GDsnp00100, GDsnp00100 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00100
dbSNP IDss475882804
SNP Array ID
480K SNP array for apple:AX-105215676
IRSC 9K SNP array for apple:GDsnp00100
20K SNP array for apple:GDsnp00100
50K SNP array for apple:AX-105215676
TypeSNP
SNP AllelesA/G
Probe 1GDsnp00100.probe: TTCATCCTTCCTAATGTCTTACGAATAATTCCTGCATTTCTCACTTCATG
5' Flanking SequenceTGTATGAATGACCTTCAAATTTAGAGTTAGAAATNAANCGGCTCCAATTATAAAATTTTT ACGGTGAAAATATATTACTTGGAAGTGAGGAATGAGCTCA
3' Flanking SequenceCATGAAGTGAGAAATGCAGGAATTATTCGTAAGACATTAGGAAGGATGAAAAAATTACTT AGTAACGCCCTAAACCTTTGGTGTGATATATATCCCACCC
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 map5N/A90.9GDsnp00100View
2Apple-C16xC17-F1-20125N/A92.61GDsnp00100View
3Apple-RosBREED-3.9K-20195N/A0.66GDsnp00100View
4Apple-NC-F15N/A2.78GDsnp00100View
5Apple-NCZFBB-consensus5N/A0.86GDsnp00100View
6Apple-ZF-F15N/A1.44GDsnp00100View
7Apple-consensus-Allard-2016LG5N/A79.01GDsnp00100View
8Apple-MM-F15N/A64.2c475882804View
9Apple-X5210X8402-F1-ConsensusLG5N/A93.7GD_SNP00100View
10Apple-X5210X8402-F1-X5210LG5N/A124GD_SNP00100View
11Apple-GDxBr-F1-2013LG5N/A79.18GD_SNP00100View
12Apple-Honeycrisp_Consensus-F15N/A80.25GDsnp00100View
Sequence
>GDsnp00100 ID=GDsnp00100; Name=GDsnp00100; organism=Malus x domestica; type=genetic_marker; length=201bp
TGTATGAATGACCTTCAAATTTAGAGTTAGAAATNAANCGGCTCCAATTA
TAAAATTTTTACGGTGAAAATATATTACTTGGAAGTGAGGAATGAGCTCA
YCATGAAGTGAGAAATGCAGGAATTATTCGTAAGACATTAGGAAGGATGA
AAAAATTACTTAGTAACGCCCTAAACCTTTGGTGTGATATATATCCCACC
C