SSR-based parentage analysis of the elite apple cultivar Golden

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SUPPLEMENTARY ELECTRONIC MATERIALS
Silvio Salvi
1,2
, Diego Micheletti 1, Pierluigi Magnago 1, Marco Fontanari 1, Roberto Viola 1,
Massimo Pindo 1, Riccardo Velasco 1
One-step reconstruction of multigeneration pedigree networks in apple (Malus × domestica
Borkh.) and the parentage of Golden Delicious
1
Centre for Research and Innovation, Fondazione Edmund Mach, via E. Mach 1, 38010 San
Michele all’Adige, Italy
2
Department of Agricultural Science, University of Bologna, viale Fanin 44, 40127 Bologna, Italy
Corresponding author: Riccardo Velasco, riccardo.velasco@fmach.it, ph. +39 0461 615257
1
Supplementary Table 1 Reported and/or reconstructed parentage of apple cultivars with reference
for reported parentages
Note on cited source of information about parentages and origin of apple cultivars
Information about apple pedigrees were drawn from sources as authoritative as possible (ie.
scientific literature, such as the collection of pedigrees reported in Evans et al. 2010). We
additionally reported source of information about apple of unknown origins, or originated as chance
seedlings, and sources of anecdotic information. All references are provided at the bottom of this
table.
Cultivar 1
Reported parentage 2
Reference 3
Ambassy
(Delbarestivale =
Delcorf = Monidel)
Ambrosia
GD x Jongrimes
Evans et al. (2010)
PE
OK
Chance seedling supposedly from
GD x Delicious
AS
AS confirmed here.
Amorosa (sport of
Aroma)
Ingrid Marie x Filippe
PE
OK
Annurca
Unknown
Antonovka
Unknown
Hampson and
Kemp (2003);
Mennell and
Mennell (1997)
GarkavaGustavsson et al.
(2008)
Morgan and
Richards (2002);
Sansavini (2008)
Bus et al. (2012)
Ariwa
GD x A849-5
Brown and
Maloney (2009)
PE
Baujade
Brina
PRI2059-101 OP
Hampson and
Kemp (2003)
Morgan and
Richards (2002)
Sansavini (2008)
PE
Ben Davis
Granny Smith x P5R42-52 (PRI
672-3 x Reinette du Mans])
Unknown
Assigned as offspring
of Saturn (closely
related to GD).
Compatible with GD
by exclusion test.
OK
Calville
Unknown
Cameo® (Camela®
= Caudle)
Catarina
GD x Delicious
PE
OK
PE
OK
Clivia
Geheimrat Dr Oldenburg x Cox
Brown and
Maloney (2003)
Evans et al. (2010)
PE
OK
Coop 36 (PRI 272018)
Cox’s Orange
Pippin
Crimson Snow
(MC38)
PRI 2050-2 x GD
Crosby et al. (1993)
PE
OK
Unknown
Hampson and
Kemp (2003)
Luby and Bedford
(2006)
AS
Assigned as offspring
of Delicious. A very
close relationship with
Cripps Pink was
suggested (See
Discussion)
Fuji x Unknown
Chance seedling supposedly
related with Cripps Pink
Morgan and
Richards (2002)
Evans (2011)
Pedigree
status 4
Reconstructed
parentage in this
study 5
2
Cripps Pink (Pink
Lady ®)
Dalinette
(Choupette®)
Delblush
(Tentation®)
Delcoros
(Autento®)
Delgrared
GD x Lady Williams
Evans et al. (2010)
X-4598 × X-3174
www.dalicom.com/
en/produits/view/76
Hampson and
Kemp (2003)
Brown and
Maloney (2009)
Morgan and
Richards (2002)
Hampson and
Kemp (2003)
Morgan and
Richards (2002)
Morgan and
Richards (2002)
www.junamiapple.com
Evans et al. (2010)
GD x Blushing Golden (Grifer)
Delicious
Delgollune (GD x Lundbytorp) x
Cox
Jenimota (GD spur) x Akane
(Primrouge)
Chance seedling
Delorina
(Harmonie®)
Discovery
Blushing Golden (Grifer) x
Florina
Seedling of Worcester Pearmain
Milwa (Faw5878,
Junami®, Diwa®)
Dorianne
(Idared x Maigold) x Elstar
Durello di Forlì
Unknown
Earlygold (Snygold)
X-6823 x X-4638
PE
OK
PE
OK
PE
OK
PE
OK
PE
OK
PE
OK
PE
AS
AS confirmed here
Elan
Chance seedling supposedly
related with GD
GD x Ingrid Marie
Tartarini et al.
(2004)
Norton and King
(1987)
Evans et al. (2010)
PE
OK
Elstar
GD x Ingrid Marie
Evans et al. (2010)
PE
OK
Enterprise (Coop30)
Crosby et al.
(1994)
Evans et al. (2010)
PE
Fiesta
Complex pedigree PRI 1661–2 x
PRI 1661–1
Cox x Idared
PE
OK
Florina
PRI 612-1 x Jonathan
Evans et al. (2010)
PE
OK
Forlady
Forum x Lady Williams
Fuji
Ralls Janet x Delicious
Sansavini et al.
(2003)
Evans et al. (2010)
PE
OK
G.41
M.27 x Robusta5
PE
OK
Gala
Kidd’s Orange Red x GD
Robinson et al.
(2003)
Evans et al. (2010)
PE
OK
Ginger Gold
Marini (1995)
AS
AS confirmed here
Evans et al. (2010)
PE
OK
Golden Delicious
(GD)
Chance seedling supposedly
related with GD
Weisser Winterglockenapfel x
Delicious
Chance seedling supposedly
related with Grimes Golden
AS
AS confirmed here
Golden Reinette
Unknown
GoldRush (Coop 38)
GD x Coop 17
Hampson and
Kemp (2003);
Cabe et al. (2005)
Morgan and
Richards 2002);
Calhoun 2010)
Evans et al. (2010)
PE
OK
Granny Smith
Chance seedling
Grimes Golden
Unknown
Idared
Jonathan x Wagenerapfel
Hampson and
Kemp (2003)
Morgan and
Richards (2002)
Evans et al. (2010)
PE
OK
Ingrid Marie
Cox x (Guldborg ?)
Evans et al. (2010)
PE
OK
James Grieve
Cox x Unknown
Evans et al. (2010)
PE
OK
Jonamac
McIntosh x Jonathan
Way (1972)
PE
OK
Jonafree (= Coop22
= PRI 2016-100)
PRI855-102 x NJ31, complex
pedigree including Jonathan and
Crosby et al.
(1992)
PE
Gloster
3
GD
Jonathan
Unknown
Jongrimes
(Jonagrimes)
Unknown, supposed Jonathan x
Grimes Golden
Kent
Cox x Jonathan
Laxton’s Superb
Wyken Pippin x Cox
Ligol
Linda x GD
Limoncini
Unknown
Lord Lambourne
M.27
James Grieve x Worcester
Pearmain
M.9 x M.13
M.9
Unknown
McIntosh
Unknown
Mela della serla
Unknown
Modì (Civg198)
Liberty x Gala
Napoleon
Unknown
P.16
Longleaf x M.9
Pearmain Dorè
Unknown
Pilot
Hampson and
Kemp (2003)
Morgan and
Richards (2002);
www.orangepippin.
com/apples/jonagri
mes
Evans et al. (2010)
AS
AS was confirmed for
Grimes Golden but
not for Jonathan
PE
Morgan and
Richards (2002)
Evans et al. (2010)
PE
Consistent with Cox
only, as also observed
in Evans et al. 2010
OK
PE
OK
Evans et al. (2010)
PE
OK
Webster and
Wertheim (2003)
Webster and
Wertheim (2003)
Hampson and
Kemp (2003)
PE
OK
Luby and Bedford
(2006)
PE
OK
PE
OK
Clivia x Undine
Webster and
Wertheim (2003)
Morgan and
Richards (2002)
Evans et al. (2010)
PE
Pinova
Clivia x GD
Evans et al. (2010)
PE
Assigned as Clivia x
Jonathan
OK
Piok
Unknown
Piros
Helios (Oldenburg × ?) × Apollo
(Cox × Oldenburg)
GD x F2 26829-2-2
Morgan and
Richards (2002)
Evans et al. (2010)
PE
OK
Evans et al. (2010)
PE
Assigned as offspring
of Renora
Primiera (Coop42)
(GD x F2 26829-2-2z) x ((Melba
x (Wealthy x Starr))x (Rome
Beauty x Melba))
GD x Coop17
PE
OK
Priscilla
Delicious x PRI 610-2
Goffreda et al.
(1995)
Evans et al. (2010)
PE
OK
Reanda
Clivia x BX 44,14
PE
OK
Rebella
GD x Remo
Pillnitzer
Obstsorten (2009);
Evans et al. (2010)
Pillnitzer
Obstsorten (2009)
PE
OK
Redearly
Coop14 x unknown
Redfield
Reinette Ananas
Wolf River x M. sieversii var.
niedzwetzkyana,
Unknown
Renora
Clivia x BX 44,2
PE
OK
PRI 14-126
Prima
Brooks and Olmo
(1972)
Morgan and
Richards (2002)
Pillnitzer
Obstsorten (2009);
Evans et al. (2010)
4
Retina
Apollo x BX 44,2
Rewena
(Cox x Oldenburg) x BX 44,14
Rome Beauty
Unknown
Rosa di Caldaro
Unknown
Rosana
Jolana x Lord Lambourne
Rubens (Civni)
Rubin
Pillnitzer
Obstsorten (2009)
Pillnitzer
Obstsorten (2009);
Noiton and Alspach
(1996)
Hampson and
Kemp (2003)
Assigned as offspring
of Reanda.
PE
OK
Gala x Elstar
Crosby et al.
(1992)
Evans et al. (2010)
PE
OK
GD x Lord Lambourne
Evans et al. (2010)
PE
OK
Rubinette
GD x Cox
Evans et al. (2010)
PE
OK
Rubinola
Prima x Rubin
Hana and Pavel
(2001); Evans et al.
(2010)
PE
Confirmed both Prima
and Rubin, differently
from Evans
San Lugano
Unknown
Sansa
Gala x Akane
PE
OK
Saturn
PRI 1235 x GD
Noiton and Alspach
(1996)
Hampson and
Kemp (2003)
PE
OK
Sila
Unknown
Brown and
Maloney (2009)
Evans et al. (2010)
PE
Gala is confirmed,
while Delicious is not
Confirmed for
McIntosh. Yellow
Newton was not
included in collection
and our data indicated
Delicious as second
parent.
®
Sonya (Nevson)
Gala x Delicious
Spartan
McIntosh x Yellow Newtown
Spitzlederer
Unknown
Stettino
Unknown
Summerfree
PRI 1956-6 x Ed Gould Golden
Bergamini and
Giongo (2002)
PE
Suncrisp
GD x (Cox x Cortland)
Marini (1995)
PE
Assigned as offspring
of Coop 36, with
which however shares
much of the pedigree
OK
Topaz
Rubin × Vanda
Evans et al. (2010)
PE
OK
Tunda
Ambassy x Liberty
PE
OK
Yellow Bellflower
Unknown
Brown and
Maloney (2009)
Morgan and
Richards (2002)
White Rosmarine
Unknown
PE
Morgan and
Richards (2002)
Common synonymous or registered names are in brackets. Golden Delicious and Cox’s Orange Pippin are indicated as
GD and Cox, respectively, in pedigrees.
2
Pedigree as known from literature. Cultivars present in this study are in bold.
3
Reference for the reported parentage.
4
AS = Anecdotic suggestion; PE = Previously established.
5
OK indicates accordance between reported and here reconstructed pedigrees. Additional comments are provided when
needed.
1
AA.VV. (2009) Pillnitzer Obstsortenbroschure. Julius Kühn-Institute, Dresden, www.jki.bund.de
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6
27
Delicious
27
Ambassy
27
Jongrimes
25
GD
Ambassy
27
Jongrimes
25
Ambrosia
27
Delicious
27
Amorosa
25
IngridMa
26
Pair LOD Parent 2
Pair LOD Parent 1
1
1
1
1
10.7
1
0.9041
27.9
6.7
1
0.0959
106
13.5
7.6
1
0.9994
82
15.8
1
1
n_m
n_f
Mismatches
Common Loci Typed
Posterior
LOD
Posterior Parent 2
27
Loci Typed
Parent 2
GD
Posterior Parent 1
GrimesG
Loci Typed
Parent 1
Loci Typed
Offspring
Supplementary Table 2 FRANz output file (‘parentage.csv’) listing the estimated parent-offspring
relationships and related parameters. GD = Golden Delicious
11.0
1
27
0
64
64
11.0
0.0
1
27
0
60
60
27
46.2
0.9041
27
0
93
93
27.9
EarlyGold
27
44.2
0.0959
27
0
93
93
GD
27
31.9
0.9994
27
0
106
15.8
1
25
0
82
Annurca
27
0.0
1
27
0
60
60
1
1
Antonovka
25
0.0
1
25
0
121
121
1
1
Ariwa
26
12.6
0.9929
26
0
114
114
0.9929
1
Belfiore
27
0.0
1
27
0
121
121
1
1
BenDavis
26
0.0
1
26
0
121
121
1
1
Baujade
27
13.1
1
27
1
111
111
1
1
Brina
27
0.0
1
27
0
120
120
1
1
Calvilla
27
0.0
1
27
0
121
121
1
1
Saturn
Grannys
26
27
27
13.1
Cameo
26
Delicious
27
33.0
0.9971
26
1
106
106
17.7
1
0.9971
Catarina
26
Fuji
26
26.2
0.9251
27
0
93
93
26.2
0.9251
1
Catarina
26
Delicious
27
23.3
0.0749
27
0
93
93
23.3
0.0749
1
Clivia
27
Coxorange
27
14.5
1
27
0
73
73
14.5
1
1
Coop36
26
GD
27
14.0
0.9915
26
0
95
95
14.0
0.9915
1
Coxorange
27
0.0
1
27
0
62
62
1
1
CrimsonS
27
14.7
1
27
0
118
118
1
1
Dalinred
26
0.0
1
26
0
121
121
1
1
Delblush
27
GD
27
15.2
0.9559
27
0
100
100
15.2
0.9559
1
Delcoros
27
Coxorange
27
15.5
1
27
0
110
110
15.5
1
1
Delgrared
27
GD
27
13.8
0.9999
27
0
121
121
13.8
0.9999
1
Delorina
26
Florina
26
14.0
1
26
1
116
116
14.0
1
1
Discove
18
0.0
1
18
0
78
78
1
1
Diwa (Milwa)
27
Elstar
27
14.6
1
27
0
121
121
14.6
1
1
Dorianne
27
GD
27
13.6
0.8805
27
0
106
106
13.6
0.8805
1
Dorianne
27
Elstar
27
11.3
0.111
27
0
106
106
11.3
0.111
1
Delicious
GD
12.6
27
5.0
14.7
DurelloFo
27
0.0
1
27
0
121
121
1
1
EarlyGold
27
GD
27
7.6
0.7009
27
0
93
93
7.6
0.7009
1
EarlyGold
27
Ambassy
27
6.7
0.2985
27
0
93
93
6.7
0.2985
1
Elan
26
IngridMa
26
GD
27
37.8
1
26
0
98
98
18.5
11.6
1
1
Elstar
27
IngridMa
26
GD
27
33.5
0.9991
27
0
83
83
15.5
12.0
1
0.9991
Enterpris
27
0.0
1
27
0
116
116
1
1
Florina
26
8.4
0.9999
26
1
99
99
0.9999
1
Jonathan
24
8.4
7
Forlady
27
0.0
1
27
0
121
121
Fiesta
26
Idared
27
43.3
1
26
0
95
95
16.5
Fuji
26
Delicious
27
24.9
1
26
0
75
75
24.9
Coxorange
27
19.0
1
1
1
1
1
1
G41
27
M27
27
28.2
1
27
0
121
121
28.2
1
1
Gala
27
GD
27
6.8
0.9769
27
0
74
74
6.8
0.9769
1
Gingergo
27
GD
27
7.9
0.999
27
0
121
121
7.9
0.999
1
Gloster
26
Delicious
27
16.8
1
26
0
88
88
16.8
1
1
GoldRei
26
0.0
1
26
0
121
121
1
1
Goldrush
26
16.2
1
26
0
82
82
1
1
Grannys
27
0.0
1
27
0
63
63
1
1
GrimesG
27
0.0
1
27
0
61
61
1
1
GD
27
16.2
Idared
27
Jonathan
24
8.8
0.9997
27
1
76
76
8.8
0.9997
1
IngridMa
26
Coxorange
27
12.5
1
26
0
70
70
12.5
1
1
JamesG
26
Coxorange
27
14.9
1
26
1
65
65
14.9
1
1
Janamac
26
McIntosh
26
46.0
1
26
0
77
77
26.5
1
1
Jonafree
26
0.0
1
26
0
97
97
1
1
Jonathan
24
0.0
1
24
0
60
60
1
1
Jongrimes
25
GrimesG
27
19.4
1
25
0
70
70
19.4
1
1
Kent
27
Coxorange
27
13.8
0.8807
27
1
82
82
13.8
0.8807
1
Jonathan
24
11.8
Kent
27
IngridMa
26
11.5
0.1193
27
1
82
82
11.5
0.1193
1
LaxtonSup
26
Coxorange
27
20.3
1
26
0
66
66
20.3
1
1
Limonc
27
0.0
1
27
0
121
121
1
1
LordLamb
23
JamesG
26
15.8
1
23
0
68
68
15.8
1
1
Ligol
26
GD
27
10.0
0.9999
26
0
121
121
10.0
0.9999
1
M27
27
M9
24
20.5
1
27
0
72
72
20.5
1
1
M9
24
0.0
1
24
0
67
67
1
1
McIntosh
26
0.0
1
26
0
60
60
1
1
MelaSerla
24
1
1
Modi
27
1
1
Napole
25
1
1
P16
26
1
1
PearmainD
27
1
1
Pilot
27
Jonathan
24
1
1
Pinklady
27
GD
27
1
1
Pinova
24
Clivia
27
1
0.9789
Gala
M9
27
24
Clivia
GD
27
27
0.0
1
24
0
121
121
13.2
1
27
0
114
114
0.0
1
25
0
121
121
22.0
1
26
0
84
84
0.0
1
27
0
121
121
27.5
1
27
2
85
85
15.6
14.2
1
27
0
93
93
14.2
34.0
0.9789
24
0
106
106
15.3
13.2
22.0
17.1
10.7
Piok
26
0.0
1
26
0
121
121
1
1
Piros
27
0.0
1
27
0
121
121
1
1
PRI14126
25
GD
27
11.1
0.9976
25
0
121
121
11.1
0.9976
1
Prima
27
Renora
27
9.7
1
27
1
93
93
9.7
1
1
Primiera
27
GD
27
15.7
0.7917
27
0
118
118
15.7
0.7917
1
Primiera
27
Goldrush
26
14.1
0.2014
27
0
118
118
14.1
0.2014
1
Priscilla
27
Delicious
27
19.4
1
27
0
97
97
19.4
1
1
Reanda
27
Clivia
27
20.2
1
27
0
121
121
20.2
1
1
Rebella
27
GD
27
9.7
0.9385
27
0
109
109
9.7
0.9385
1
Rebella
27
Elstar
27
6.7
0.0612
27
1
109
109
6.7
0.0612
1
8
Redearly
26
0.0
1
26
0
121
121
1
1
Redfield
27
0.0
1
27
0
121
121
1
1
Renettana
26
0.0
1
26
0
121
121
1
1
Renora
27
19.4
1
27
0
121
121
1
1
Retina
27
0.0
1
27
0
121
121
1
1
Rewena
26
16.8
1
26
1
108
108
1
1
Romebe
27
0.0
1
27
0
60
60
1
1
RosaCald
27
0.0
1
27
0
121
121
1
1
Rosana
26
LordLamb
23
19.7
1
26
0
114
114
19.7
1
1
WhiteRosm
26
4054a
27
26.7
0.5011
26
1
121
121
26.7
0.5011
1
WhiteRosm
26
0.0
0.4989
26
0
121
121
0.4989
1
Rubens
27
Gala
27
Elstar
27
34.1
0.9996
27
0
108
108
16.8
13.2
1
0.9996
Rubin
27
LordLamb
23
GD
27
27.5
0.9989
27
1
121
121
15.1
4.8
1
0.9989
Rubinette
26
Coxorange
27
GD
27
25.8
1
26
2
86
86
11.9
8.8
1
1
Rubinola
26
Rubin
27
Prima
27
37.0
1
26
0
121
121
14.0
15.9
1
1
SanLuga
26
0.0
1
26
0
121
121
1
1
Sansa
27
Gala
27
14.2
1
27
0
88
88
14.2
1
1
Saturn
26
GD
27
12.0
0.9997
26
0
82
82
12.0
0.9997
1
Sila
27
0.0
1
27
0
121
121
1
1
15.5
0.9918
26
0
121
121
15.5
0.9918
1
54.9
1
26
0
71
71
23.4
1
1
Clivia
Reanda
27
27
19.4
16.8
Sonya
26
Gala
27
Spartan
26
McIntosh
26
Spitzlede
26
0.0
1
26
0
121
121
1
1
Stettino
25
0.0
1
25
0
121
121
1
1
SummerFr
27
Coop36
26
18.5
0.9989
27
0
120
120
18.5
0.9989
1
Suncrisp
27
GD
27
13.5
0.9998
27
0
106
106
13.5
0.9998
1
Topaz
26
Rubin
27
14.1
1
26
1
121
121
14.1
1
1
Tunda
27
Ambassy
27
16.1
1
27
1
106
106
16.1
1
1
Delicious
27
18.3
3685e
27
0.0
1
27
0
121
121
1
1
3688h
27
0.0
1
27
0
121
121
1
1
3691f
26
0.0
1
26
0
121
121
1
1
3762g
22
0.0
1
22
0
121
121
1
1
4054a
27
0.0
0.5011
27
0
121
121
0.5011
1
4054a
27
26.7
0.4989
27
1
121
121
0.4989
1
4103a
26
0.0
1
26
0
121
121
1
1
4304e
27
0.0
1
27
0
121
121
1
1
WhiteRosm
26
26.7
4309c
27
0.0
1
27
0
121
121
1
1
4309d
27
0.0
1
27
0
121
121
1
1
sy4495f
26
0.0
1
26
0
121
121
1
1
sy4496w
25
0.0
1
25
0
121
121
1
1
sy4497a
26
0.0
1
26
0
121
121
1
1
syCRA
25
0.0
1
25
0
121
121
1
1
syM781
21
0.0
1
21
0
121
121
1
1
syM790
25
0.0
1
25
0
121
121
1
1
syM900
27
0.0
1
27
0
121
121
1
1
syNO1
27
0.0
1
27
0
121
121
1
1
9
syNO3
26
0.0
1
26
0
121
121
1
1
syNO4
27
0.0
1
27
0
121
121
1
1
syNO5
27
0.0
1
27
0
121
121
1
1
syPOL
26
0.0
1
26
0
121
121
1
1
10
Supplemental Figure 1
11
Supplemental Figure 2
12
Supplemental Figure 3
13
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