GDsnp01813, GDsnp01813 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp01813
dbSNP IDss475882532
SNP Array ID
480K SNP array for apple:AX-105192403
IRSC 9K SNP array for apple:GDsnp01813
20K SNP array for apple:GDsnp01813
50K SNP array for apple:AX-105192403
TypeSNP
SNP AllelesA/G
Probe 1GDsnp01813.probe: TTCAAGTGATGTAAATTCAATGAGCAGTCCAAGTAGCGAATTCAGCATCG
5' Flanking SequenceGTAATCATCTAACCATACAACAAGAACGCATATGCATCCAGAAGACTCATTTCAAGTGAT GTAAATTCAATGAGCAGTCCAAGTAGCGAATTCAGCATCG
3' Flanking SequenceAACAAAAGGTACCTGAGCAGATTTATTGAGCTGGAGGAGAGTGCAAAACCGCGGCATATG CACCGATATCGAATTGCTGTTGATGGGCTGACTAAGCTGC
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.
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.
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-RGxBr-Braeburn-F1LG15N/A45.6GDsnp01813View
2Apple Integrated map15N/A64.8GDsnp01813View
3Apple-B-F1-2014B15N/A45.6GDsnp01813View
4Apple-FjxPL-F1-2013LG15N/A56.79GDsnp01813View
5Apple-RosBREED-3.9K-201915N/A64.45GDsnp01813View
6Apple-BB-F115N/A75.57GDsnp01813View
7Apple-NC-F115N/A83.94GDsnp01813View
8Apple-NCZFBB-consensus15N/A83.44GDsnp01813View
9Apple-consensus-Allard-2016LG15N/A70.21GDsnp01813View
10Apple-MM-F115N/A73.9c475882532View
11Apple-Honeycrisp_Consensus-F115N/A64.45GDsnp01813View
Sequence
>GDsnp01813 ID=GDsnp01813; Name=GDsnp01813; organism=Malus x domestica; type=genetic_marker; length=75bp
TTCAATGAGCAGTCCAAGTAGCGAATTCAGCATCG[A/G]AACAAAAGGT
ACCTGAGCAGATTTATTGAGCTGGA
Alignments
Feature NameTypeLocationAnalysis
MDC003829.708 contig MDC003829.708:5743..5743. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr15 chromosome Chr15:22704837..22704837+ Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr15 chromosome Chr15:22704787..22704887- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation