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Similaire à Micheletti et al., 2012. application of high throughput genotyping, pag xx san diego
Similaire à Micheletti et al., 2012. application of high throughput genotyping, pag xx san diego (20)
Plus de fruitbreedomics (20)
Micheletti et al., 2012. application of high throughput genotyping, pag xx san diego
- 1. Application of High Throughput Genotyping
Techniques in Peach Germplasm and Breeding
Lines within the FruitBreedomics Project
Diego 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 all'Adige , Italy. 4. INRA. UR419, Unité de Recherches sur les Espèces Fruitières, Villenave d'Ornon,
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.cat
Abstract
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit Material and Methods
crops in temperate areas. Every year new varieties are released from breeding
programmes 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 peach
efficiency but, although nowadays many Mendelian traits are mapped in peach and and 6 interspecific) for QTL mapping through pedigree based association using flexQTL
(http://www.biometris.wur.nl/UK/Software/FlexQTL/).
SSR 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 the
in 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-high
degree 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 chip
scientific 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 Analysis
SNP 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 in
about 1,500 individuals belonging to eighteen Prunus crosses (12 peach x peach and 6
interspecific) and in 1,300 peach cultivars from different origins, including some of the
founders 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_317001
Number 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_298541
FruitBreedomics. 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_296682
The 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_295978
crosses (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
Monomorphic
Number of polymorphic SNPs in each chromosome in 16 of the 18 crosses of analyzed 416
Polymorphic
in 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
5 230 219 188 176 172 135 101 165 209 153 119 194 149 174 113 120 Conclusion:
6 335 290 182 282 281 221 213 328 117 310 258 345 294 137 209 251
Considering the 16 segregating populations already analyzed, the average number of
7 243 278 286 311 251 137 208
![Application of High Throughput Genotyping
Techniques in Peach Germplasm and Breeding
Lines within the FruitBreedomics Project
Diego 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 all'Adige , Italy. 4. INRA. UR419, Unité de Recherches sur les Espèces Fruitières, Villenave d'Ornon,
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.cat
Abstract
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit Material and Methods
crops in temperate areas. Every year new varieties are released from breeding
programmes 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 peach
efficiency but, although nowadays many Mendelian traits are mapped in peach and and 6 interspecific) for QTL mapping through pedigree based association using flexQTL
(http://www.biometris.wur.nl/UK/Software/FlexQTL/).
SSR 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 the
in 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-high
degree 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 chip
scientific 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 Analysis
SNP 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 in
about 1,500 individuals belonging to eighteen Prunus crosses (12 peach x peach and 6
interspecific) and in 1,300 peach cultivars from different origins, including some of the
founders 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_317001
Number 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_298541
FruitBreedomics. 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_296682
The 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_295978
crosses (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
Monomorphic
Number of polymorphic SNPs in each chromosome in 16 of the 18 crosses of analyzed 416
Polymorphic
in 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
5 230 219 188 176 172 135 101 165 209 153 119 194 149 174 113 120 Conclusion:
6 335 290 182 282 281 221 213 328 117 310 258 345 294 137 209 251
Considering the 16 segregating populations already analyzed, the average number of
7 243 278 286 311 251 137 208](https://image.slidesharecdn.com/michelettietal-2012-applicationofhighthroughputgenotypingpagxxsandiego-120203013619-phpapp01/85/micheletti-et-al-2012-application-of-high-throughput-genotyping-pag-xx-san-diego-1-320.jpg)
