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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
eF
lam
me
e
Pu
rple
Cla
ba
sh
Bla
ck
Fro
mT
ula
Ch
ero
ke
eP
urp
le
Go
ldB
all
Ye
llo
wS
tuff
er
Kin
gH
um
be
rt
Ail
sa
Cra
ig
Ox
he
art
Gru
sh
ov
ka
Op
alk
a
Co
sto
luto
Ge
no
ve
se
Be
au
ty
Mo
ne
ym
ak
er
Po
nd
ero
sa
Am
ish
Pa
ste
Fa
vo
rite
Tre
sC
an
tos
VF
NT
Ch
err
y
T1
69
7
Glo
be
Ma
rglo
be
Ma
rve
ille
de
sM
arc
he
s
Ro
ma
VF
T1
69
3
Stu
pic
e
Pe
ron
Sp
on
zil
lo
D'O
lvia
xIn
du
str
ia
Pri
nc
ipe
Bo
rgh
es
e
Bra
nd
yw
ine
Ta
ina
n(A
VR
DC
#6
)
Ru
tge
rs
LY
C1
90
3
Ho
wa
rdG
erm
an
T1
00
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
Ail
sa
Cra
ig
Gru
sh
ov
ka
Bu
rba
nk
Kin
gH
um
be
rt
Ro
ma
VF
Ma
rve
ille
de
sM
arc
he
s
Mo
ne
ym
ak
er
Ma
rglo
be
D'O
lvia
xIn
du
str
ia
Sa
nM
arz
an
o
Pe
ron
T1
00
3
Pa
rag
on
Bla
ck
Fro
mT
ula
Po
nd
ero
sa
VF
NT
Ch
err
y
Glo
be
Ora
ng
eS
tra
wb
err
y
Ch
ero
ke
eP
urp
le
Stu
pic
e
T1
69
7
Tre
sC
an
tos
Ju
an
eF
lam
me
e
Fa
vo
rite
Am
ish
Pa
ste
Be
au
ty
Ho
wa
rdG
erm
an
Ak
er'
sW
es
tVir
gin
ia
Ye
llo
wP
ea
r
Bla
ck
Plu
m
Op
alk
a
Bra
nd
yw
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
gH
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
rdG
erm
an
S
an
Ma
rza
no
P
urp
leC
lab
as
h
T1
69
7
Pa
rag
on
B
lac
kP
lum
M
arv
eil
led
es
Ma
…
Bu
rba
nk
Am
ish
Pa
ste
F
av
ori
te
Ye
llo
wP
ea
r G
lob
e
Ail
sa
Cra
ig
Pri
nc
ipe
Bo
rgh
e…
T
10
03
C
he
rok
ee
Pu
rple
G
old
Ba
ll
Bra
nd
yw
ine
B
ea
uty
Y
ell
ow
Stu
ffe
r B
lac
kF
rom
Tu
la
Po
nd
ero
sa
M
arg
lob
e
Wh
ite
Qu
ee
n
Stu
pic
e
Ora
ng
eS
tra
wb
e…
P
ero
n
D'O
lvia
xIn
du
str
ia
Ta
ina
n(A
VR
DC
#6
) 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
Ye
llo
wS
tuff
er
Sa
nM
arz
an
o
Co
sto
luto
Ge
no
ve
se
Ro
ma
VF
Ora
ng
eS
tra
wb
err
y
Ch
ero
ke
eP
urp
le
Am
ish
Pa
ste
T1
69
3
Bu
rba
nk
Stu
pic
e
Mo
ne
ym
ak
er
Ma
rglo
be
Ail
sa
Cra
ig
Be
au
ty
Ak
er'
sW
es
tVir
gin
ia
Glo
be
VF
NT
Ch
err
y
Ye
llo
wP
ea
r
Pe
ron
Tre
sC
an
tos
Fa
vo
rite
Ta
ina
n(A
VR
DC
#6
)
Bla
ck
Plu
m
Sp
on
zil
lo
Bla
ck
Fro
mT
ula
Bra
nd
yw
ine
Pa
rag
on
T1
00
3
Po
nd
ero
sa
Go
ldB
all
Kin
gH
um
be
rt
Pri
nc
ipe
Bo
rgh
es
e
D'O
lvia
xIn
du
str
ia
T1
69
7
Ma
rve
ille
de
sM
arc
he
s
Ju
an
eF
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
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