GDsnp00565, GDsnp00565 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00565
dbSNP IDss475882428
SNP Array ID
480K SNP array for apple:AX-105220205
IRSC 9K SNP array for apple:GDsnp00565
20K SNP array for apple:GDsnp00565
50K SNP array for apple:AX-105220205
TypeSNP
SNP AllelesA/G
Probe 1GDsnp00565.probe: TCTGGAAGGACAGGTTACTGTTACTGTGGAGACGACAAAAAGAGAATGCC
5' Flanking SequenceTGGATTTCCGAAAATGCCCTTGGCGTTTTGACAAGCAAGAACTACTTGGGCGGAGCCAAG TGGCTGATTTGAGGAATAGCGTGGCGACACGTAGCCTGAC
3' Flanking SequenceGGCATTCTCTTTTTGTCGTCTCCACAGTAACAGTAACCTGTCCTTCCAGAGACACGTTTC GGGAGGAGACTGAATGAGGGGGATAGAACCACGTGTCGGT
SpeciesMalus x domestica
Product Length563
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.
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.
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 map13N/A19.1GDsnp00565View
2Apple-C16xC17-F1-201213N/A65.39GDsnp00565View
3Apple-RGTxGD-F1-2015GD_13N/A22.16GDsnp00565View
4Apple-JGxWSH-F1LG13N/A20GDsnp00565View
5Apple-RosBREED-3.9K-201913N/A11.97GDsnp00565View
6Apple-BB-F113N/A19.01GDsnp00565View
7Apple-NC-F113N/A26.94GDsnp00565View
8Apple-NCZFBB-consensus13N/A19.33GDsnp00565View
9Apple-consensus-Allard-2016LG13N/A12.12GDsnp00565View
10Apple-MM-F113N/A16.5c475882428View
11Apple-Honeycrisp_Consensus-F113N/A11.97GDsnp00565View
Sequence
>GDsnp00565 ID=GDsnp00565; Name=GDsnp00565; organism=Malus x domestica; type=genetic_marker; length=75bp
GATTTGAGGAATAGCGTGGCGACACGTAGCCTGAC[C/T]GGCATTCTCT
TTTTGTCGTCTCCACAGTAACAGTA
Alignments
Feature NameTypeLocationAnalysis
MDC017572.200 contig MDC017572.200:4033..4033. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr13 chromosome Chr13:4334692..4334692+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr13 chromosome Chr13:4334642..4334742- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation