GDsnp00183, GDsnp00183 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00183
dbSNP IDss475882277
SNP Array ID
480K SNP array for apple:AX-115181965
IRSC 9K SNP array for apple:GDsnp00183
20K SNP array for apple:GDsnp00183
50K SNP array for apple:AX-105221583
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00183.probe: TCCTGGCCCTCTTCAAGGAGAAAAAGGAAAAGCCAAGGTCTTAAGCTTGT
5' Flanking SequenceAGATATTCCCGGAGTCAGGTTCAAGGTTGTGAAGGTATCCGGTGTCTCTCTCCTGGCCCT CTTCAAGGAGAAAAAGGAAAAGCCAAGGTCTTAAGCTTGT
GGAAAAGCCAAGGTCT TAAGCTTGT
3' Flanking SequenceAAGGAAGCTCATCTATGCCTAAGTCTCTGTCGTTGTAGCGTAGTTTTTCGTTTAGATCAT AGTTGTAACAACTTATCAGTTTCTCTTCTTTTGGTGAGAA
AAGGAAGCTCATCTAT GCCTAAGTC
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_HCGA_F11N/A33.62GDsnp00183View
2Apple_HC64_F11N/A26.43GDsnp00183View
3Apple_HCMO_F11N/A25.44GDsnp00183View
4Apple_HGMM_Consenus1N/A30.2GDsnp00183View
5Apple Integrated map1N/A33.9GDsnp00183View
6Apple-RosBREED-3.9K-20191N/A24.68GDsnp00183View
7Apple-BB-F11N/A31.29GDsnp00183View
8Apple-NC-F11N/A45.83GDsnp00183View
9Apple-NCZFBB-consensus1N/A28.68GDsnp00183View
10Apple-ZF-F11N/A32.68GDsnp00183View
11Apple-MM-F11N/A27c475882277View
12Apple-X3259X3263-F11N/A40.03GD_SNP00183View
13Apple-X5210X8402-F1-ConsensusLG1N/A34.7GD_SNP00183View
14Apple-GDxBr-F1-2013LG1N/A42.3GD_SNP00183View
15Apple-Honeycrisp_Consensus-F11N/A24.68GDsnp00183View
Sequence
>GDsnp00183 ID=GDsnp00183; Name=GDsnp00183; organism=Malus x domestica; type=genetic_marker; length=201bp
AGATATTCCCGGAGTCAGGTTCAAGGTTGTGAAGGTATCCGGTGTCTCTC
TCCTGGCCCTCTTCAAGGAGAAAAAGGAAAAGCCAAGGTCTTAAGCTTGT
YAAGGAAGCTCATCTATGCCTAAGTCTCTGTCGTTGTAGCGTAGTTTTTC
GTTTAGATCATAGTTGTAACAACTTATCAGTTTCTCTTCTTTTGGTGAGA
A