GDsnp00488, GDsnp00488 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00488
dbSNP IDss475882823
SNP Array ID
480K SNP array for apple:AX-105192056
IRSC 9K SNP array for apple:GDsnp00488
20K SNP array for apple:GDsnp00488
50K SNP array for apple:AX-105192056
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00488.probe: TTAGGAAGGCTTCGTTGAACAGCATGATGTGCTCAGTTTTTGGACGTAAA
5' Flanking SequenceGGAAGGTGATCGGACCAGTTCAACTTTCCCAACATATCATAACCTTCATCGACAAGTCGA CTCAACTCCTCGGTCTCTTCATTCGACGAACTCAGCTCGT
3' Flanking SequenceTTTACGTCCAAAAACTGAGCACATCATGCTGTTCAACGAAGCCTTCCTAAGTATGTCGCG GACAAGGAAGCTGTTGTTACAACTTGTCCAGATAAGGGAC
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 map6N/A43.1GDsnp00488View
2Apple-RosBREED-3.9K-20196N/A33.08GDsnp00488View
3Apple-BB-F16N/A38.14GDsnp00488View
4Apple-NC-F16N/A41.78GDsnp00488View
5Apple-NCZFBB-consensus6N/A38.02GDsnp00488View
6Apple-ZF-F16N/A17.06GDsnp00488View
7Apple-consensus-Allard-2016LG6N/A20GDsnp00488View
8Apple-Honeycrisp_Consensus-F16N/A33.08GDsnp00488View
Sequence
>GDsnp00488 ID=GDsnp00488; Name=GDsnp00488; organism=Malus x domestica; type=genetic_marker; length=75bp
CTCCTCGGTCTCTTCATTCGACGAACTCAGCTCGT[A/G]TTTACGTCCA
AAAACTGAGCACATCATGCTGTTCA
Alignments
Feature NameTypeLocationAnalysis
MDC012901.372 contig MDC012901.372:6414..6414. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr06 chromosome Chr06:25791597..25791597- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr06 chromosome Chr06:25791547..25791647+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation