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