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Analysis of genetic control of fruit size in using both multiple, pedigree-related and single full- sib families Hélène MURANTY, François LAURENS, Marco C.A.M. BINK , Eric van de WEG

Hélène MURANTY RGC8 21-23 June 2016 Introduction

• Fruit size = appearance + yield component • QTL for marker-assisted selection – large population  precise location – large diversity  consistency across genetic backgrounds

Pedigree-based analysis

• Bink et al 2002, 2008, 2014 • Rosyara et al 2013 • Fresnedo-Ramírez et al 2015, 2016 • Roach et al 2016 • Allard et al 2016

2 Hélène MURANTY RGC8 21-23 June2 2016 Previous studies

reference cross pop fruit trait linkage group size 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Liebhard et al × 251 weight (2003) X X X X X X X X

Kenis et al (2008) Telamon × 199 / weight, X X X X X X X 165 diameter, height Royal × 572 Devoghalaere et al Braeburn weight X X X X X X (2012) Starkrimson × 123 Chang et al (2014) × Golden 144 / weight, X X X X Delicious 140 diameter, length × Delearly 86 Fuji × 73 size, weight, Costa (2015) × 185 X X X X X X X Scarlet diameter, height Golden Delicious × 75 Braeburn

3 Hélène MURANTY RGC8 21-23 June3 2016 Material

Z185 BVIII_34.16 GoldenDel X-4355 X-6820 PRI612-1 F_X-4355 Generos 12_E AntonovkaOB Chantecler X-6681

Delicious PRI672-3 X-6683 26 related F_B8_34.16 X-3177 Baujade PRI14-126 ReiDuMans I_M Clochard PRI14-152 X-6799 TN_R10A8 families X-3259 X-6398 HiDRAS Jonathan Crandall O53T136 X-6564 I_W Wines_Prima Galarina X-3305 F_Delicious F_O53T136 Gala Wagenerap X-6679 X-3143 F2_26829-2-2 X-2771 Coop-17 X-6417 12_N KidsOrRed Rubinette X-3263 EsopSpitz Fuji RedWinter RedWinterX3177 X-3318 RomBeauty 12_P F_Jonathan PRI668-100 Linda X-6823 Fantazja Prima Primula Sawa RallsJan F_Linda U1065 12_B GranSmith F_Wealthy PRI1661-2 Priam 12_O Cox Alwa F_Enterprise 12_L Macoun X-6808 McIntosh X-4638 GaEn F_Alwa D1955-44-220 2 families Dorianne F_Melba IngMarie PRI54-12 I_BB 12_K Ligol phenotyped JerseyBla Lobo D3_DLO D1972-10-33 F_Priscilla-NL Priscilla-NL I_CC F_IngMarie D1973-01-41 12_F separately LadyWill PinkLady D1980-15-25 F_Lobo Sampion 12_I FuGa 12_J F_LadyWill Lambourne FuPi JamesGr Braeburn LiAl DrOldenbu TeBr GaCr Telamon Rewena I_J F_JamesGr F_Braeburn RePir GaPi Pirol MeLi 67-47 WorcPearm Reanda AlPi PiGa Sa10 BX44.14 DLO-12 JoPr BeautBath PiRea AlSz Discovery DiPr

founders intermediate ancestors parents related FS families separate FS families supplementary FS families

4 Hélène MURANTY RGC8 21-23 June 2016 Phenotypes • 6 sites • 30 control varieties • 3 harvests (2003  2005) HiDRAS • fruit size scored on a 1-5 scale

• well-shaped distributions

5 Hélène MURANTY RGC8 21-23 June 2016 Phenotypes • 6 sites • 30 control varieties • 3 harvests (2003  2005) HiDRAS • fruit size scored on a 1-5 scale

• 2 harvests (2006 – 2007) DLO-12 • fruit weight

• well-shaped distributions • moderate to high correlations between years

6 Hélène MURANTY RGC8 21-23 June 2016 Phenotypes • 6 sites • 30 control varieties • 3 harvests (2003  2005) HiDRAS • fruit size scored on a 1-5 scale

• 2 harvests (2006 – 2007) DLO-12 • fruit weight

• 3 harvests (2004  2006) Te x Br • fruit weight • fruit height (H) and diameter (D)

• well-shaped distributions • moderate to high correlations between years • high correlation between diameter and weight within year

7 Hélène MURANTY RGC8 21-23 June 2016 Marker data

20K SNP array (Bianco et al 2014) scrutinizing for Mendelian inconsistencies

genetic mapping in 20 FS families scrutinizing for double recombinants

null-alleles focal point mapping across families additional SNP at the probe set (E. di Piero et al, in prep.) paralogous loci

haploblock markers building

8 Hélène MURANTY RGC8 21-23 June 2016 Marker data

20K SNP array (Bianco et al 2014) scrutinizing for Mendelian inconsistencies

genetic mapping in 20 FS families scrutinizing for double recombinants

null-alleles focal point mapping across families additional SNP at the probe set (E. di Piero et al, in prep.) paralogous loci

haploblock markers building with ~7 K robust markers

1112 haploblocks, 1281 cM 1.2 cM between adjacent HB

9 Hélène MURANTY RGC8 21-23 June 2016 Data analysis

• Phenotypic analysis 푌~푠푖푡푒 × 푦푒푎푟 + 푔푒푛표푡푦푝푒

adjusted means

• Pedigree-based QTL mapping : FlexQTL (Bink et al, 2014) – transmission of alleles through generations (IBD) – Bayesian method for QTL mapping • Bayes factor: test statistic to infer which model is more likely, e.g. 1 QTL vs. 0 QTL • Report QTL for Bayes factor ≥ 5 – additive QTL effects

10 Hélène MURANTY RGC8 21-23 June 2016 Bayes factor 1 QTL vs. 0 QTL QTL location, at chromosome level Fruit size Fruit weight HiDRAS DLO-12 TeBr

3 yrs 2003 2004 2005 2006 2007 2004 2005 2006

studies previous previous # indiv. 1059 678 623 677 220 164 105 96 111 LG1 30.2 29.9 9.3 3.4 2 LG2 5.8 1 LG9 7.1 10.6 1 LG10 4.6 8.8 5.3 2 LG11 10.9 3.9 3 LG12 10.2 8.2 5.3 4.6 1 LG14 8.6 10.1 0 LG15 8.6 5.8 5 LG16 7.7 9.1 2 LG17 4.2 10.6 3 Some QTL stable over years within datasets Most QTL specific of each dataset, except LG12 11 2 yearHélène-specific MURANTY QTL on LG15 RGC8 21-23 June 2016 Part of variance explained by QTL Fruit size Fruit weight HiDRAS DLO-12 TeBr 3 yrs 2003 2004 2005 2006 2007 2004 2005 2006 # indiv. 1059 678 623 677 220 164 105 96 111 LG1 25% 19% 9% 5% LG2 9% LG9 7% 15% LG10 13% 21% 15% LG11 5% 2% LG12 3% 5% 6% 8% LG14 9% 18% LG15 14% 15% LG16 7% 12% LG17 3% 14% Moderate to small effect QTL 12 Hélène MURANTY RGC8 21-23 June 2016 LG1: Rvi6 region 1 0 HB-01-1 HB-01-2 HB-01-2b HB-01-3 Q-haplotype q-haplotype HB-01-3b HB-01-4 2-2-2-Q-2-2-2 HB-01-4b HB-01-5 Dorianne, X-6808, X- 2-2-2-Q-2-4-2 HB-01-5b

HB-01-6 Qq 2-2-2-Q-2-4-3 HB-01-7 6564, X-3305, Galarina, HB-01-8 2-4-2-Q-4-4-2 13-9-3-q-8-3-3 HB-01-9 X-6683, RedWinterX3177, HB-01-10 4-4-2-Q-2-4-2 2-14-3-q-8-3-3 HB-01-11 X-3263, X-6679, X-6681, 4-4-2-Q-4-4-2 20 HB-01-12 HB-01-13 X-3259, X-6398 5-4-2-Q-4-4-2 HB-01-13b HB-01-14 7-6-2-Q-2-2-2

HB-01-15 Heterozygotes HB-01-16 2-2-2-Q-2-4-2 HB-01-17 Pirol, Sampion 2-2-2-q-2-9-2 HB-01-17b 4-4-2-Q-4-4-2 HB-01-18 HB-01-19 HB-01-20 HB-01-21 HB-01-22 13 different haplotypes in the 9 qq parents HB-01-23 HB-01-23b 7 different haplotypes in the 5 QQ parents 40 HB-01-24 FS-2004 HB-01-25

FS-2005

HB-01-25b FS-2003 HB-01-26 HB-01-27 FS-3yrs HB-01-28 HB-01-28b HB-01-29 HB-01-30 HB-01-31 HB-01-31b HB-01-32 HB-01-32b 9.1 cM 60 HB-01-32c HB-01-33 HB-01-34 HB-01-35 13 Hélène MURANTY RGC8 21-23 June 2016 Rvi6 region: linkage drag or effect of R gene ?

GoldenDel Clochard F2_26829-2-2 Cox D3_DLO McIntosh 2 4 5 4 13 4 4 5 * * 2 2 2 4 2 4 9 5 4 4 * * 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 4 2 4 Rvi6 8 7 12 4 4 20 2 2 4 4 5 4 3 4 9 4 3 5 2 5 2 2 3 2 3 2 2 2 3 3 2 3

X-6823 PRI14-152 IngMarie Lobo 2 4 2 13 5 4 2 4 2 4 2 9 4 4 2 4 2 2 2 3 2 2 2 2 2 4 4 8 4 12 2 4 4 4 4 3 4 9 5 18 2 2 2 3 2 2 3 4

PRI672-3 Elstar Priscilla-NL 13 4 4 4 2 5 9 2 4 4 2 9 3 2 2 2 2 3 8 2 4 12 2 8 3 4 4 9 5 4 3 2 2 2 3 2

X-4638 D1972-10-33 4 13 * * 4 9 4 29 2 3 2 2 4 8 * * 4 3 * * 2 3 2 3

Dorianne D1980-15-25 2.5 cM 4 13 2 5 9.1 cM 4 9 29 9 2 3 2 3 4 8 20 8 Rvi6 4 3 5 4 2 3 3 2

Soriano et al (2009) 14 Hélène MURANTY RGC8 21-23 June 2016 Rvi6 region: linkage drag or effect of R gene ?

GoldenDel Clochard F2_26829-2-2 Cox D3_DLO McIntosh 2 4 5 4 13 4 4 5 * * 2 2 2 4 2 4 9 5 4 4 * * 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 4 2 4 Rvi6 8 7 12 4 4 20 2 2 4 4 5 4 3 4 9 4 3 5 Vd3 2 5 2 2 3 2 3 2 2 2 3 3 2 3

X-6823 PRI14-152 IngMarie Lobo 2 4 2 13 5 4 2 4 2 4 2 9 4 4 2 4 2 2 2 3 2 2 2 2 2 4 4 8 4 12 2 4 4 4 4 3 4 9 5 18 2 2 2 3 2 2 3 4

PRI672-3 Elstar Priscilla-NL 13 4 4 4 2 5 9 2 4 4 2 9 3 2 2 2 2 3 8 2 4 12 2 8 3 4 4 9 5 4 3 2 2 2 3 2

X-4638 D1972-10-33 4 13 * * 4 9 4 29 2 3 2 2 4 8 * * 4 3 * * 2 3 2 3

Dorianne D1980-15-25 2.5 cM Parent D1980-15-25 segregates for 4 13 2 5 9.1 cM 4 9 29 9 Rvi6 but not for fruit weight  2 3 2 3 4 8 20 8 Rvi6 4 3 5 4 linkage drag 2 3 Vd3 3 2

Soriano et al (2009) 15 Hélène MURANTY RGC8 21-23 June 2016 LG12:12 a q allele coming from Golden Delicious

HB-12-1

HB-12-1b HB-12-2 FS-3yrs FW-2006 HB-12-3 HB-12-4 GoldenDel Clochard RomBeauty EsopSpitz F_Jonathan F_O53T136 F2_26829-2-2 Cox F_IngMarie Coop-17 FW-2007 HB-12-5 HB-12-6 HB-12-7 HB-12-8 HB-12-9 DLO-12 HB-12-10 HB-12-10b HB-12-11 HB-12-12 HB-12-13 Jonathan PRI14-152 X-6823 IngMarie Chantecler HB-12-14 HB-12-15 20 HB-12-15b HB-12-16 HB-12-16b HB-12-17 HB-12-18 HB-12-18b HB-12-19 FW HB-12-19b

HB-12-19c - Crandall PRI672-3 D1955-44-220 Elstar X-3259 DLO HB-12-20 FW HB-12-20b

HB-12-21 -

- DLO

HB-12-21b 12

HB-12-22 -

HB-12-23 2006 -

HB-12-24 12

HB-12-25 HB-12-26 -

HB-12-26b 2007

HB-12-27 FS

HB-12-28 O53T136 X-4638 D1973-01-41 -

40 HB-12-28b HiDRAS HB-12-28c HB-12-28d HB-12-29 HB-12-30 HB-12-30b

HB-12-31 -

HB-12-32 3yrs HB-12-32b HB-12-33 HB-12-33b HB-12-33c TN_R10A8 X-6808 Dorianne HB-12-33d HB-12-33e HB-12-33f HB-12-34 HB-12-35 HB-12-35b HB-12-35c HB-12-36 HB-12-37 HB-12-37b HB-12-38 60 X-6417 HB-12-39 HB-12-39b HB-12-40 16 HB-12-41 HB-12-41b Hélène MURANTY RGC8 21-23 June 2016 Conclusion

• QTL spread over 10 chromosomes • Stable over years and year-specific QTL • Moderate to small effects • Many regions too wide for MAS (except on LG1 and LG14)

• Use recombinants in Rvi6 region to reduce linkage drag

17 Hélène MURANTY RGC8 21-23 June 2016 Acknowledgements

 Genotypic data  Phenotypic data . M. Troggio, E. Banchi . Y. Noordijk . HiDRAS project HiDRAS . IsaFruit project  Genetic mapping . H. Koehorst- van Putten  Telamon x Braeburn pop° . M. di Guardo, S. Longhi . M. Davey, W. Keulemans . F. Costa, G. Pagliarani, T. Letschka, L. Lozano-Luis . S. Tartarini, E. di Pierro, L. Gianfranceschi Thank you for  Haploblock building . J. Kruisselbrink listening

18 Hélène MURANTY RGC8 21-23 June 2016