GDsnp01867, GDsnp01867 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp01867
Aliasss475882305
rs267615250
GD_01867_L10_PA
c475882305
dbSNP IDss475882305
SNP Array ID
480K SNP array for apple:AX-115182079
IRSC 9K SNP array for apple:GDsnp01867
20K SNP array for apple:GDsnp01867
TypeSNP
SNP AllelesT/G
Probe 1GDsnp01867.probe: TCCTTGTCGAGGAGGAAGTGATGCTAGCTAATCTTGTTCCTTTGGACATC
5' Flanking SequenceAATAATTGGTGAATTGTCGTAAAAANGAAGTTACGTTCCAGAGACTTAGCAAGCCTACCG TGACGCAGCCAATCTGTACCCAAGATAACATCAAAATCCG
3' Flanking SequenceGATGTCCAAAGGAACAAGATTAGCTAGCATCACTTCCTCCTCGACAAGGANGGGACATCT TTGGTACTCCCCTTGTAANAAACTTCACATCTAGGCATTG
SpeciesMalus x domestica
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.
2012Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC genomics. 2012; 13:203.
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.
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
GDsnp01867GDsnp01867Malus x domesticamarker_locus
c475882305c475882305Malus x domesticamarker_locus
GD_SNP01867GD_SNP01867Malus x domesticamarker_locus
GDsnp01867GDsnp01867-14.639Malus x domesticamarker_locus


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

Feature NameUnique NameSpeciesType
probeGDsnp01867.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
>GDsnp01867 ID=GDsnp01867|Name=GDsnp01867|organism=Malus x domestica|type=genetic_marker|length=75bp
CAGCCAATCTGTACCCAAGATAACATCAAAATCCG[A/C]GATGTCCAAA
GGAACAAGATTAGCTAGCATCACTT
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple Integrated map10N/A18.2GDsnp01867View
2Apple_HCGA_F110N/A55.53GDsnp01867View
3Apple_HC64_F110N/A73.9GDsnp01867View
4Apple_HCMO_F110N/A15.26GDsnp01867View
5Apple_HGMM_Consenus10N/A17.01GDsnp01867View
6Apple-Rg-F1-2014RG10N/A12GDsnp01867View
7Apple-FjxPL-F1-2013LG10N/A18.92GDsnp01867View
8Apple-MM-F110N/A20.4c475882305View
9Apple-GB-F1LG_10N/A15.1GD_SNP01867View
10Apple-GDxBr-F1-2013LG10N/A15.11GD_SNP01867View
11Apple-Honeycrisp_Consensus-F110N/A14.64GDsnp01867-14.639View
Alignments
Feature NameTypeLocationAnalysis
MDC013691.233 contig MDC013691.233:4564..4564. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr10 chromosome Chr10:7859599..7859599+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr10 chromosome Chr10:7859549..7859649- 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