GDsnp00087, GDsnp00087 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00087
dbSNP IDss475882282
SNP Array ID
480K SNP array for apple:AX-105219527
IRSC 9K SNP array for apple:GDsnp00087
50K SNP array for apple:AX-105219527
TypeSNP
SNP AllelesA/G
5' Flanking SequenceGCTTAAGTGCCAAAGTGAGAGCTCA
3' Flanking SequenceTCACACCTACATGTCCAACTCTTGA
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
480K SNP array for appleSNP_chip
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.
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_HCGA_F11N/A29.5GDsnp00087View
2Apple_HC64_F11N/A24.63GDsnp00087View
3Apple_HCMO_F11N/A29.22GDsnp00087View
4Apple_HGMM_Consenus1N/A33.41GDsnp00087View
5Apple Integrated map1N/A41.2GDsnp00087View
6Apple-JGxWSH-F1LG1N/A27GDsnp00087View
7Apple-WSH-F1LG1N/A30GDsnp00087View
8Apple-RosBREED-3.9K-20191N/A27.81GDsnp00087View
9Apple-X3263xBr-F11N/A38.7GD_SNP00087View
10Apple-X3259X3263-F11N/A45.3GD_SNP00087View
11Apple-X5210X8402-F1-ConsensusLG1N/A36.3GD_SNP00087View
12Apple-X5210X8402-F1-X8402LG1N/A43.6GD_SNP00087View
13Apple-GDxBr-F1-2013LG1N/A46.86GD_SNP00087View
14Apple-MM-F11N/A33.7b475882282View
15Apple-Honeycrisp_Consensus-F11N/A27.81GDsnp00087View
Sequence
>GDsnp00087 ID=GDsnp00087; Name=GDsnp00087; organism=Malus x domestica; type=genetic_marker; length=201bp
TGAATACTAAGACGACATGAAAACCTCATAAATGGTAGCAAAATCTGAGG
AGGCTAAAGTTACTTAGTACTTTATGCTTAAGTGCCAAAGTGAGAGCTCA
RTCACACCTACATGTCCAACTCTTGATATTAAACAGTAGGTAAACAGGTC
ACAAGGAAACTCGGCAATGTTTTGGTCAGATGGATTGGTCGAGAGTAAGA
G