GDsnp00098, GDsnp00098 (genetic_marker) Malus x domestica

Marker Overview
NameGDsnp00098
dbSNP IDss475882425
SNP Array ID
480K SNP array for apple:AX-105219948
IRSC 9K SNP array for apple:GDsnp00098
20K SNP array for apple:GDsnp00098
50K SNP array for apple:AX-105219948
TypeSNP
SNP AllelesT/C
Probe 1GDsnp00098.probe: AGCAAGGCCACTAAAGCAATGGTTTCAACATCATGCTACAATTCACATAA
5' Flanking SequenceTCCTTTTGTGATTGAGTTTCAGCAGCGAAGCATGGTTCATAAAAGTAGGTAGCAAGGCCA CTAAAGCAATGGTTTCAACATCATGCTACAATTCACATAA
CAACATCATGCTACAA TTCACATAA
3' Flanking SequenceATGTTGTGCTCTCCCTTTAATCAACATCACATTATCTAGCTTTCTGGAGCATGAGAATCC CGAGAGGGGCAACAAATTTACATAGATAGAAAAAGATCCA
ATGTTGTGCTCTCCCT TTAATCAAC
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
Nicola Harrison
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
Nicola Harrison
First name:Nicola
Last name:Harrison
Address:East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
Email:nicola.harrison@emr.ac.uk
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.
2016Harrison N, Harrison RJ, Barber-Perez N, Cascant-Lopez E, Cobo-Medina M, Lipska M, Conde-Ruíz R, Brain P, Gregory PJ, Fernández-Fernández F. A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage. Journal of experimental botany. 2016 Jan 29; 67(6):1871-1881.
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 map13N/A9.4GDsnp00098View
2Apple_HCGA_F113N/A100.64GDsnp00098View
3Apple_HC64_F113N/A63.23GDsnp00098View
4Apple_HCMO_F113N/A1.25GDsnp00098View
5Apple_HGMM_Consenus13N/A4.04GDsnp00098View
6Apple-FjxPL-F1-2013LG13N/A8.66GDsnp00098View
7Apple-RosBREED-3.9K-201913N/A5.52GDsnp00098View
8Apple-BB-F113N/A11.88GDsnp00098View
9Apple-NC-F113N/A15.37GDsnp00098View
10Apple-NCZFBB-consensus13N/A10.67GDsnp00098View
11Apple-ZF-F113N/A7.56GDsnp00098View
12Apple-consensus-Allard-2016LG13N/A8.02GDsnp00098View
13Apple-MM-F113N/A9.1c475882425View
14Apple-X3259X3263-F113N/A12.25GD_SNP00098View
15Apple-M27xM116-2016LG13N/A6.4RBsnp2640View
16Apple-Honeycrisp_Consensus-F113N/A5.52GDsnp00098View
Sequence
>GDsnp00098 ID=GDsnp00098; Name=GDsnp00098; organism=Malus x domestica; type=genetic_marker; length=201bp
TCCTTTTGTGATTGAGTTTCAGCAGCGAAGCATGGTTCATAAAAGTAGGT
AGCAAGGCCACTAAAGCAATGGTTTCAACATCATGCTACAATTCACATAA
YATGTTGTGCTCTCCCTTTAATCAACATCACATTATCTAGCTTTCTGGAG
CATGAGAATCCCGAGAGGGGCAACAAATTTACATAGATAGAAAAAGATCC
A