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Loci Important for Peach and Cherry Fruit Size and Quality What is known about their functional alleles? Ksenija Gasic, peach demonstration breeder, Clemson University Outline of Presentation Important Loci for Peach Important Loci for Cherry Functional alleles Jewels Important Loci Peach “How to” for Rosaceae Breeders? Peach fruit texture type • Freestone vs. clingstone and melting flesh vs. non-melting flesh • Freestone-Melting flesh (F-M) locus near the bottom of Prunus chromosome 4; − controlled by endoPG genes at the locus (and thus also referred to as “endoPG locus” or F-M-endoPG locus) Peach Fruit Texture Type - Marker • Primary alleles - Simple PCR-based SCAR marker targeting small indels in the first intron of two adjacent endoPG genes (“endoPG-6”). • Secondary alleles - SSR marker targeting a (CA)n di-nucleotide microsatellite in the promoters of two adjacent endoPG genes - (“endoPG-1-SSR”). This marker also distinguishes primary alleles, but can be readily PCR-multiplexed with the endoPG-6 marker “How To” for Rosaceae Breeders Example here is for peach fruit texture type Tables of functional genotypes (www.rosbreed.org/breeding/jewel-use) “How To” for Rosaceae Breeders Peach fruit texture type Important Loci Cherry “How to” for Rosaceae Breeders? The same gene responsible for red color in apple is thought to be responsible for red color in cherry and peach. Apple L9 Cherry G3 Peach G3 Cs locus MYB1/10 Fruit skin & flesh color MYB1/10 Fruit skin & flesh color (red color around stone) & QTL for flesh bleeding MYB1/10 Fruit skin color “How To” for Rosaceae Breeders Cherry fruit size Jewels Peach Important regions in the Prunus genome G1 G2 G3 G4 Mi D G6 G7 D Nl Dw Ps Ma Pi Evg G8 Cs Ag Y sharka G5 Pcp Fc Lb Sk G Sc Gr Sf E Br Dl F-M Peach, Nectarine S B Almond Si Apricot Important regions in the Prunus genome G1 G2 Sugars Mi G3 Flwg date G4 G5 Ripe date G6 D Xap Acidity Ripe date Sugars Sugars Skin blush D Xap Y Skin blush sharka Bruising Mealiness Pcp Fc Pl Acidity Xap Flwg date Ripe date Sugars Lb Xap Sc Gr Sk G Sf E Sugars Acidity Acidity Br Dl F-M Mealiness Bleeding Peach, Nectarine Flwg date Flwg date S Sugars B Xap Ripe date Sugars Evg G8 Nl Fruit size Acidity Ripe Dw date Ma Sugars Ps Skin blush Browning Ag Pi Flwg date Cs Bruising Ripe date Mealiness G7 Bruising Almond Si Apricot After QTL Discovery... Xap.Pp.CO-4.2 F-M locus QTL discovery - location Parent A Parent B R+ R+ 3 1 F f1 r -2 r-2 f f Segregating alleles - genetic variation Functional Allelic Variation Parent genepool RipeDate.Pp-4.1 Xap.Pp.CO-4.2 F-M locus Building blocks Available alleles - genetic variation Breeding with Valuable Alleles F_M RD Xap RD Xap blush New Cultivar Jewels Crafted masterpieces Jewels Cherry QTL Discovery... LG2 LG6 07FW EAA-MCCC-295 PR85 EPPCU3855-PR72 ME1-EM2-575 EMPaS01 UDP96-001 EAT-MCTC-375 BPPCT008 Ma014a PR127 EAA-MCCC-160 EAC-MCTA-225 CPPCT029 UDA-471 BPPCT006 EMPA004 CPSCT029 EAT-MCTC-272 BPPCT009 CPPCT023 EPPCU2828 PR86 EPPCU3090 EAA-MCAC-420 EAA-MCCC-130 UDAp-413 EAT-MCCC-100 UDP98-021 EPPB4227 Ma040a PrPFT PR93 EPPCU4092-PR56 EAC-MCTA-350 EAT-MCTC-142 EAC-MCTA-185 S-locus PR121 06FW 113.3 07Cell BPPCT006 EPPCU6536-PR69 EAA-MCAC-110 EAC-MCTA-525 EAC-MCTA-148 EPPCU8702 EAT-MCCC-150 Ma069a CPSCT038 PR96 UDA-059 BPPCT034 MA005c EAA-MCCC-370 UDAp-461 BPPCT002 MA007a PCHGMS1 UDA-005 CPSCT021 UCD-CH12 PceGA34 CPSCT034 06Cell 17.5 26.3 29.1 29.7 30.5 31.3 32.2 35.7 37.1 38.9 39.8 46.7 48.4 49.3 51.5 59.4 68.1 75.3 76.4 80.5 82.1 91.3 95.3 07FW EAC-MCTA-260 EPPCU9366-PR70 06FW 0.0 2.9 0.0 4.0 9.5 11.9 16.5 19.2 25.3 28.3 31.9 33.3 35.7 37.8 37.9 39.6 40.3 43.0 44.7 44.9 48.5 50.1 55.6 55.9 57.2 59.6 59.7 62.2 62.7 63.3 71.4 74.8 75.5 76.5 78.0 78.2 79.3 82.4 Simple Validation and Functional Genotype Effects Ran FlexQTL for simple validation Simple Validation and Functional Genotype Effects Calculated functional genotype effects probability BL BN AB AA AL fruit size probability 0 g BN AA AB AL BL firmness g/mm Alleles Genotypes Haplotypes Diplotypes EF NY UDA059 134 138 134 134 PR96 192 194 192 192 204 Gene190 controlling cell number 255 235 190 192 255 225 QTL CPSCT038 BPPCT034 BPPCT002 184 185 184 168 Ma007a 116 104 110 93 UDA005 222 218 222 218 In sweet cherry, 3 linkage group regions have been identified that contain genes that control fruit size. LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 Fruit Color Self Fertility Pollen & egg types for LGs 2, 3, & 6 Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture Questions? www.rosbreed.org