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Analysis of genetic control of fruit size in apple 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 Discovery × Fiesta 251 weight (2003) X X X X X X X X Kenis et al (2008) Telamon × Braeburn 199 / weight, X X X X X X X 165 diameter, height Royal Gala × 572 Devoghalaere et al Braeburn weight X X X X X X (2012) Starkrimson × 123 Granny Smith Chang et al (2014) Jonathan × Golden 144 / weight, X X X X Delicious 140 diameter, length Fuji × Delearly 86 Fuji × Cripps Pink 73 size, weight, Costa (2015) Golden Delicious × 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 Idared Florina 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 Winesap 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 Wealthy Fantazja Prima Primula Sawa RallsJan F_Linda U1065 12_B GranSmith F_Wealthy PRI1661-2 Priam Enterprise 12_O Melba Cox Alwa F_Enterprise 12_L Macoun Melrose X-6808 McIntosh X-4638 GaEn F_Alwa D1955-44-220 2 families Dorianne F_Melba IngMarie Elstar PRI54-12 I_BB 12_K Ligol phenotyped JerseyBla Lobo D3_DLO D1972-10-33 F_Priscilla-NL Priscilla-NL Liberty I_CC F_IngMarie D1973-01-41 12_F separately LadyWill PinkLady D1980-15-25 F_Lobo Sampion Alkmene Pinova 12_I Clivia 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 .
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    PROGRESS IN APPLE IMPROVEMENT J. R. MAGNESS, Principal Pomologisi, 13ivision of Fruit and Vegetable Crops and Diseases, liureau of Plant Industry ^ A HE apple we liave today is J^u" rciuovod from tlic "gift of the gods'' wliich prehistoric man found in roaming the woods of western Asia and temperate Europe. We can judge that apple only by the wild apples that grow today in the area between tlie Caspian Sea and Europe, which is believed to be the original habitat of the apple. These apples are generally onl>r 1 to 2 inches in diameter, are acici and astringent, and are far inferior io the choice modern horticultural varieties. The improvement of the apple through tlie selection of the best types of the wild seedlings goes far baclv to the very beginning of history. Methods of budding and grafting fiiiits were Icnown more than 2,000 years ago. According to linger, C^ato (third century, B. C.) knew seven different apple varieties, l^liny (first centiuy, A. D.) knew^ 36 different kinds. By tlie time the iirst settlers froni Europe were coming to the sliores of North America., himdreds of apple varieties had been named in European <M)unt]*ies, The superior varieties grown in l^^urope in the seventeenth century had, so far as is known, all developed as chance seedlings, but garden- ers had selected the best of the s(>edling trees îvnd propagated them vegetatively. The early American settlers, ptirticiilarly those from the temperate portions of Europe, who came to the eastern coast of North Amer- ica, brought with them seeds and in some cases grafted trees of European varieties.
  • INF03 Reduce Lists of Apple Varieites

    INF03 Reduce Lists of Apple Varieites

    ECE/TRADE/C/WP.7/GE.1/2009/INF.3 Specialized Section on Standardization of Fresh Fruit and Vegetables Fifty-fifth session Geneva, 4 - 8 May 2009 Items 4(a) of the provisional agenda REVISION OF UNECE STANDARDS Proposals on the list of apple varieties This note has been put together by the secretariat following the decision taken by the Specialized Section at its fifty-fourth session to collect information from countries on varieties that are important in international trade. Replies have been received from the following countries: Canada, Czech Republic, Finland, France, Germany, Italy, Netherlands, New Zealand, Poland, Slovakia, South Africa, Sweden, Switzerland and the USA. This note also includes the documents compiled for the same purpose and submitted to the fifty-second session of the Specialized Section. I. Documents submitted to the 52nd session of the Specialized Section A. UNECE Standard for Apples – List of Varieties At the last meeting the 51 st session of the Specialized Section GE.1 the delegation of the United Kingdom offered to coordinate efforts to simplify the list of apple varieties. The aim was to see what the result would be if we only include the most important varieties that are produced and traded. The list is designed to help distinguish apple varieties by colour groups, size and russeting it is not exhaustive, non-listed varieties can still be marketed. The idea should not be to list every variety grown in every country. The UK asked for views on what were considered to be the most important top thirty varieties. Eight countries sent their views, Italy, Spain, the Netherlands, USA, Slovakia, Germany Finland and the Czech Republic.
  • Molecular and Genetic Regulation of Sensory Quality of Climacteric Fruit

    Molecular and Genetic Regulation of Sensory Quality of Climacteric Fruit

    Molecular and Genetic Regulation of Sensory Quality of Climacteric Fruit I. El-Sharkawy, D. Manriquez, F.B. Flores, A. Latché and J.C. Pech INRA/INPT-ENSAT "Génétique et Biotechnologie des fruits" (UMR 990) 31326 Castanet-Tolosan Cédex France Keywords: quality, shelf life, flavor, breeding, melon, aroma biosynthesis, ethylene Abstract The sensory quality of fruit has become a major criterion in making the purchasing decision by consumers. Breeding programs have mainly been directed, from the post-harvest stand point, towards improving shelf-life. Chance seedlings or mutants with improved agronomic traits and/or extended shelf-life have been used for introgressing the long shelf-life character and eventually improved sensory quality traits in commercial genotypes of apple, melon or tomato. Because the plant hormone ethylene plays a central role in both storability and ripening of climacteric fruit, the generation by biotechnology of ethylene-inhibited fruit has offered a powerful tool to better understand, at the molecular and genetic level, the inter- relations between storability and sensory quality. In the melon, inhibition of ethylene synthesis results is a strong inhibition of the synthesis of aroma volatiles while the accumulation of sugars is not affected or is even improved. The softening of the flesh is strongly affected but not abolished. Mid or long shelf-life melons generated by classical breeding present the same behavior. The generation of recombinant inbred lines by crossing a typical climacteric melon (Cantaloupe Charentais of the cantalupensis group) with a non climacteric melon (PI161375 of the agrestis chinensis group) allowed to demonstrate that the climacteric character is conferred by 2 duplicated loci only, which are of great importance for the regulation of storability and sensory quality.
  • Summer Apple Varieties

    Summer Apple Varieties

    Summer Apple Varieties Quentin B. Zielinski Andrea Mackey Joy Stockman Sue Joiner Agricultural Experiment Station Oregon State College Corvallis Circular of Information 586 January 1958 Neat Summer Apple Varieties Quentin B. Zielinski, Andrea Mackey, Joy Stockman, and Sue Joiner* Introduction Home gardeners are showing an increasing interest in new summer apple varieties. Many make attractive additions to the yard and also produce an abundance of fruit with good eating and cooking qualities. These new apples {ire improved crosses or are sports of such older varieties as Astrachan, Early Harvest, and Duchess; some are introductions from other growing areas. Characteristics of raw fruit and results of cooking tests are presented here. Judges evaluated flavor, color, and texture for the apples when raw, as sauce, or as pie. Yellow Transparent was used as a standard of comparison for early varieties ripening before August 15th; while Gravenstein was used for the later ripening apples. By making compari- sons with these well-known varieties it is possible to say whether the new apples are as well, or better suited for home use. Twenty new apples, as well as Gravenstein and Yellow Transparent, are described. Varieties are arranged according to their dates of ripening, beginning in early July and ex- tending through the middle of September. Details regarding cultural requirements of trees and other information may be found in Oregon Agricultural Experiment Station Bulletin No. 563, Apple Varieties for Oregon. Most summer apples are firm and tart when first picked. They do not store well at room temperature however, becoming mealy after a few days.
  • Pipfruit in Holland (Slideshow)

    Pipfruit in Holland (Slideshow)

    Fruitconsult - www.fruitconsult.com Fruitconsult - www.fruitconsult.com • Dutch consulting company • Working area • Based in Randwijk, – Holland Netherlands – Belgium • 7 advisors – Germany – pip- and stone fruits – Scandinavia – different specialists – Poland • nutrition/irrigation – Tsjechien • plant management – Hungary • plant protection – Italy – United Kingdom Pip fruit industry in Holland - mainly situated on river or sea sedi- Pip fruit industry in Holland ments (high pH -clays soils) - 700-900 mm rainfall/yr - 1500 professional growers - moderate climate # family run businesses - 5 main area’s - 17.000 ha pip fruit - Betuwe (Tiel/Geldermalsen) - Average farm size 11 ha - Utrecht - Zeeland (Goes) - number of growers decreases - Noord Holland (Hoorn) - average farm size increases quite fast - Zuid Limburg (Maastricht) Average production level: Apple industry in Holland 1990: 34.000kg/ha 1990: 20.000 ha 2009:45.000 kg/ha 2010: 8.500 ha Upper 10%: 60-65.000 kg/ha 1 Development in apple varieties in Nl Club varieties – Elstar 40% of production – Jonagold30% – Golden delicious6% – Boskoop6% – Cox‘s, Delcorf etc8% – New varieties • Kanzi400 ha • Rubens150 ha • Junami400 ha • Wellant100 ha • Pinova - Evelina • Topaz - Evita • Maribelle Club varieties Club varieties – only superior quality is sold • Strong tendency to club varieties – apples with minor deficiencies: <45% colour, light hail damage etc • 2009 -> 1000 ha = 12-13% -> industry • In 2009 10.000 tonnes premium • High and early production in order to keep the quality of different