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. 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In: Ferree DC, Warrington IJ (eds) Apples: botany, production, and uses. CAB International, Wallingford UK, pp 91-124 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