GDsnp01229, GDsnp01229 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp01229
dbSNP IDss475882525
SNP Array ID
480K SNP array for apple:AX-115182031
IRSC 9K SNP array for apple:GDsnp01229
20K SNP array for apple:GDsnp01229
50K SNP array for apple:AX-105223982
TypeSNP
SNP AllelesA/G
Probe 1GDsnp01229.probe: CCAGAATCTCATGTTACTCATCCTGATCTTGTCCATGGAAGAGAATCAGC
5' Flanking SequenceCCTTTGCTACATTTGGTTCTACATGGAAGTATGTGTTCTTAGTTTGCAGACCAGAATCTC ATGTTACTCATCCTGATCTTGTCCATGGAAGAGAATCAGC
ATCTTGTCCATGGAAG AGAATCAGC
3' Flanking SequenceGTTGTGTAATAAATGAAACCTCATCCATCCAAACCATGCCTTACCCTCTTGACACTTTTA AATCAATGCAGCCTTATCTCCACGAGTCTCGCCATCTTCA
GTTGTGTAATAAATGA AACCTCATC
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.
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.
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 map15N/A53.5GDsnp01229View
2Apple-FjxPL-F1-2013LG15N/A21.06GDsnp01229View
3Apple-NC-F115N/A63.41GDsnp01229View
4Apple-NCZFBB-consensus15N/A68.49GDsnp01229View
5Apple-ZF-F115N/A61GDsnp01229View
6Apple-X3259X3263-F115N/A49.53GD_SNP01229View
7Apple-GB-F1LG_15N/A45.2GD_SNP01229View
8Apple-GDxBr-F1-2013LG15N/A45.24GD_SNP01229View
9Apple-Honeycrisp_Consensus-F115N/A50.72GDsnp01229View
Sequence
>GDsnp01229 ID=GDsnp01229; Name=GDsnp01229; organism=Malus x domestica; type=genetic_marker; length=201bp
CCTTTGCTACATTTGGTTCTACATGGAAGTATGTGTTCTTAGTTTGCAGA
CCAGAATCTCATGTTACTCATCCTGATCTTGTCCATGGAAGAGAATCAGC
RGTTGTGTAATAAATGAAACCTCATCCATCCAAACCATGCCTTACCCTCT
TGACACTTTTAAATCAATGCAGCCTTATCTCCACGAGTCTCGCCATCTTC
A
Alignments
Feature NameTypeLocationAnalysis
MDC009940.479 contig MDC009940.479:2251..2251. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr15 chromosome Chr15:17123284..17123384- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr15 chromosome Chr15:17123310..17123310. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr15 chromosome Chr15:17123334..17123334. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation