GDsnp00388, GDsnp00388 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00388
dbSNP IDss475882758
SNP Array ID
480K SNP array for apple:AX-105176054
IRSC 9K SNP array for apple:GDsnp00388
20K SNP array for apple:GDsnp00388
50K SNP array for apple:AX-105176054
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00388.probe: GCCGAAAGCGTCAGCTTTGATCCATTCCTAACACTTACCACAGAATTCAA
5' Flanking SequenceAGCACTCCATCTTTGCAATTTACCCTAATTCATCGTCCGAAATCTGGGGTGCCGAAAGCG TCAGCTTTGATCCATTCCTAACACTTACCACAGAATTCAA
3' Flanking SequenceTTGTTGGCTTGTAGTATAGCTGATGGAGCACTTCTCTTCCCTTCGAGTTCCTCAATGCTC GTTGGGAACTTAGGCTGCTCCACCGGTCCATATACATCAT
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.
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 Integrated map4N/A58.6GDsnp00388View
2Apple-RosBREED-3.9K-20194N/A55.68GDsnp00388View
3Apple-BB-F14N/A63.37GDsnp00388View
4Apple-NC-F14N/A73.28GDsnp00388View
5Apple-NCZFBB-consensus4N/A61.61GDsnp00388View
6Apple-ZF-F14N/A74.66GDsnp00388View
7Apple-consensus-Allard-2016LG4N/A70.05GDsnp00388View
8Apple-Honeycrisp_Consensus-F14N/A55.68GDsnp00388View
9Apple-GDxBr-F1-2013LG4N/A64.63GD_SNP00388View
Sequence
>GDsnp00388 ID=GDsnp00388; Name=GDsnp00388; organism=Malus x domestica; type=genetic_marker; length=75bp
TTTGATCCATTCCTAACACTTACCACAGAATTCAA[C/T]TTGTTGGCTT
GTAGTATAGCTGATGGAGCACTTCT
Alignments
Feature NameTypeLocationAnalysis
MDC011727.163 contig MDC011727.163:17780..17780. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr04 chromosome Chr04:30478166..30478166- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr04 chromosome Chr04:30478116..30478216- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr04 chromosome Chr04:30478168..30478168. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation