Phenotypic and Molecular Variation in 44 Vintage

Tomato Varieties

JA Labate1, DR Panthee2, MT McGrath3, DM Francis4,

AP Breksa III5, and LD Robertson1

1USDA-ARS Plant Genetic Resources Unit, Geneva, NY 2MHCR & EC, NC State University 3LIHREC, Cornell University 4OARDC, The Ohio State University 5USDA-ARS PFRU, Albany, CA

2011

Heirloom tomatoes:

• appealing through their diverse

range of color, size, shape, texture

and flavor

• largely unimproved for traits such

as yield or disease resistance

• as such they have attracted efforts

of breeding for niche markets

The National Plant Germplasm System (NPGS) Plant

Genetic Resources Unit (PGRU) holds the largest

public tomato (Solanum lycopersicum L.) collection in

the U.S., many of which are heirlooms.

Characterization of the collection will increase its

efficiency of use.

• 44 heirloom varieties (SolCAP panel), replicate

plots in OH, NC, NY (2009), NC (2010)

• scored highly heritable horticultural traits

• scanned fruit for Tomato Analyzer

• fruit quality traits: lycopene, total soluble solids,

ascorbic acid (Vit C), titratable acid

LSmean (min, max) trait values across 4 environments

9.31 9.39 8.00

13.90

0

5

10

15

20

25

30

35

NC09 NY09 OH09 NC10

lyc

op

en

e (

ug

/g)

LSmean (min, max) trait values across 4 environments

TS

S (

bri

x)

5.35 5.84 6.11

4.48

0

1

2

3

4

5

6

7

8

9

10

NC09 NY09 OH09 NC10

LSmean (min, max) trait values across 4 environments

VIT

C (

ug

/ml)

32.74

58.48

34.22 34.99

0

20

40

60

80

100

120

NC09 NY09 OH09 NC10

LSmean (min, max) trait values across 4 environments

TA

(%

)

0.37 0.38 0.42

0.37

0.00

0.10

0.20

0.30

0.40

0.50

0.60

0.70

0.80

NC09 NY09 OH09 NC10

Mean trait values

44 entries across 4 environments

0

2

4

6

8

10

12

14

16

Ye

llo

wP

ea

r

Wh

ite

Qu

ee

n

Ora

ng

eS

tra

wb

err

y

Bla

ck

Plu

m

Ju

an

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lam

me

e

Pu

rple

Cla

ba

sh

Bla

ck

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Ch

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ldB

all

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llo

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tuff

er

Kin

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um

be

rt

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sa

Cra

ig

Ox

he

art

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sh

ov

ka

Op

alk

a

Co

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luto

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no

ve

se

Be

au

ty

Mo

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ym

ak

er

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sa

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err

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69

7

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be

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rglo

be

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rve

ille

de

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s

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pic

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ron

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)

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3

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3

Pa

rag

on

Sa

nM

arz

an

o

Bu

rba

nk

Ak

er'

sW

es

tVir

gin

ia

Lycopene (ug/g)

Mean trait values

44 entries across 4 environments

0

1

2

3

4

5

6

7

8

9

T1

69

3

LY

C1

90

3

Ye

llo

wS

tuff

er

Wh

ite

Qu

ee

n

Ru

tge

rs

Co

sto

luto

Ge

no

ve

se

Ox

he

art

Pri

nc

ipe

Bo

rgh

es

e

Go

ldB

all

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sa

Cra

ig

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sh

ov

ka

Bu

rba

nk

Kin

gH

um

be

rt

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ma

VF

Ma

rve

ille

de

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arc

he

s

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ne

ym

ak

er

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rglo

be

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lvia

xIn

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nM

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o

Pe

ron

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00

3

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T1

69

7

Tre

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an

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an

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Fa

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rite

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ish

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ste

Be

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ty

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ea

r

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ck

Plu

m

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alk

a

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ine

Pu

rple

Cla

ba

sh

Ta

ina

n(A

VR

DC

#6

)

Sp

on

zil

lo

TSS (brix)

Mean trait values

44 entries across 4 environments

0

10

20

30

40

50

60

70

Ro

ma

VF

LY

C1

90

3

T1

69

3

Op

alk

a

Gru

sh

ov

ka

O

xh

ea

rt

Kin

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um

be

rt

Co

sto

luto

Ge

no

…

Ru

tge

rs

Mo

ne

ym

ak

er

Tre

sC

an

tos

A

ke

r's

We

stV

irg

…

Ho

wa

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erm

an

S

an

Ma

rza

no

P

urp

leC

lab

as

h

T1

69

7

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rag

on

B

lac

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arv

eil

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…

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nk

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ish

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av

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r G

lob

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sa

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ig

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T

10

03

C

he

rok

ee

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rple

G

old

Ba

ll

Bra

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ine

B

ea

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ell

ow

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r B

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rom

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la

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arg

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) J

ua

ne

Fla

mm

ee

V

FN

TC

he

rry

S

po

nz

illo

VITC (ug/ml)

Mean trait values

44 entries across 4 environments

0

0.1

0.2

0.3

0.4

0.5

0.6

LY

C1

90

3

Ho

wa

rdG

erm

an

Ru

tge

rs

Wh

ite

Qu

ee

n

Gru

sh

ov

ka

Op

alk

a

Ox

he

art

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llo

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tuff

er

Sa

nM

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an

o

Co

sto

luto

Ge

no

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se

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ng

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tra

wb

err

y

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ero

ke

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urp

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ish

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ak

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be

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sa

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au

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es

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gin

ia

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err

y

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llo

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ea

r

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ron

Tre

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an

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vo

rite

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ina

n(A

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#6

)

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ck

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m

Sp

on

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lo

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ck

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ula

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nd

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ine

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rag

on

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3

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nd

ero

sa

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ldB

all

Kin

gH

um

be

rt

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nc

ipe

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rgh

es

e

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lvia

xIn

du

str

ia

T1

69

7

Ma

rve

ille

de

sM

arc

he

s

Ju

an

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lam

me

e

Pu

rple

Cla

ba

sh

TA (%)

VITC (ug/ml x 10-1 )

LYC (ug/g)

TA (% x 101 )

TSS (ºbrix)

0

2

4

6

8

10

12

14

16

Ail

sa

Cra

ig

Ak

er'

sW

es

tVir

gin

ia

Am

ish

Pa

ste

Be

au

ty

Bla

ck

Fro

mT

ula

Bla

ck

Plu

m

Bra

nd

yw

ine

Bu

rba

nk

Ch

ero

ke

eP

urp

le

Co

sto

luto

Ge

no

ve

se

D'O

lvia

xIn

du

str

ia

Fa

vo

rite

Glo

be

Go

ldB

all

Gru

sh

ov

ka

Ho

wa

rdG

erm

an

Ju

an

eF

lam

me

e

Kin

gH

um

be

rt

LY

C1

90

3

Ma

rglo

be

Ma

rve

ille

de

sM

arc

he

s

Mo

ne

ym

ak

er

Op

alk

a

Ora

ng

eS

tra

wb

err

y

Ox

he

art

Pa

rag

on

Pe

ron

Po

nd

ero

sa

Pri

nc

ipe

Bo

rgh

es

e

Pu

rple

Cla

ba

sh

Ro

ma

VF

Ru

tge

rs

Sa

nM

arz

an

o

Sp

on

zil

lo

Stu

pic

e

T1

00

3

T1

69

3

T1

69

7

Ta

ina

n(A

VR

DC

#6

)

Tre

sC

an

tos

VF

NT

Ch

err

y

Wh

ite

Qu

ee

n

Ye

llo

wP

ea

r

Ye

llo

wS

tuff

er

Mean trait values

44 entries over 4 environments

ANOVA, 44 entries x 4 locations

Source

Genotype

G x E

df a

43,

164

127,

164

TA

8.89***

2.63***

TSS

10.96***

5.03***

VITC

8.07***

6.18***

LYC

2.05***

1.84***

a numerator, denominator degrees of freedom

Descriptive statistics and heritability estimates for fruit quality

traits in 44 vintage varieties of tomato

LYC (ug/g)

TSS (%)

VITC (ug/ml)

TA (%)

Mean Min Max StDev Heritability (%)

10.2 5.8 50.9 4.9 49.8

5.5 2.9 9.0 1.0 88.7

40.4 8.9 104.6 16.2 79.9

0.4 0.2 0.8 0.1 73.9

Trait

Genetic (below diagonal) and phenotypic (above

diagonal) correlation coefficients of 44 entries across 4

environments

LYC

TSS

VITC

TA

LYC TSS VITC TA

0.01 -0.15 -0.11

-0.02 0.49 0.29

-0.28 0.53 0.37

-0.16 0.27 0.52

Germplasm No. SNP Freq of major

samplea n markers He F allele

1) Vintage

2) Vintage

3) Geodiversity

4) Geodiversity

44

20

50

30

18

86

68

49

0.110

0.076

0.199

0.171

0.827

0.798

0.717

0.965

0.895

0.835

0.848

0.852

a 1) current study, 2) Sim et al. 2011, 3) Baldo et al. 2011, 4) Labate et al. 2011

Diversity estimates of tomato germplasm based on SNP markers

High resolution scans for Tomato Analyzer

VFNT Cherry

Purple Clabash Marveille des Marches Howard German Juane Flammee

Brandywine

Opalka Aker’s West Virginia King Humbert Yellow Pear

Sponzillo

Digital images for GRIN database

VFNT Cherry

Purple Clabash

Marveille des Marches

Howard German

Juane Flammee

Brandywine

Opalka Aker’s West Virginia

King Humbert Yellow Pear

Sponzillo

Digital images for GRIN database

Summary

• Four fruit quality traits were assayed for 44 heirloom tomato

varieties in replicate plots, 4 environments

• Extensive variation among entries, significant Genotype and GxE

effects for all traits

• All traits showed high heritability (50-89%)

• Traits were positively correlated with the exception of lycopene

• Molecular genetic diversity estimates were similar to tomato

geodiversity samples

• Phenotypic characterization data of 44 tomato heirloom varieties

will be available in GRIN http://www.ars-grin.gov/

• Accessions have been regenerated and are listed in PGRU Tomato

Core Set http://www.ars.usda.gov/SP2UserFiles/Place/19100500/TomatoCoreListing.pdf

PGRU

T. Balch

S. Tennies

S. Sheffer

C. Pigeat

Funded by Tomato CGC 2009 and CRIS project 1910-21000-019-00D

Cornell Univ

G.M. Fox

Ohio State

Univ

T. Aldrich

NC State Univ

P. Sanders

C. Anderson

K. Gaskill

Thank you!

PFRU

B. Cain