GDsnp00522, GDsnp00522 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00522
dbSNP IDss475882476
SNP Array ID
IRSC 9K SNP array for apple:GDsnp00522
50K SNP array for apple:AX-105201516
TypeSNP
SNP AllelesA/G
5' Flanking SequenceCCTCAAAGCACTTCTACTGGTCTGT
3' Flanking SequenceTATATCCCCCTTCATACTTACTCTC
SpeciesMalus x domestica
Publication[view all]
ContactCindy F. Verdu
Contact
NameDetails
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
Libraries
Library NameType
IRSC 9K SNP array for appleSNP_chip
50K SNP array for appleSNP_chip
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.
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.
2013Troggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin. PloS one. 2013; 8(6):e67407.
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.
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 map14N/A46.9GDsnp00522View
2Apple-M432-201314N/A36.07GDsnp00522View
3Apple-M432-2013-physical-Malus-domestica14N/A22011006GDsnp00522View
4Apple-FjxPL-F1-2013LG14N/A57.73GDsnp00522View
5Apple-X3259X3263-F114N/A54.74GD_SNP00522View
6Apple-Honeycrisp_Consensus-F114N/A48.01GDsnp00522View
Sequence
>GDsnp00522 ID=GDsnp00522; Name=GDsnp00522; organism=Malus x domestica; type=genetic_marker; length=201bp
TCGCAAGAAGGATTTCGTGGATATTCTCCTCCAAGTTCAAAAGGATGGCA
ATGACTTTGAGCTCAAAAGTGACCACCTCAAAGCACTTCTACTGGTCTGT
RTATATCCCCCTTCATACTTACTCTCTTTAACAATAACATTATATATATG
GCTGAAGATTGATTTGGCTTCTTAAGTTACGATTTCAGGACATGTTTGTC
G
Alignments
Feature NameTypeLocationAnalysis
MDC013874.464 contig MDC013874.464:1290..1290. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr14 chromosome Chr14:26310094..26310094. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation