GDsnp02030, GDsnp02030 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp02030
dbSNP IDss475882722
SNP Array ID
480K SNP array for apple:AX-115182095
IRSC 9K SNP array for apple:GDsnp02030
20K SNP array for apple:GDsnp02030
50K SNP array for apple:AX-105185014
TypeSNP
SNP AllelesA/G
Probe 1GDsnp02030.probe: TCAAAACGAGATGAGGAATGAGCAATGAGGATTCCCAGCACAAGCCTATT
5' Flanking SequenceTGGACTCAGAATTTATAATAATCAATNATTTATAGAGAGAAGCTTCCCACACTCCAAAAG TTAATATGTATATACATGCGATTATGAAAAGAAACATAGT
3' Flanking SequenceAATAGGCTTGTGCTGGGAATCCTCATTGCTCATTCCTCATCTCGTTTTGAATTCGGACCA AGAAATTGAATAAAGAAAAATACTTTCAAAATTGTTCAAT
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.
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.
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 map3N/A77.2GDsnp02030View
2Apple-RGTxGD-F1-2015GD_3N/A62.23GDsnp02030View
3Apple-FjxPL-F1-2013LG3N/A67.7GDsnp02030View
4Apple-RosBREED-3.9K-20193N/A63.09GDsnp02030View
5Apple-NC-F13N/A84.58GDsnp02030View
6Apple-NCZFBB-consensus3N/A68.36GDsnp02030View
7Apple-ZF-F13N/A79.25GDsnp02030View
8Apple-MM-F13N/A58b475882722View
9Apple-Honeycrisp_Consensus-F13N/A63.09GDsnp02030View
Sequence
>GDsnp02030 ID=GDsnp02030; Name=GDsnp02030; organism=Malus x domestica; type=genetic_marker; length=201bp
TGGACTCAGAATTTATAATAATCAATNATTTATAGAGAGAAGCTTCCCAC
ACTCCAAAAGTTAATATGTATATACATGCGATTATGAAAAGAAACATAGT
YAATAGGCTTGTGCTGGGAATCCTCATTGCTCATTCCTCATCTCGTTTTG
AATTCGGACCAAGAAATTGAATAAAGAAAAATACTTTCAAAATTGTTCAA
T
Alignments
Feature NameTypeLocationAnalysis
MDC010599.294 contig MDC010599.294:5636..5636. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr00 chromosome Chr00:44158326..44158326+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr03 chromosome Chr03:34070935..34070935- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr00 chromosome Chr00:44158328..44158328. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation