GDsnp00505, GDsnp00505 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00505
dbSNP IDss475882643
SNP Array ID
480K SNP array for apple:AX-105197740
IRSC 9K SNP array for apple:GDsnp00505
20K SNP array for apple:GDsnp00505
50K SNP array for apple:AX-105197740
TypeSNP
SNP AllelesT/G
Probe 1GDsnp00505.probe: ATTAGCTCTATATTTGTCTGCCATATTATAGATCTAACTGTTGGTTAATC
5' Flanking SequenceAAGAAAAGGTAGATTTATTTTTAAAAAGTTCAAAATTATATCATTAATAATTGAATTCCT TCCATCAAAAGCTTAATTACATGCTTACATATACTAATTA
3' Flanking SequenceGATTAACCAACAGTTAGATCTATAATATGGCAGACAAATATAGAGCTAATGGTACCTCCG GGCTTAAATTAAACCCGCCAAAATTGAAAAACATAGCAGG
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
Contact
NameDetails
Michela Troggio
First name:Michela
Last name:Troggio
Title:Researcher
Institution:Research and Innovation Centre, Fondazione Edmund Mach
Address:Via Edmund Mach, 1, 38010 San Michele All'adige TN, Italy
Country:Italy
Email:ti.hcamf@oiggort.alehcim
Phone:+39 0461 615111
Fax:+39 0461 650218
Analyses
This genetic_marker is derived from or has results from the following analyses
Analysis NameDate Performed
RosBREED SNP development2011-01-01
Publications
YearPublication
2010Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics. 2010 Oct; 42(10):833-839.
2014Bianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh). PloS one. 2014; 9(10):e110377.
2012Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC genomics. 2012; 13:203.
2016Bianco L, Cestaro A, Linsmith G, Muranty H, Denance C, Théron A, Poncet C, Micheletti D, Kerschbamer E, Di Pierro EA, Larger S, Pindo M, van de Weg E, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M. Development and validation of the Axiom(®) Apple480K SNP genotyping array. The Plant journal : for cell and molecular biology. 2016 Feb 26.
2020Rymenants M, van de Weg E, Auwerkerken A, De Wit I, Czech A, Nijland B, Heuven H, De Storme N, and Keulemans W. Detection of QTL for apple fruit acidity and sweetness using sensorial evaluation in multiple pedigreed full-sib families. Tree Genetics & Genomes 16, 71 (2020). https://doi.org/10.1007/s11295-020-01466-8
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple_HCGA_F12N/A8.23GDsnp00505View
2Apple_HC64_F12N/A9.28GDsnp00505View
3Apple_HCMO_F12N/A4.99GDsnp00505View
4Apple_HGMM_Consenus2N/A10.72GDsnp00505View
5Apple Integrated map2N/A27.4GDsnp00505View
6Apple-MM-F12N/A22c475882643View
7Apple-Honeycrisp_Consensus-F12N/A14.97GDsnp00505View
Sequence
>GDsnp00505 ID=GDsnp00505; Name=GDsnp00505; organism=Malus x domestica; type=genetic_marker; length=75bp
CAAAAGCTTAATTACATGCTTACATATACTAATTA[A/C]GATTAACCAA
CAGTTAGATCTATAATATGGCAGAC
Alignments
Feature NameTypeLocationAnalysis
MDC008933.302 contig MDC008933.302:3909..3909. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr02 chromosome Chr02:7602641..7602641+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr02 chromosome Chr02:7602591..7602691+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr02 chromosome Chr02:7602643..7602643. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation