Application of High Throughput Genotyping                                                                    Techniques in...
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Micheletti et al., 2012. application of high throughput genotyping, pag xx san diego


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Micheletti et al., 2012. application of high throughput genotyping, pag xx san diego

  1. 1. Application of High Throughput Genotyping Techniques in Peach Germplasm and Breeding Lines within the FruitBreedomics ProjectDiego Micheletti1 , Valeria Aramini2 , Pere Arús1 , Elisa Banchi3 , Teresa Barreneche4 , Daniele 1. IRTA. Centre of Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain.Bassi5 , Elisabeth Dirlewanger4 , Zhongshan Gao6 , Laura Gazza2 , Patrick Lambert7 , François 2. CRA - Fruit Tree Research Center, Roma, Italy. 3. IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele allAdige , Italy. 4. INRA. UR419, Unité de Recherches sur les Espèces Fruitières, Villenave dOrnon,Laurens8 , Xiongwei Li6 , Thierry Pascal7, Bénédicte Quilot-Turion7 , Laura Rossini5 , Michela France. 5. University of Milan, Milano, Italy. 6. Zhejiang University. Department of Horticulture, Hangzhou, China. 7.Troggio3 , Eric Van de Weg9 , Ignazio Verde2 , Maria Jose Aranzana1,£ INRA. UR1052, Génétique et Amélioration des Fruits et Légumes, Montfavet, France. 8. INRA, Institut de Recherche en Horticulture et Semences, Beaucouze, France. 9. Plant Breeding Wageningen University & Research centre, Wageningen, Netherlands £. Corresponding Author: mariajose.aranzana@irta.catAbstractPeach (Prunus persica (L.) Batsch) is one of the most economically important fruit Material and Methodscrops in temperate areas. Every year new varieties are released from breedingprogrammes trying to meet the requirements imposed by the market. Classical fruit tree Plant Material:breeding is generally slow and inefficient. Molecular markers could improve its FruitBreedomics WP3: about 1,500 individual belonging 18 Prunus crosses (12 peach x peachefficiency but, although nowadays many Mendelian traits are mapped in peach and and 6 interspecific) for QTL mapping through pedigree based association using flexQTL ( markers have been found to be linked to some of the key major genes, their use FruitBreedomics WP4: 1,300 peach cultivars from different origins, including some of thein breeding programmes is still limited. Main reasons for that are insufficient linkage founders of the current breeding programs for genome wide association mapping (GWA)between the markers and the genes and the lack of markers suitable for medium-highdegree of multiplexing. FruitBreedomics is a European project conceived with the Genotyping and data analysis:strategic goal to improve the efficiency of fruit breeding by bridging the gap between The 2,800 accessions of WP3 and WP4 were genotyped using the 9K peach SNP chipscientific knowledge and application in breeding. In the frame of this project, and with (Illumina Inc.), developed by the International Peach SNP Consortium (IPSC).the goal of obtaining SNPs closely linked to agronomic interesting traits, the 9K peach SNP genotypes were scored with the Genotyping Module of GenomeStudio Data AnalysisSNP chip (Illumina Inc.) developed by the International Peach SNP Consortium (IPSC) software (Illumina, Inc.) using the default parameters. The data obtained were filtered using:has been used in both segregating populations and in germplasm collections. This GenTrain Score > 0.4, GenCall 10% > 0.2 and missing data < 5%.chip, containing 8,144 SNPs scattered on the 8 peach chromosomes, has been used inabout 1,500 individuals belonging to eighteen Prunus crosses (12 peach x peach and 6interspecific) and in 1,300 peach cultivars from different origins, including some of thefounders of the current breeding programs. Comparison of the genetic map of chromosome 3 of two different crosses (P13 [Belbinette x Nectalady] and P01 [(IF7319828 x P. ferganensis) x IF7310828]).List of crosses genotyped in the WP3 of FruitBreedomics P01_Chr_3 P13_Chr_3 P01_Chr_3 P13_Chr_3 PopID Owner Type Parents 0.0 SNP_IGA_360780 SNP_IGA_360734 SNP_IGA_360658 SNP_IGA_361247 2.2 SNP_IGA_363408 P01 CRA-FRU (Rome) BC1 (IF7319828 x P. ferganensis) x IF7310828 SNP_IGA_363732 SNP_IGA_364777 SNP_IGA_363920 SNP_IGA_364517 SNP_IGA_364036 SNP_IGA_365173 SNP_IGA_364066 SNP_IGA_364441 2.7 SNP_IGA_364100 SNP_IGA_364601 SNP_IGA_364119 SNP_IGA_365180 SNP_IGA_364138 SNP_IGA_364502 SNP_IGA_364330 SNP_IGA_365146 P02 CRA-FRU (Rome) BC2 Romestar (P. persica x P.ferganensis) x BC125 3.6 0.0 2.2 SNP_IGA_360780 SNP_IGA_360734 SNP_IGA_360658 SNP_IGA_361247 SNP_IGA_364370 SNP_IGA_364562 SNP_IGA_363595 SNP_IGA_363408 SNP_IGA_365200 SNP_IGA_363732 SNP_IGA_364777 SNP_IGA_363920 SNP_IGA_364517 0.0 SNP_IGA_366432 SNP_IGA_366639 SNP_IGA_366151 SNP_IGA_365933 SNP_IGA_365455 SNP_IGA_364036 SNP_IGA_365173 SNP_IGA_364066 SNP_IGA_364441 SNP_IGA_367214 SNP_IGA_367668 SNP_IGA_367728 SNP_IGA_368077 4.9 P03 CRA-FRU (Rome) BC2 Romestar (P. persica x P. ferganensis) x BC161 5.9 2.7 SNP_IGA_364100 SNP_IGA_364601 SNP_IGA_364119 SNP_IGA_365180 SNP_IGA_366354 SNP_IGA_366041 SNP_IGA_365485 SNP_IGA_366141 SNP_IGA_364138 SNP_IGA_364502 SNP_IGA_364330 SNP_IGA_365146 SNP_IGA_367214 SNP_IGA_367359 SNP_IGA_367351 SNP_IGA_367365 SNP_IGA_364370 SNP_IGA_364562 SNP_IGA_363595 2.1 SNP_IGA_366639 snp_3_21905073 SNP_IGA_367684 SNP_IGA_367325 SNP_IGA_367365 SNP_IGA_367373 SNP_IGA_367351 SNP_IGA_367359 SNP_IGA_367373 SNP_IGA_367325 SNP_IGA_364441 SNP_IGA_364100 SNP_IGA_364562 SNP_IGA_364370 10.7 3.6 SNP_IGA_365200 SNP_IGA_360665 SNP_IGA_361595 SNP_IGA_366432 5.70.0 SNP_IGA_364138 SNP_IGA_364517 SNP_IGA_364601 SNP_IGA_364119 P04 INRA (Bordeaux) F2 Ferjalou Jalousia (P. persica) x Fantasia (P. persica) 11.6 12.4 4.9 SNP_IGA_366639 SNP_IGA_366151 SNP_IGA_365933 SNP_IGA_365455 snp_3_18270229 SNP_IGA_366354 SNP_IGA_366041 SNP_IGA_365485 SNP_IGA_366141 SNP_IGA_359881 SNP_IGA_359875 SNP_IGA_367214 SNP_IGA_367359 SNP_IGA_367351 SNP_IGA_367365 2.1 SNP_IGA_364330 SNP_IGA_365200SNP_IGA_367728 SNP_IGA_368077 SNP_IGA_367214 SNP_IGA_367668 SNP_IGA_364502 SNP_IGA_366639 snp_3_21905073 SNP_IGA_367684 SNP_IGA_367325 SNP_IGA_365485 SNP_IGA_365557 SNP_IGA_365647 SNP_IGA_365780 5.9 SNP_IGA_355801 SNP_IGA_358726 snp_scaffold_3_17617694 SNP_IGA_355957 SNP_IGA_367365 SNP_IGA_367373 SNP_IGA_367351 SNP_IGA_367359 13.2 SNP_IGA_367373 SNP_IGA_367325 SNP_IGA_365933 SNP_IGA_366041SNP_IGA_364562 SNP_IGA_364370 SNP_IGA_364441 SNP_IGA_364100 SNP_IGA_366151 SNP_IGA_366141 SNP_IGA_359035 P05 INRA (Avignon) BC2 (P. davidiana x Summergrand (P. persica)) x Zephyr (P. persica) 14.0 10.7 11.6 12.4 SNP_IGA_360665 SNP_IGA_361595 SNP_IGA_356344 SNP_IGA_359462 SNP_IGA_356179 SNP_IGA_357326 snp_3_18270229 SNP_IGA_355814 SNP_IGA_356407 SNP_IGA_357381 SNP_IGA_357335 SNP_IGA_359881 SNP_IGA_359875 7.35.7 SNP_IGA_363920 SNP_IGA_364066SNP_IGA_364601 SNP_IGA_364119 SNP_IGA_364138 SNP_IGA_364517 SNP_IGA_365357 SNP_IGA_365048 SNP_IGA_366354 SNP_IGA_365389SNP_IGA_364502 SNP_IGA_365180 SNP_IGA_364330 SNP_IGA_365200 SNP_IGA_364036 SNP_IGA_365455 SNP_IGA_365557 SNP_IGA_365647 SNP_IGA_365780 SNP_IGA_354647 SNP_IGA_355382 SNP_IGA_355590 SNP_IGA_354802 SNP_IGA_365485 15.7 SNP_IGA_355801 SNP_IGA_358726 snp_scaffold_3_17617694 SNP_IGA_355957 8.2 SNP_IGA_365173 SNP_IGA_365146SNP_IGA_366151 SNP_IGA_366141 SNP_IGA_365933 SNP_IGA_366041 13.2 SNP_IGA_354950 SNP_IGA_354980 P06 INRA (Avignon) F2 Summergrand (P. persica) x P. davidiana 16.5 14.0 SNP_IGA_359035 SNP_IGA_353861 SNP_IGA_353395 SNP_IGA_353457 SNP_IGA_353674 SNP_IGA_356344 SNP_IGA_359462 SNP_IGA_356179 SNP_IGA_357326 SNP_IGA_353937 SNP_IGA_354028 SNP_IGA_354000 SNP_IGA_354229 SNP_IGA_355814 SNP_IGA_356407 SNP_IGA_357381 SNP_IGA_357335 8.57.3 9.6 SNP_IGA_363203 SNP_IGA_363595SNP_IGA_365357 SNP_IGA_365048 SNP_IGA_363920 SNP_IGA_364066 SNP_IGA_363732 SNP_IGA_363408 SNP_IGA_363089 SNP_IGA_699172SNP_IGA_364036 SNP_IGA_365180 SNP_IGA_366354 SNP_IGA_365389 SNP_IGA_363060 SNP_IGA_365455 SNP_IGA_358419 SNP_IGA_358498 SNP_IGA_358948 SNP_IGA_358781 SNP_IGA_354647 SNP_IGA_355382 SNP_IGA_355590 SNP_IGA_354802 SNP_IGA_352618 SNP_IGA_352778 SNP_IGA_352841 SNP_IGA_352789 17.78.2 SNP_IGA_365173 SNP_IGA_365146 15.7 SNP_IGA_358339 SNP_IGA_358448 P07 INRA (Avignon) F2 Pamirskij (P. persica) x Rubira (P. persica) 17.3 16.5 SNP_IGA_354950 SNP_IGA_354980 SNP_IGA_352942 SNP_IGA_352749 SNP_IGA_353324 SNP_IGA_353088 SNP_IGA_353861 SNP_IGA_353395 SNP_IGA_353457 SNP_IGA_353674 SNP_IGA_353328 SNP_IGA_353369 SNP_IGA_353937 SNP_IGA_354028 SNP_IGA_354000 SNP_IGA_354229 8.5 9.6 SNP_IGA_356407 SNP_IGA_356442SNP_IGA_363732 SNP_IGA_363408 SNP_IGA_363203 SNP_IGA_363595 SNP_IGA_356701 SNP_IGA_356713 SNP_IGA_357013 SNP_IGA_356484SNP_IGA_363060 SNP_IGA_357326 SNP_IGA_363089 SNP_IGA_699172 SNP_IGA_356767 18.1 SNP_IGA_352362 SNP_IGA_352413 SNP_IGA_352122 SNP_IGA_357156 SNP_IGA_358033SNP_IGA_358948 SNP_IGA_358781 SNP_IGA_358419 SNP_IGA_358498 SNP_IGA_357396 SNP_IGA_357381 SNP_IGA_352618 SNP_IGA_352778 SNP_IGA_352841 SNP_IGA_352789 19.9 17.7 20.6 SNP_IGA_351612 SNP_IGA_358339 SNP_IGA_358448 SNP_IGA_357415 SNP_IGA_356947 SNP_IGA_357409 SNP_IGA_356469 P08 INRA (Avignon) F1 P. davidiana x Rubira (P. persica) 21.4 17.3 SNP_IGA_352942 SNP_IGA_352749 SNP_IGA_353324 SNP_IGA_353088 SNP_IGA_350488 SNP_IGA_350842 SNP_IGA_353328 SNP_IGA_353369 SNP_IGA_349233 SNP_IGA_349682 SNP_IGA_348931 SNP_IGA_349757 SNP_IGA_356407 SNP_IGA_356442 SNP_IGA_356701 SNP_IGA_356713 SNP_IGA_357423 SNP_IGA_357013 SNP_IGA_356484 SNP_IGA_356767 SNP_IGA_357326 SNP_IGA_355590 SNP_IGA_355382SNP_IGA_357396 SNP_IGA_357381 18.1 SNP_IGA_352362 SNP_IGA_352413 SNP_IGA_352122 SNP_IGA_350280 SNP_IGA_349789 SNP_IGA_350827 SNP_IGA_349707 19.9 21.1 SNP_IGA_357156 SNP_IGA_358033 SNP_IGA_357335 SNP_IGA_355801 23.0 20.6 SNP_IGA_351612 SNP_IGA_355814 SNP_IGA_356344SNP_IGA_357409 SNP_IGA_356469 SNP_IGA_357415 SNP_IGA_356947 SNP_IGA_356179 SNP_IGA_350620 SNP_IGA_349097 SNP_IGA_350573 SNP_IGA_349831 P09 INRA (Avignon) F1 Bolinia (P. persica) x Bolinia (P. persica) 24.7 21.4 SNP_IGA_350488 SNP_IGA_350842 SNP_IGA_350137 SNP_IGA_349932 SNP_IGA_351038 SNP_IGA_349233 SNP_IGA_349682 SNP_IGA_348931 SNP_IGA_349757 SNP_IGA_346608 SNP_IGA_350280 SNP_IGA_349789 SNP_IGA_350827 SNP_IGA_349707 22.2 23.3 21.1 SNP_IGA_354647 SNP_IGA_354980 SNP_IGA_354950 SNP_IGA_357423 SNP_IGA_353674 SNP_IGA_353457SNP_IGA_357335 SNP_IGA_355801 SNP_IGA_355590 SNP_IGA_355382 SNP_IGA_353937 SNP_IGA_353861 23.0 SNP_IGA_354028 SNP_IGA_354229SNP_IGA_356179 SNP_IGA_355814 SNP_IGA_356344 SNP_IGA_354000 25.5 SNP_IGA_346196 SNP_IGA_346164 SNP_IGA_350620 SNP_IGA_349097 SNP_IGA_350573 SNP_IGA_349831 SNP_IGA_352413 SNP_IGA_352362SNP_IGA_354950 SNP_IGA_352618 22.2 SNP_IGA_354647 SNP_IGA_354980 SNP_IGA_352749 P10 INRA (Avignon) F2 Weeping Flower Peach (P. persica) x Pamirskij (P. persica) 27.1 24.7 25.5 SNP_IGA_345700 SNP_IGA_343311 SNP_IGA_343501 SNP_IGA_345809 SNP_IGA_350137 SNP_IGA_349932 SNP_IGA_351038 SNP_IGA_346608 SNP_IGA_343432 SNP_IGA_343773 SNP_IGA_344064 SNP_IGA_344612 SNP_IGA_346196 SNP_IGA_346164 SNP_IGA_344712 SNP_IGA_344789 SNP_IGA_345704 SNP_IGA_343534 24.5 23.3 SNP_IGA_352841 SNP_IGA_352789SNP_IGA_353937 SNP_IGA_353861 SNP_IGA_353674 SNP_IGA_353457 SNP_IGA_353088 SNP_IGA_352942 SNP_IGA_353328 SNP_IGA_353324SNP_IGA_354000 SNP_IGA_353369 SNP_IGA_354028 SNP_IGA_354229 SNP_IGA_353395 25.6 SNP_IGA_351612 SNP_IGA_352122SNP_IGA_352749 SNP_IGA_352618 SNP_IGA_352413 SNP_IGA_352362 SNP_IGA_345797 Pp19Cl SNP_IGA_343311 SNP_IGA_343501 SNP_IGA_345809 SNP_IGA_345700 24.5 SNP_IGA_349996 SNP_IGA_312205SNP_IGA_353088 SNP_IGA_352942 SNP_IGA_352841 SNP_IGA_352789 SNP_IGA_350280 SNP_IGA_350137 P11 IRTA (Barcelona) F1 Big Top (P. persica) x Armking (P. persica) 29.6 27.1 SNP_IGA_343432 SNP_IGA_343773 SNP_IGA_344064 SNP_IGA_344612 SNP_IGA_332830 SNP_IGA_332587 SNP_IGA_332889 SNP_IGA_340471 SNP_IGA_344712 SNP_IGA_344789 SNP_IGA_345704 SNP_IGA_343534 SNP_IGA_332632 SNP_IGA_333074 SNP_IGA_332847 SNP_IGA_333908 SNP_IGA_345797 Pp19Cl 26.7 25.6 SNP_IGA_350620 SNP_IGA_350488SNP_IGA_353395 SNP_IGA_353369 SNP_IGA_353328 SNP_IGA_353324 SNP_IGA_350842 SNP_IGA_350827 SNP_IGA_351612 SNP_IGA_352122 SNP_IGA_351494 SNP_IGA_350909 SNP_IGA_351548 SNP_IGA_351567 30.4 SNP_IGA_331956 SNP_IGA_331961 SNP_IGA_332146 SNP_IGA_351542 SNP_IGA_349861SNP_IGA_350280 SNP_IGA_350137 SNP_IGA_349996 SNP_IGA_312205 SNP_IGA_350573 SNP_IGA_332830 SNP_IGA_332587 SNP_IGA_332889 SNP_IGA_340471 SNP_IGA_350620 SNP_IGA_350488 SNP_IGA_350842 SNP_IGA_350827 35.3 29.6 SNP_IGA_429668 SNP_IGA_429299 SNP_IGA_916433 SNP_IGA_913769 P12 IRTA (Barcelona) F1 Big Top (P. persica) x Nectaross (P. persica) 36.2 30.4 SNP_IGA_332632 SNP_IGA_333074 SNP_IGA_332847 SNP_IGA_333908 SNP_IGA_756400 SNP_IGA_432210 SNP_IGA_431437 SNP_IGA_331956 SNP_IGA_331961 SNP_IGA_332146 SNP_IGA_433036 SNP_IGA_432632 SNP_IGA_319344 Pp12Cl SNP_IGA_429668 SNP_IGA_429299 SNP_IGA_916433 SNP_IGA_913769 27.9 26.7 30.1 SNP_IGA_349932 SNP_IGA_351494 SNP_IGA_350909 SNP_IGA_351548 SNP_IGA_351567 SNP_IGA_348418 SNP_IGA_348289SNP_IGA_350573 SNP_IGA_351542 SNP_IGA_349861 SNP_IGA_348533 35.3 27.9 SNP_IGA_346432 SNP_IGA_346608 SNP_IGA_347013 SNP_IGA_346440 SNP_IGA_349932 36.2 SNP_IGA_319280 SNP_IGA_323191 SNP_IGA_319883 SNP_IGA_324067 SNP_IGA_756400 SNP_IGA_432210 SNP_IGA_431437 31.2 SNP_IGA_346745 SNP_IGA_348289 SNP_IGA_348533 30.1 SNP_IGA_348418 P13 IRTA (Barcelona) F1 Belbinette (P. persica) x Nectalady (P. persica) 37.0 SNP_IGA_324347 SNP_IGA_322925 SNP_IGA_324340 SNP_IGA_432536 SNP_IGA_433036 SNP_IGA_432632 SNP_IGA_319344 Pp12Cl SNP_IGA_433045 SNP_IGA_433050 SNP_IGA_433059 SNP_IGA_433063 SNP_IGA_319280 SNP_IGA_323191 SNP_IGA_319883 SNP_IGA_324067 SNP_IGA_433191 SNP_IGA_433197 SNP_IGA_433205 SNP_IGA_433302 SNP_IGA_324347 SNP_IGA_322925 SNP_IGA_324340 SNP_IGA_432536 31.2 33.5 SNP_IGA_344628 SNP_IGA_344712SNP_IGA_347013 SNP_IGA_346440 SNP_IGA_346432 SNP_IGA_346608 SNP_IGA_344789 SNP_IGA_344755 SNP_IGA_345700 SNP_IGA_345704 SNP_IGA_345419 SNP_IGA_345666 SNP_IGA_346745 SNP_IGA_345797 SNP_IGA_345809SNP_IGA_344789 SNP_IGA_344755 SNP_IGA_344628 SNP_IGA_344712 SNP_IGA_433542 SNP_IGA_433555 SNP_IGA_433575 SNP_IGA_433588 SNP_IGA_433045 SNP_IGA_433050 SNP_IGA_433059 SNP_IGA_433063 SNP_IGA_344612 SNP_IGA_345704 SNP_IGA_345419 SNP_IGA_345666 SNP_IGA_345700 37.0 34.6 33.5 P14 IRTA (Barcelona) F2 Texas (P. dulcis) x Earlygold (P. persica) SNP_IGA_433191 SNP_IGA_433197 SNP_IGA_433205 SNP_IGA_433302 SNP_IGA_433760 SNP_IGA_433596 SNP_IGA_433600 SNP_IGA_433772 SNP_IGA_433542 SNP_IGA_433555 SNP_IGA_433575 SNP_IGA_433588 SNP_IGA_435008 SNP_IGA_433760 SNP_IGA_433596 SNP_IGA_433600 SNP_IGA_433772 43.4 34.6 SNP_IGA_327678 SNP_IGA_345809 SNP_IGA_345797 SNP_IGA_344612 SNP_IGA_325166 SNP_IGA_325718 SNP_IGA_327093 SNP_IGA_325855 SNP_IGA_314521 SNP_IGA_314544 SNP_IGA_314503 SNP_IGA_314598 43.4 SNP_IGA_327678 SNP_IGA_326457 SNP_IGA_338469 SNP_IGA_325305 SNP_IGA_338615 SNP_IGA_435008 SNP_IGA_314588 SNP_IGA_314509 SNP_IGA_314631 SNP_IGA_315904 SNP_IGA_338533 SNP_IGA_860196SNP_IGA_327093 SNP_IGA_325855 SNP_IGA_325166 SNP_IGA_325718 SNP_IGA_339170 SNP_IGA_339037 P15 IRTA (Barcelona) BC1 MB1.37 (P. persica x P. dulcis) x Earlygold (P. persica) 38.6 38.6 SNP_IGA_314521 SNP_IGA_314544 SNP_IGA_314503 SNP_IGA_314598 SNP_IGA_316025 SNP_IGA_316047 SNP_IGA_317114 SNP_IGA_316877 SNP_IGA_314588 SNP_IGA_314509 SNP_IGA_314631 SNP_IGA_315904 SNP_IGA_317001 44.4 44.4 SNP_IGA_339178 SNP_IGA_339568SNP_IGA_325305 SNP_IGA_338615 SNP_IGA_326457 SNP_IGA_338469 SNP_IGA_367738 SNP_IGA_325850 SNP_IGA_339719 SNP_IGA_339586SNP_IGA_339170 SNP_IGA_339037 SNP_IGA_338533 SNP_IGA_860196 SNP_IGA_340016 SNP_IGA_316025 SNP_IGA_316047 SNP_IGA_317114 SNP_IGA_316877 SNP_IGA_339178 SNP_IGA_339568 SNP_IGA_367738 SNP_IGA_325850 40.3 SNP_IGA_314353 SNP_IGA_101376 SNP_IGA_321601 SNP_IGA_321580 SNP_IGA_336711 SNP_IGA_317001 SNP_IGA_339719 SNP_IGA_339586 SNP_IGA_340016 SNP_IGA_309338 SNP_IGA_309462 SNP_IGA_309473 SNP_IGA_309872 45.3 P16 UniMi-PTP (Milan) F1 Bolero (P. persica) x Oro (P. persica) 40.3 SNP_IGA_314353 SNP_IGA_309881 SNP_IGA_309554 SNP_IGA_310057 SNP_IGA_309635 SNP_IGA_309338 SNP_IGA_309462 SNP_IGA_309473 SNP_IGA_309872 SNP_IGA_310338 SNP_IGA_310467 SNP_IGA_310548 SNP_IGA_310553 45.3 47.7 SNP_IGA_700961 SNP_IGA_321565SNP_IGA_321580 SNP_IGA_336711 SNP_IGA_101376 SNP_IGA_321601 SNP_IGA_887061 SNP_IGA_894039 SNP_IGA_700961 SNP_IGA_321565 42.7 SNP_IGA_309881 SNP_IGA_309554 SNP_IGA_310057 SNP_IGA_309635 SNP_IGA_429127 SNP_IGA_428047 SNP_IGA_913769 SNP_IGA_428088 SNP_IGA_887061 SNP_IGA_894039 SNP_IGA_310566 SNP_IGA_310760 SNP_IGA_311336 SNP_IGA_311537 47.7 48.2 SNP_IGA_310338 SNP_IGA_310467 SNP_IGA_310548 SNP_IGA_310553 SNP_IGA_916433 SNP_IGA_428056SNP_IGA_913769 SNP_IGA_428088 SNP_IGA_429127 SNP_IGA_428047 42.7 P17 UniMi-PTP (Milan) F1 Contender (P. persica) x Elegant Lady (P. persica) SNP_IGA_311645 SNP_IGA_311856 SNP_IGA_312052 SNP_IGA_309737 SNP_IGA_310566 SNP_IGA_310760 SNP_IGA_311336 SNP_IGA_311537 SNP_IGA_312409 SNP_IGA_311645 SNP_IGA_311856 SNP_IGA_312052 SNP_IGA_309737 48.2 48.7 50.3 48.7 SNP_IGA_429299 SNP_IGA_429668 SNP_IGA_916433 SNP_IGA_428056 SNP_IGA_432210 SNP_IGA_429668 SNP_IGA_429299 SNP_IGA_307422 SNP_IGA_306400 SNP_IGA_306593 SNP_IGA_306604 SNP_IGA_312409 50.3 Pp12Cl SNP_IGA_433045 SNP_IGA_322925 SNP_IGA_433191 SNP_IGA_432210 43.5 SNP_IGA_307422 SNP_IGA_306400 SNP_IGA_306593 SNP_IGA_306604 SNP_IGA_306856 SNP_IGA_306650 SNP_IGA_306640 SNP_IGA_306900 Pp12Cl SNP_IGA_433045 SNP_IGA_322925 SNP_IGA_433191 SNP_IGA_324067 SNP_IGA_433205 SNP_IGA_433059 SNP_IGA_433542 P18 UniMi-PTP (Milan) F1 Max (P. persica) x Rebus (P. persica) 44.4 43.5 SNP_IGA_306856 SNP_IGA_306650 SNP_IGA_306640 SNP_IGA_306900 SNP_IGA_307037 SNP_IGA_307983 SNP_IGA_307230 SNP_IGA_307918 SNP_IGA_307037 SNP_IGA_307983 SNP_IGA_307230 SNP_IGA_307918 SNP_IGA_306024 SNP_IGA_305762 SNP_IGA_306147 SNP_IGA_305895 50.8 SNP_IGA_433555 SNP_IGA_433197SNP_IGA_433059 SNP_IGA_433542 SNP_IGA_324067 SNP_IGA_433205 SNP_IGA_433588 SNP_IGA_433302 SNP_IGA_433600 SNP_IGA_433575SNP_IGA_433588 SNP_IGA_433302 SNP_IGA_433555 SNP_IGA_433197 SNP_IGA_433772 SNP_IGA_433596 45.2 44.4 SNP_IGA_306024 SNP_IGA_305762 SNP_IGA_306147 SNP_IGA_305895 SNP_IGA_305449 SNP_IGA_305427 SNP_IGA_304930 50.8 45.2 SNP_IGA_305449 SNP_IGA_305427 SNP_IGA_304930 SNP_IGA_433760 SNP_IGA_324340SNP_IGA_433772 SNP_IGA_433596 SNP_IGA_433600 SNP_IGA_433575 SNP_IGA_433063 SNP_IGA_432632 46.0 SNP_IGA_304755 SNP_IGA_304773 SNP_IGA_304790 SNP_IGA_433036 SNP_IGA_433050SNP_IGA_433063 SNP_IGA_432632 SNP_IGA_433760 SNP_IGA_324340 SNP_IGA_435008 46.0 SNP_IGA_304755 SNP_IGA_304773 SNP_IGA_304790 SNP_IGA_300851 SNP_IGA_300877 SNP_IGA_300953 SNP_IGA_301843 SNP_IGA_300851 SNP_IGA_300877 SNP_IGA_300953 SNP_IGA_301843 SNP_IGA_319280 SNP_IGA_319883SNP_IGA_435008 SNP_IGA_320761 SNP_IGA_433036 SNP_IGA_433050 SNP_IGA_319344 SNP_IGA_301473 SNP_IGA_301707 SNP_IGA_301956 SNP_IGA_301913 52.4 SNP_IGA_319280 SNP_IGA_319883 SNP_IGA_319344 SNP_IGA_320761 SNP_IGA_301473 SNP_IGA_301707 SNP_IGA_301956 SNP_IGA_301913 52.4 SNP_IGA_650359 SNP_IGA_319294 SNP_IGA_650359 SNP_IGA_319294 47.6 SNP_IGA_302042 SNP_IGA_302772 SNP_IGA_302823 SNP_IGA_302830 SNP_IGA_317404 SNP_IGA_317307SNP_IGA_317281 SNP_IGA_317774 47.6 SNP_IGA_302042 SNP_IGA_302772 SNP_IGA_302823 SNP_IGA_302830 SNP_IGA_303514 SNP_IGA_303527 SNP_IGA_303535 SNP_IGA_303564 54.1 SNP_IGA_317404 SNP_IGA_317307 SNP_IGA_317281 SNP_IGA_317774 SNP_IGA_303514 SNP_IGA_303527 SNP_IGA_303535 SNP_IGA_303564 54.1 SNP_IGA_317767 SNP_IGA_317767 SNP_IGA_304082 SNP_IGA_304227 SNP_IGA_304307 snp_3_3770195 SNP_IGA_304082 SNP_IGA_304227 SNP_IGA_304307 snp_3_3770195 SNP_IGA_316315 SNP_IGA_316047SNP_IGA_316301 SNP_IGA_317001 SNP_IGA_316315 SNP_IGA_316047 SNP_IGA_316301 SNP_IGA_317001Number of polymorphic SNPs in 16 of the 18 crosses analyzed in 49.3 49.3 SNP_IGA_299341 SNP_IGA_300098 SNP_IGA_298943 SNP_IGA_299003 SNP_IGA_299341 SNP_IGA_300098 SNP_IGA_298943 SNP_IGA_299003 SNP_IGA_300389 SNP_IGA_300389 SNP_IGA_298139 SNP_IGA_297841 SNP_IGA_298109 SNP_IGA_298287 SNP_IGA_298139 SNP_IGA_297841 SNP_IGA_298109 SNP_IGA_298287 55.8 55.8 56.7 56.7 SNP_IGA_317114 SNP_IGA_316615 SNP_IGA_317114 SNP_IGA_316615 SNP_IGA_315904 SNP_IGA_314503SNP_IGA_314353 SNP_IGA_314509 SNP_IGA_315904 SNP_IGA_314503 SNP_IGA_314353 SNP_IGA_314509 SNP_IGA_314521 SNP_IGA_314544SNP_IGA_314588 SNP_IGA_314631 SNP_IGA_314521 SNP_IGA_314544 SNP_IGA_314588 SNP_IGA_314631 SNP_IGA_298449 SNP_IGA_298417 SNP_IGA_298154 SNP_IGA_298541FruitBreedomics. 50.1 50.1 SNP_IGA_298449 SNP_IGA_298417 SNP_IGA_298154 SNP_IGA_298541 SNP_IGA_298636 SNP_IGA_298575 SNP_IGA_298580 SNP_IGA_298636 SNP_IGA_298575 SNP_IGA_298580 SNP_IGA_296900 SNP_IGA_297128 SNP_IGA_296886 SNP_IGA_297495 SNP_IGA_296900 SNP_IGA_297128 SNP_IGA_296886 SNP_IGA_297495 51.7 51.7 SNP_IGA_297497 SNP_IGA_297507 SNP_IGA_296682 SNP_IGA_297497 SNP_IGA_297507 SNP_IGA_296682The inter-specific crosses (P. persica x other Prunus) are reported in red and the intra-specific 52.6 52.6 55.8 SNP_IGA_296290 SNP_IGA_296355 SNP_IGA_296562 SNP_IGA_296203 SNP_IGA_296290 SNP_IGA_296355 SNP_IGA_296562 SNP_IGA_296203 SNP_IGA_296553 SNP_IGA_296553 SNP_IGA_295978 67.2 67.2 68.2 68.2 SNP_IGA_291021 SNP_IGA_898654SNP_IGA_291055 SNP_IGA_291021 SNP_IGA_898654 SNP_IGA_291055 SNP_IGA_897342 SNP_IGA_897342 55.8 SNP_IGA_295978crosses (P. persica x P. persica) are reported in blue. 56.7 56.7 59.1 SNP_IGA_295145 SNP_IGA_295649 SNP_IGA_295644 SNP_IGA_295658 SNP_IGA_295145 SNP_IGA_295649 SNP_IGA_295644 SNP_IGA_295658 SNP_IGA_295664 SNP_IGA_295763 SNP_IGA_295664 SNP_IGA_295763 SNP_IGA_294410 SNP_IGA_294410 59.1 SNP_IGA_291055 SNP_IGA_291021 SNP_IGA_291987 SNP_IGA_292008 60.8 SNP_IGA_291055 SNP_IGA_291021 SNP_IGA_291987 SNP_IGA_292008 60.8 SNP_IGA_292307 SNP_IGA_898654 SNP_IGA_293254 SNP_IGA_292307 SNP_IGA_898654 SNP_IGA_293254 SNP_IGA_311537 SNP_IGA_311645 SNP_IGA_311856 SNP_IGA_311941 76.6 SNP_IGA_311537 SNP_IGA_311645 SNP_IGA_311856 SNP_IGA_311941 SNP_IGA_312052 76.6 3000 77.6 77.6 SNP_IGA_312052 SNP_IGA_313464 SNP_IGA_313615 SNP_IGA_313623 SNP_IGA_313117 SNP_IGA_313117 SNP_IGA_313464 SNP_IGA_313615 SNP_IGA_313623 2500 2000 Preliminary results from the genotyping of the 8,144 SNP of the 9k array on 1500 1,300 accessions of Prunus 1000 500 Failed 1975 0 MonomorphicNumber of polymorphic SNPs in each chromosome in 16 of the 18 crosses of analyzed 416 Polymorphicin FruitBreedomics (WP3). 5753 P06 and P07 not yet analyzed Chro P01 P02 P03 P04 P05 P08 P09 P10 P11 P12 P13 P14 P15 P16 P17 P18 moso me 1 458 243 315 194 315 301 219 341 200 336 308 399 376 235 196 259 MAF 2 488 463 435 222 442 135 267 184 175 377 390 496 354 343 463 256 3 257 320 225 103 229 222 165 218 200 356 281 272 262 62 290 178 4 596 597 516 366 441 378 259 296 365 429 367 572 525 599 450 430 5 230 219 188 176 172 135 101 165 209 153 119 194