GDsnp01116, GDsnp01116 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp01116
dbSNP IDss475882558
SNP Array ID
480K SNP array for apple:AX-115182025
IRSC 9K SNP array for apple:GDsnp01116
20K SNP array for apple:GDsnp01116
50K SNP array for apple:AX-105199745
TypeSNP
SNP AllelesT/C
Probe 1GDsnp01116.probe: ACACATGAATCCACAGACTGACATACGTTACCTCAGATTAAACCCCATCT
5' Flanking SequenceTTTAAATATCAAATATTATAACATAAATAACTAGATATTTAAAAAAAAATGTCAATCACT TGTATTACGACACATAATCTATCACACTAAAATTTCTTAA
3' Flanking SequenceAGATGGGGTTTAATCTGAGGTAACGTATGTCAGTCTGTGGATTCATGTGTTTGTTCAGAG CAATAAATTAGGCTCTCATATAATTCTTTCTATTTGATCT
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
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
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.
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 map16N/A12GDsnp01116View
2Apple-B-F1-2014B16N/A42.1GDsnp01116View
3Apple-FjxPL-F1-2013LG16N/A35GDsnp01116View
4Apple-BB-F116N/A18.57GDsnp01116View
5Apple-NC-F116N/A24.59GDsnp01116View
6Apple-NCZFBB-consensus16N/A23.25GDsnp01116View
7Apple-ZF-F116N/A16.59GDsnp01116View
8Apple-consensus-Allard-2016LG16N/A18.05GDsnp01116View
9Apple-MM-F116N/A12.2b475882558View
10Apple-GDxBr-F1-2013LG16N/A5.62GD_SNP01116View
Sequence
>GDsnp01116 ID=GDsnp01116; Name=GDsnp01116; organism=Malus x domestica; type=genetic_marker; length=75bp
TACGACACATAATCTATCACACTAAAATTTCTTAA[A/G]AGATGGGGTT
TAATCTGAGGTAACGTATGTCAGTC
Alignments
Feature NameTypeLocationAnalysis
MDC014221.239 contig MDC014221.239:14611..14611. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr16 chromosome Chr16:5117877..5117976- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr16 chromosome Chr16:5117928..5117928. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation