GDsnp02291, GDsnp02291 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp02291
dbSNP IDss475882861
SNP Array ID
480K SNP array for apple:AX-115181903
IRSC 9K SNP array for apple:GDsnp02291
20K SNP array for apple:GDsnp02291
50K SNP array for apple:AX-105183569
TypeSNP
SNP AllelesA/C
Probe 1GDsnp02291.probe: TGCTCGGAAAAAAAGTTAAAGAGAATAATGGGGAATGATGTTAATGCAGT
5' Flanking SequenceTCCAGGTAAATCTAGGTATTCTTCTTCTCTTGCACAAAATGTGAAATTGTTCCACCCACA ATGAAATAAGAATAAATTAGTCAATTCCCTGTATAAAGTG
ATTAGTCAATTCCCTG TATAAAGTG
3' Flanking SequenceACTGCATTAACATCATTCCCCATTATTCTCTTTAACTTTTTTTCCGAGCAGAAAGAGGTC ATGAAAAAGGCAGTTTTGGAAGGGTATTCTTGCAGTTAGT
ACTGCATTAACATCAT TCCCCATTA
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.
2012Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PloS one. 2012; 7(2):e31745.
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 map7N/A52.7GDsnp02291View
2Apple-JG-F1LG7N/A35.5GDsnp02291View
3Apple-JGxWSH-F1LG7N/A36.4GDsnp02291View
4Apple-FjxPL-F1-2013LG7N/A57.62GDsnp02291View
5Apple-BB-F17N/A38.93GDsnp02291View
6Apple-NC-F17N/A66.76GDsnp02291View
7Apple-NCZFBB-consensus7N/A50.33GDsnp02291View
8Apple-ZF-F17N/A55.76GDsnp02291View
9Apple-MM-F17N/A43.1c475882861View
10Apple-X3259X3263-F17N/A64.87GD_SNP02291View
11Apple-X5210X8402-F1-X8402LG7N/A38.2GD_SNP02291View
12Apple-GDxBr-F1-2013LG7N/A59.66GD_SNP02291View
Sequence
>GDsnp02291 ID=GDsnp02291; Name=GDsnp02291; organism=Malus x domestica; type=genetic_marker; length=201bp
TCCAGGTAAATCTAGGTATTCTTCTTCTCTTGCACAAAATGTGAAATTGT
TCCACCCACAATGAAATAAGAATAAATTAGTCAATTCCCTGTATAAAGTG
MACTGCATTAACATCATTCCCCATTATTCTCTTTAACTTTTTTTCCGAGC
AGAAAGAGGTCATGAAAAAGGCAGTTTTGGAAGGGTATTCTTGCAGTTAG
T
Alignments
Feature NameTypeLocationAnalysis
MDC019622.281 contig MDC019622.281:4126..4126. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr07 chromosome Chr07:25962578..25962578+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr07 chromosome Chr07:25962528..25962628- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr07 chromosome Chr07:25962580..25962580. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation