GDsnp00405, GDsnp00405 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00405
dbSNP IDss475882330
SNP Array ID
480K SNP array for apple:AX-105218663
IRSC 9K SNP array for apple:GDsnp00405
20K SNP array for apple:GDsnp00405
50K SNP array for apple:AX-105218663
TypeSNP
SNP AllelesA/G
Probe 1GDsnp00405.probe: GTCATAATTCTACAGAAACTAACGCAGCACCATAAAACTGAGCAACTAGG
5' Flanking SequenceTCACCAGCTTCAGTTATTTACACACAAAAGAGTTAGAAACACATAGAAATGTCATAATTC TACAGAAACTAACGCAGCACCATAAAACTGAGCAACTAGG
3' Flanking SequenceCGGCGCATTTGTTTTCCGACCCTCTTGCGCTTAGAGACAGATTTACTTTACAGATTTCCC CTCTAAGCACACGAGGGGCGGACGTCTAGTTGGTGCCTCG
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.
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.
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 map10N/A93.1GDsnp00405View
2Apple_HCGA_F110N/A0.81GDsnp00405View
3Apple_HC64_F110N/A1.82GDsnp00405View
4Apple_HCMO_F110N/A66.8GDsnp00405View
5Apple_HGMM_Consenus10N/A90.38GDsnp00405View
6Apple-RosBREED-3.9K-201910N/A76.97GDsnp00405View
7Apple-BB-F110N/A83.74GDsnp00405View
8Apple-NC-F110N/A106.38GDsnp00405View
9Apple-NCZFBB-consensus10N/A105.94GDsnp00405View
10Apple-ZF-F110N/A118.97GDsnp00405View
11Apple-consensus-Allard-2016LG10N/A76.12GDsnp00405View
12Apple-GB-F1LG_10N/A86.8GD_SNP00405View
13Apple-X5210X8402-F1-X5210LG10N/A86GD_SNP00405View
14Apple-GDxBr-F1-2013LG10N/A86.73GD_SNP00405View
15Apple-Honeycrisp_Consensus-F110N/A76.97GDsnp00405View
Sequence
>GDsnp00405 ID=GDsnp00405; Name=GDsnp00405; organism=Malus x domestica; type=genetic_marker; length=201bp
TCACCAGCTTCAGTTATTTACACACAAAAGAGTTAGAAACACATAGAAAT
GTCATAATTCTACAGAAACTAACGCAGCACCATAAAACTGAGCAACTAGG
RCGGCGCATTTGTTTTCCGACCCTCTTGCGCTTAGAGACAGATTTACTTT
ACAGATTTCCCCTCTAAGCACACGAGGGGCGGACGTCTAGTTGGTGCCTC
G
Alignments
Feature NameTypeLocationAnalysis
MDC015139.29 contig MDC015139.29:23073..23073. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr10 chromosome Chr10:40755204..40755204- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr10 chromosome Chr10:40755154..40755254- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr10 chromosome Chr10:40755206..40755206. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation