GDsnp00053, GDsnp00053 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00053
Aliasss475882935
rs267615875
GD_00053_L9_PA
dbSNP IDss475882935
SNP Array ID
480K SNP array for apple:GDsnp00053
IRSC 9K SNP array for apple:GDsnp00053
20K SNP array for apple:GDsnp00053
50K SNP array for apple:GDsnp00053
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00053.probe: AGCCTTCAGCTTCACTCCAAACCGATCTCTTCATCTTACGTCCTTTTTAA
5' Flanking SequenceAGAAAATAGATTTGACAACCTGGATCGTATCGTTAAATTACGTACTCCCTAGCCTTCAGC TTCACTCCAAACCGATCTCTTCATCTTACGTCCTTTTTAA
3' Flanking SequenceCTCGCAACAGTGGGCCTCCTCCACATCCCAGTGCTGCAGATGAGGAAAAGACCCCTTCAA CTTTTGCCAATCTTTGTCCCATTTCTTCAAGTACTTGAGA
SpeciesMalus x domestica
PolymorphismP_ GDsnp00053
Publication[view all]
ContactMichela Troggio
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.
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
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
Relationships

The following marker_locus feature(s) are an instance of this genetic_marker:

Feature NameUnique NameSpeciesType
GDsnp00053GDsnp00053Malus x domesticamarker_locus
GD_SNP00053GD_SNP00053Malus x domesticamarker_locus
GDsnp00053GDsnp00053-47.652Malus x domesticamarker_locus


The following probe feature(s) are associated with this genetic_marker:

Feature NameUnique NameSpeciesType
probeGDsnp00053.probeMalus x domesticaprobe


Analyses
This genetic_marker is derived from or has results from the following analyses
Analysis NameDate Performed
RosBREED SNP development2011-01-01
Sequence
>GDsnp00053 ID=GDsnp00053|Name=GDsnp00053|organism=Malus x domestica|type=genetic_marker|length=75bp
TCCAAACCGATCTCTTCATCTTACGTCCTTTTTAA[C/T]CTCGCAACAG
TGGGCCTCCTCCACATCCCAGTGCT
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple Integrated map9N/A53.4GDsnp00053View
2Apple-RGxPI6-F1LG9N/A56.5GDsnp00053View
3Apple-FjxPL-F1-2013LG9N/A58.94GDsnp00053View
4Apple-RosBREED-3.9K-20199N/A47.65GDsnp00053View
5Apple-GDxBr-F1-2013LG9N/A50.56GD_SNP00053View
6Apple-Honeycrisp_Consensus-F19N/A47.65GDsnp00053View
Alignments
Feature NameTypeLocationAnalysis
MDC015142.561 contig MDC015142.561:12179..12179. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr09 chromosome Chr09:25961454..25961454- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr09 chromosome Chr09:25961404..25961504+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr09 chromosome Chr09:25961456..25961456. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation