GDsnp00430, GDsnp00430 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00430
dbSNP IDss475882378
SNP Array ID
480K SNP array for apple:AX-115181984
IRSC 9K SNP array for apple:GDsnp00430
20K SNP array for apple:GDsnp00430
50K SNP array for apple:AX-105216974
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00430.probe: ATACGAGTTTTTTTTTGTGTTTGCTGTAATGTTTGCTAGGCATATCTCGA
5' Flanking SequenceAGCTAAATCATATTGTGCACATGTCACTTGTATTAACACATATAGAAATAATTTGATGAG TGATATCGAGATAATTTTTTTAGTGTTGTCAATGCAACTT
3' Flanking SequenceTCGAGATATGCCTAGCAAACATTACAGCAAACACAAAAAAAAACTCGTATCAAACATTCA AAGAGTCATTAGAACAAGTGTTTTTCAAACCCGAACCACC
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
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
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.
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 map12N/A10.3GDsnp00430View
2Pear-PM-F1-Moonglow12N/A2.23GDsnp00430View
3Apple-RGTxGD-F1-2015GD_12N/A11.4GDsnp00430View
4Apple-B-F1-2014B12N/A0GDsnp00430View
5Apple-BB-F112N/A9.36GDsnp00430View
6Apple-NC-F112N/A12.83GDsnp00430View
7Apple-NCZFBB-consensus12N/A10.5GDsnp00430View
8Apple-ZF-F112N/A15.48GDsnp00430View
9Apple-Honeycrisp_Consensus-F112N/A8.12GDsnp00430View
10Pear-PH-CG-2017LG12N/A76.01GDsnp00430View
Sequence
>GDsnp00430 ID=GDsnp00430; Name=GDsnp00430; organism=Malus x domestica; type=genetic_marker; length=75bp
TCGAGATAATTTTTTTAGTGTTGTCAATGCAACTT[A/G]TCGAGATATG
CCTAGCAAACATTACAGCAAACACA
Alignments
Feature NameTypeLocationAnalysis
MDC000512.417 contig MDC000512.417:14210..14210. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr12 chromosome Chr12:4002686..4002686+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr12 chromosome Chr12:4002683..4002683. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation