GDsnp00875, GDsnp00875 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00875
Aliasss475882304
rs267615249
GD_00875_L10_PA
dbSNP IDss475882304
SNP Array ID
480K SNP array for apple:AX-105224249
IRSC 9K SNP array for apple:GDsnp00875
20K SNP array for apple:GDsnp00875
TypeSNP
SNP AllelesT/G
Probe 1GDsnp00875.probe: ATTCTCCCATTGCGGCATAAATTTTGGTTGTAACTAATGTTGGGTGTCTT
5' Flanking SequenceTGACCTTGTATGTATCTGGGAGTTAAACCAAATTCTTTTGAAGGCCATAGATTCTCCCAT TGCGGCATAAATTTTGGTTGTAACTAATGTTGGGTGTCTT
3' Flanking SequenceTATTATAAAAGGATGCTCCAGATTCATAAAAAATGTTGCCCATATTGAATGATATCCTTG TGCAGGAATCAATCAACCGTTCGTTGTTGAATCTGCTCAC
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
Cindy F. Verdu
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.
2011Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, Velasco R, Salvi S. Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genetics & Genomes. 2011; 7(4):857-868.
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.
Relationships

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

Feature NameUnique NameSpeciesType
GDsnp00875GDsnp00875Malus x domesticamarker_locus
GD_SNP00875GD_SNP00875Malus x domesticamarker_locus


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

Feature NameUnique NameSpeciesType
probeGDsnp00875.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
>GDsnp00875 ID=GDsnp00875|Name=GDsnp00875|organism=Malus x domestica|type=genetic_marker|length=201bp
TGACCTTGTATGTATCTGGGAGTTAAACCAAATTCTTTTGAAGGCCATAG
ATTCTCCCATTGCGGCATAAATTTTGGTTGTAACTAATGTTGGGTGTCTT
KTATTATAAAAGGATGCTCCAGATTCATAAAAAATGTTGCCCATATTGAA
TGATATCCTTGTGCAGGAATCAATCAACCGTTCGTTGTTGAATCTGCTCA
C
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple Integrated map10N/A16.3GDsnp00875View
2Apple-FjxPL-F1-2013LG10N/A20.01GDsnp00875View
3Apple-GB-F1LG_10N/A15.7GD_SNP00875View
4Apple-X5210X8402-F1-X8402LG10N/A13.2GD_SNP00875View
5Apple-GDxBr-F1-2013LG10N/A15.74GD_SNP00875View
Alignments
Feature NameTypeLocationAnalysis
MDC010254.244 contig MDC010254.244:8452..8452. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr10 chromosome Chr10:7351117..7351217+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
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