GDsnp00619, GDsnp00619 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00619
dbSNP IDss475882742
SNP Array ID
480K SNP array for apple:AX-115181993
IRSC 9K SNP array for apple:GDsnp00619
20K SNP array for apple:GDsnp00619
50K SNP array for apple:AX-105221532
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00619.probe: CGTGGAGTCAAACCTATTTTGATGAGCCATGCATACAAAACATACTCCGA
5' Flanking SequenceTACTAGAATGCCCTCAACTTTATCCGGATTTATATTAAGTTTGACTCGGTATGAATTCAG GATTATCTTACCGTTTAACGACAATTCTTATGCTTACTTC
3' Flanking SequenceTCGGAGTATGTTTTGTATGCATGGCTCATCAAAATAGGTTTGACTCCACGTTTGCGTTCT CCATTAGAGATGATCTAATAAGAGCATTCACTCTAACATT
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
Cindy F. Verdu
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
Cindy F. Verdu
First name:Cindy
Last name:Verdu
Title:Researcher
Institution:INRA
Address:INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouze, France
Country:France
Email:cindyverdu@gmail.com
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.
2013Troggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin. PloS one. 2013; 8(6):e67407.
2014Verdu CF, Guyot S, Childebrand N, Bahut M, Celton J-M, Gaillard S, Lasserre-Zuber P, Troggio M, Guilet D, Laurens F. QTL Analysis and Candidate Gene Mapping for the Polyphenol Content in Cider Apple. PLoS ONE. 2014; 9(10):e107103.
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/A49.8GDsnp00619View
2Apple-M432-20134N/A55.95GDsnp00619View
3Apple-M432-2013-physical-Malus-domestica4N/A18467352GDsnp00619View
4Apple-BB-F14N/A56.25GDsnp00619View
5Apple-NC-F14N/A63.97GDsnp00619View
6Apple-NCZFBB-consensus4N/A54.55GDsnp00619View
7Apple-ZF-F14N/A65.07GDsnp00619View
8Apple-X5210X8402-F1-X5210LG4N/A63.5GD_SNP00619View
Sequence
>GDsnp00619 ID=GDsnp00619; Name=GDsnp00619; organism=Malus x domestica; type=genetic_marker; length=201bp
TACTAGAATGCCCTCAACTTTATCCGGATTTATATTAAGTTTGACTCGGT
ATGAATTCAGGATTATCTTACCGTTTAACGACAATTCTTATGCTTACTTC
RTCGGAGTATGTTTTGTATGCATGGCTCATCAAAATAGGTTTGACTCCAC
GTTTGCGTTCTCCATTAGAGATGATCTAATAAGAGCATTCACTCTAACAT
T
Alignments
Feature NameTypeLocationAnalysis
MDC010871.402 contig MDC010871.402:19632..19632. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr04 chromosome Chr04:28623344..28623344- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation