GDsnp00159, GDsnp00159 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00159
Aliasss475882647
rs267615590
b475882647
GD_00159_L2_PA
dbSNP IDss475882647
SNP Array ID
480K SNP array for apple:GDsnp00159
IRSC 9K SNP array for apple:GDsnp00159
20K SNP array for apple:GDsnp00159
50K SNP array for apple:GDsnp00159
TypeSNP
SNP AllelesA/G
Probe 1GDsnp00159.probe: ATCACTTATGGCTTGTTTTACTATTTCGGAATCAGAATTGGATGAATTGA
5' Flanking SequenceTCTGCTTAAGTTTGCATAAAAATGATTATGAAACTGGTTTTTAAGATAAGATCACTTATG GCTTGTTTTACTATTTCGGAATCAGAATTGGATGAATTGA
3' Flanking SequenceTTGAGCATGAGGAGGAATGTGACATAAATTGTTTACTACTTTTTTATTAGATTTTTGTCG AAGTTTTGTACTAAATTTTACGTGATACCATATATAGTTT
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.
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.
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
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
Relationships

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

Feature NameUnique NameSpeciesType
GDsnp00159GDsnp00159Malus x domesticamarker_locus
GD_SNP00159GD_SNP00159Malus x domesticamarker_locus
GDsnp00159GDsnp00159-19.885Malus x domesticamarker_locus


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

Feature NameUnique NameSpeciesType
probeGDsnp00159.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
>GDsnp00159 ID=GDsnp00159|Name=GDsnp00159|organism=Malus x domestica|type=genetic_marker|length=75bp
TTTTACTATTTCGGAATCAGAATTGGATGAATTGA[A/G]TTGAGCATGA
GGAGGAATGTGACATAAATTGTTTA
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Apple Integrated map2N/A31.8GDsnp00159View
2Apple-M432-20132N/A30GDsnp00159View
3Apple-M432-2013-physical-Malus-domestica2N/A11416721GDsnp00159View
4Apple-BB-F12N/A29.02GDsnp00159View
5Apple-NC-F12N/A19.57GDsnp00159View
6Apple-NCZFBB-consensus2N/A23.28GDsnp00159View
7Apple-GDxBr-F1-2013LG2N/A30.74GD_SNP00159View
8Apple-Honeycrisp_Consensus-F12N/A19.89GDsnp00159View
Alignments
Feature NameTypeLocationAnalysis
MDC011279.298 contig MDC011279.298:4156..4156. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr02 chromosome Chr02:10217411..10217411- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr10 chromosome Chr10:4839669..4839818- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr02 chromosome Chr02:10217361..10217461- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr02 chromosome Chr02:10217413..10217413. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation