant Germplasm
Comprehensive & Standardized
Performance Information
Performance-Predictive DNA Information
Genebanks as Conduits to Utilization
Value of Genebanks
to Crop Improvement
Value of Genebanks
to Crop ImprovementWILD POPULATIONS
GENEBANK
BREEDING
Ultimate source
of useful alleles,
less protected
Security
of crop
production
Output is basis of
crop production
Utilization is rare
for tree fruit
Value of Genebanks
to Crop Improvement
• Allelic diversity is not useful if not used
• Primary users for crop improvement
= BREEDERS
• Encourage utilization by breeders!
Think Like a Breeder
Select parents
Cross
Select seedlings
Release commercially
Think Like a Breeder
Select parents
Genebank accessions Cultivars and selections
Think Like a Breeder
I can’t see any
value in that!
Think Like a Breeder
Do I need that trait?
Even if I want it, it’s a
lot of work to chip it
out and polish it up!
Think Like a Breeder
Much better! I can
incorporate that!
Think Like a Breeder
Select parents
Genebank accessions Cultivars and selections
Think Like a Breeder
Select parents
Genebank accessions Cultivars and selections
Think Like a Breeder
Select parents
Genebank accessions Cultivars and selections
• To support “Use as parent/Ignore” decisions
(and encourage “Use”), need to get into
breeders’ heads!
Think Like a Breeder
What are the
actual allele effects?
Is it dominant?
Recessive? Additive?
Is there pleiotropy with
other traits? Linkage?
Those genebank
accessions could
be useful, but…
SWEET SOMETIMES,
V. HIGH YIELD
MID SWEETNESS,
LARGE SIZE
POOR
TASTE,
SMALL
G
• Phenotype is an incomplete predictor of
underlying genetics
Think Like a Breeder
cold
summer
sweetens
slightly if
picked early
soil
ripens early
when cold
immature
taster
P
• Phenotype is an incomplete predictor of
underlying genetics
Think Like a Breeder
G
taster
cold
summer
ripens early
when cold
immature
sweetens
slightly if
picked early
soil
P
Contributors to variation
among trees
Env
GxEGen
Normal
view
Breeders’
optimal view
+2
-18
-1
+5
-5
-8
(+6)
0
Sweetness
Weight
+2
+10
-1
+5
Genetic
Block 2C
recessiveness
+3
SWEET SOMETIMES,
V. HIGH YIELD
MID SWEETNESS,
LARGE SIZE
POOR
TASTE,
SMALL
pleiotropy
epistasis
Think Like a Breeder
Think Like a Breeder
Breeders’
optimal view
+2
+10
-1
+5
-5
-8
(+6)
0
+3
+2
-18
-1
+5
Think Like a Breeder
Breeders’
optimal view
+2
+10
-1
+5
-5
-8
(+6)
0
+3
+2
-18
-1
+5
Putting the jewels
together…
Think Like a Breeder
Breeders’
optimal view
+2
+10
-1
+5
-5
-8
(+6)
0
+3
+2
-18
-1
+5
Putting the jewels
together…
Provide Segregating Descendant Germplasm
1. Marker-trait association approaches require
enough contrasting individuals for statistical
power
F1 mapping population: 516 seedlings
e.g. Red flesh and the MYB10 gene in apple
NPGS genebank: >50 accessions (>30 red)
(red-flesh allele dominant)
Provide Segregating Descendant Germplasm
2. Cryptic alleles – not detected by phenotype
If favorable allele is recessive or epistatic, then
- not detected, or
- mistaken for dominance or additive effect
Wild forest
cherry
Typical
cultivar
QTL study found a tiny-fruited wild
cherry accession contains common
large-fruit allele at major locus
e.g. Fruit size in sweet cherry
(large-fruit allele masked
by another locus)
Provide Segregating Descendant Germplasm
3. Wild germplasm, even if carrying wonderful
alleles, is far from being cultivar-producing
parents. How can breeders rapidly respond??
e.g. Malus floribunda-derived disease resistance in apple
A modern cultivar Scab-resistant
wild relative
First cross
made <1940
<- - - - - 5 generations
Provide Segregating Descendant Germplasm
• Genebanks need to have, or else
energetically facilitate, availability of
descendant segregating germplasm
SOLUTION
Enough contrasting individuals
Reveal cryptic alleles
Closer to elite
Useful alleles
easier to find
Useful alleles
easier to extract
Goldrush
WSU5
Raritan
Enterprise
CornellPop03
AE0202
AE0207
AE0227
AE0235
AE0237
AE0247
AE0242
AE0103
AE0104
NY08
MN2031
AE_HCxJonf
WSU7
Redfree
Pop_AurxEnt
Pop_EntxArl
Pop_HCxEnt
WSU38
Pop_CPxWSU5
AE0219
AE0248
CornellPop12
AE0254
CornellPop01
Pop_CPxWSU7
Pop_WSU7xWSU5
GoldenDel
LadyWill
RomBeauty
Mavis
McIntosh
LivelRasp
F_Spartan
EsopSpitz
Delicious
Mflor821
Splendour
Wealthy
Starr
Cox
Frostbite
NorthSpy
Tetofsky
YelTransp
Longfield
DuchOlden
F_PattenGr
JerseyBla
F_GingerGold
Edgewood
RallsJan
YellNewtown
LangfBeauty
F_Linda
BenDavis
Montgomery
P14-126
F_JamesGr
M_NY632
Malinda
BlushiGol
F_Beacon
Jongrimes
74-6-77
F_MN1764
F_WSU3
M.sieversii
dummy1
F_Tsugaru
dummy3
F_IngMarie
dummy2
dummy4
NY247
NY66305-289
F_MN1760
MN1706
Sundowner
CrippsPink
NJ35934
F_NJ15
Melba
Spartan
Jonathan
F1_9433-2-2
F1_9433-2-8
NJ130o
Sonora
OR38T610
KidsOrRed
Wagener
Sweet16
Keepsake
MN1628
F_Honeycrisp
Mantet
Oriole
Sharon
Fireside
PattenGr
F_Goodland
Macoun
PRI54-12
GingerGold
MN1627
MN1636
RedBaron
NJ14
NJ19237
Fuji
NJ60837
NJ31
Linda
WorcPearm
Cortland
Lodi
Empire
NY55158-002
dummy6
Clivia
Braeburn
Antonovka
JamesGr
NY632
Haralson
M_Sunrise
PCF-3-120
Delblush
Wijcik
Suncrisp
Ambrosia
Cameo
Beacon
Delcorf
MN1764
WSU3
Regent
GMAL4327
Tsugaru
GMAL4329
Kildare
IngMarie
GMAL4332
GMAL4328
Dolgo
NY76406-007
CoromandelRed
BeautBath
MN1760
NJ15
Melrose
F2_26829-2-2
NJ117637
NJ12
VistaBella
NJ67634
Jolana
F_Williams
Gala
Idared
MN1708
Honeycrisp
StateFair
Goodland
sibLiberty
Liberty
Monroe
Crandall
NJ35437
Snowsweet
MN1702
Fantazja
Primula
Monark
Akane
Jonamac
EarlyCortland
Blackjon
RussianSeedling
Pinova
NY18491
NY18492
Lambourne
Honeygold
Sunrise
NY06
NY92607-16
MN1789
Hatsuaki
Jonagold
NY543
PitmPine
Britemac
NJ303955
Elstar
Fortune
AE0213
AE0211
CornellPop07
Pop_CPxWSU3
Pop_CPxDel
Kerr
NY09
Discovery
NJ136055
Winesap
F_Ill#2
NY49821-46
PRI14-126
PRI14-226
PRI14-510
PRI14-644
PRI16-144
NJ123249
NJ27
Williams
NJ16-109
PRI47-147
DgR23T35
PacQueen
PacRose
AurGoldGa
Arlet
MN1691
NY65707-19
Sonya
NY88
NJ37848
NJ440249
MN1802
MN1915
Nicola
WSU2
BC-8S-27-2
BC8S-27-43
Chinook
Sawa
Sansa
Empress
AutumnCrisp
NY59333-006
WintBanana
PRI2-19
Rubin
Vanda
GranSmith
Burgundy
Silken
Scifresh
WSU24
WSU37
NY04
AE0403
CornellPop04
NY05
NY07
CornellPop08
CornellPop02
NY11
MN1971
Delorgue
AE0304
WSU46
Fiesta
MN1942
MN1955
MN2034
AE0401
MN1965
MN2062
AE0407
MN1980
MN2036
MN1984
MN2056
MN2057
MN2063
AE0408
Pop_CPxHC
WSU65
Pop_DelxHC
Pop_HCxCP
Pop_HCxSPL
Pop_WSU3xHC
WSU34
AE_HCx1702
AE_HCx1764
AE_HCxMon
AE_HCxPit(692)
AE0115
AE0116
AE0118
AE0250
AE0306
AE0405
AE0402
AE0210
MN1836
MN1899
NJ90
Ill#2
PRI668-100
PRI612-1
NJ53
PRI1018-101
Zestar
NY913
NY752
MN1837
MN1888
PCFW2-134
PRI669-205
669NJ5
PRI1235-100
Prima
NY53705-021
PRI855-102
CornellPop05
NY03
NY70712-53
NY02
Hudson
Freedom
PRI1050-201
Topaz
WSU30
AE0233
AE0236
AE0245
AE0251
WSU17
WSU36
WSU49
WSU50
WSU52
WSU57
Pop_AurxArl
Pop_AurxCP
Pop_AurxHC
Pop_CPxAur
AE0234
AE0246
AE0252
CornellPop13
AE0305
AE0404
Pop_HCxAr
WSU35
WSU48
MN2000
MN2042
AE0113
AE0406
NY13
Coop-17
Coop-15
NJ110037
PRI1661-1
PRI1661-2
NY01
NY14
NY241
CrimsCrisp
PixieCrunch
Dayton
MN1839
Coop-18
NY61345
Jonafree
AE0204
AE0301
AE0307
AE0109
AE0240
AE0215
AE0226
AE0229
AE0230
AE0241
AE0308
MN1914
MN1925
MN2033
MN2041
MN2044
MN2050
AE_HCxZest
AE0122
MN1937
MN1940
MN2016
MN2046
AE0206
CornellPop10
CornellPop11
NY15
NY10
CornellPop09
NY12
CornellPop06
MN1964
MN1988
Sundance
Provide Segregating Descendant Germplasm
• RosBREED’s reference
germplasm set of apple
merges breeding & NPGS
85 NPGS accessions
135 cultivars (breeding progs)
260 seedlings (breeding progs)
• NPGS accessions =
ancestors. Allow joining of
many populations in stats
Provide Comprehensive & Standardized
Performance Information
• Phenotypic evaluation:
performance, not descriptors
acute apex
petiole length
= 24 mm
At harvest
Storage 10w+7d
Storage 20w+7d
5 fruit (reps) per evaluation
Firmness – Instr, Sens
Crispness – Instr, Sens
Juiciness – Sens
Harvest date
Maturity
Fruit size
Sweetness
Internal
ethylene conc
Acidity
Relevant to breeding
Provide Comprehensive & Standardized
Performance Information
• Excellent quality phenotypic information
(and available in GRIN) is critical
Reduces unpredictable components of
performance
…needed by researchers to develop excellent
quality genetic tests for performance
Env
GxE
Gen
Contributors to variation among trees
EnvGxE
Gen
Provide Comprehensive & Standardized
Performance Information
• Standardized phenotyping for Rosaceae (led by Gayle Volk, USDA-ARS Fort Collins)
First presented
at ASHS
July 2009
For:
Provide Comprehensive & Standardized
Performance Information
• Protocolswww.rosbreed.org/resources/
fruit-evaluation/
Crop Germplasm Committees:
trait priorities -> + protocols?
Provide Performance-Predictive
DNA Information
Breeders’ optimal view
+2
+10
-1
+5
+2
-18
-1
+5
-5
-8
(+6)
0
• Research required
to develop genetic
tests that provide
functional genotypes
for valuable traits
+3
Provide Performance-Predictive
DNA Information
• Target appropriate traits
Provide Performance-Predictive
DNA Information
• Need excellent quality phenotypic data
At harvest
Storage 10w+7d
Storage 20w+7d
5 fruit (reps) per evaluation
Firmness – Instr, Sens
Crispness – Instr, SensJuiciness – SensHarvest date
Maturity
Fruit size
Sweetness
Internal
ethylene conc
Acidity
Multiple harvests
Multiple locations
Multiple years
Multiple tree reps
Provide Performance-Predictive
DNA Information
• Need efficient DNA technologies
Provide Performance-Predictive
DNA Information
• Need appropriate germplasm
Segregating descendant germplasm
o Associations are discovered and
characterized in training set(s)
o Then extrapolated to the rest of the
crop – breeding material, repositories,
wild populations
Provide Performance-Predictive
DNA Information
• A jewel for sweet cherry
237
190
marker 1 allele
marker 2 allele
255
190
235
204single source
Some functional genotypes (haplotypes) in cultivars
common common
Using already in breeding
Screening Davis Repository cherrieso further sources of the good haplotype?
o new useful haplotypes?
o tag bad haplotypes (avoid in introgression)
Replace this
SWEET SOMETIMES (8.4-14 oBrix)
V. HIGH YIELD but TINY (19-31 g)
MID SWEETNESS (11.5-13.4 oBrix)
LARGE SIZE (140-180 g)
LOW SWEETNESS
(6.7-9.0 oBrix)
SMALL (45-68 g)
+2
-18
-1
+5
+2
+10
-1
+5
-5
-8
(+6)
0
+3
Provide Performance-Predictive
DNA Information
…with this
WILD POPULATIONS
GENEBANK
BREEDING
Ultimate source
of useful alleles,
less protected
Security
of crop
production
Output is basis of
crop production
The Current System
4. Provide
performance-predictive
DNA informationWILD POPULATIONS
GENEBANK
3. Provide
comprehensive
& standardized
performance
information1. Think like
a breeder
BREEDING
2. Provide segregating
descendant populations
WILD POPULATIONS
REPOSITORY
BREEDING
Genebanks as Conduits
to Utilization
SEGREGATING
DESCENDANT
GERMPLASM
Ultimate source
of useful alleles
Output is
basis of crop
production
Safeguarded source
of useful alleles
Training sets for
genetic test development
Allele providers for
breeding
Genebanks as Conduits
to Utilization
WILD POPULATIONS
REPOSITORY
BREEDING
SEGREGATING
DESCENDANT
GERMPLASM