RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16, RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16 (genetic_marker) Malus x domestica

Marker Overview
NameRosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16
dbSNP IDss475878172
SNP Array ID
480K SNP array for apple:AX-105219139
IRSC 9K SNP array for apple:RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16
20K SNP array for apple:RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16
50K SNP array for apple:AX-105219139
TypeSNP
SNP AllelesA/C
Probe 1RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16.probe: TCAATCTCTCCCTTGAACTCCCAAATATGAACGCGACTCCCATTGACCAC
5' Flanking SequenceAGTTTCCTTCCTCAATCTCTCCCTTGAACTCCCAAATATGAACGCGACTCCCATTGACCA C
3' Flanking SequenceCCTGTGAGGCACAAACAGCCTCGCCGCACACATAAGCGTCTAGATCTAGAGTAATCCGAT T
SpeciesMalus x domestica
Publication[view all]
ContactMichela Troggio
Nicola Harrison
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
Analyses
This genetic_marker is derived from or has results from the following analyses
Analysis NameDate Performed
RosBREED SNP development2011-01-01
Publications
YearPublication
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.
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.
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_HCGA_F15N/A64.19SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
2Apple_HC64_F15N/A5.46SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
3Apple_HCMO_F15N/A10.33SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
4Apple_HGMM_Consenus5N/A21.03SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
5Apple-RosBREED-3.9K-20195N/A75.17SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
6Apple-BB-F15N/A74.67SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
7Apple-NC-F15N/A110.76SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
8Apple-NCZFBB-consensus5N/A83.34SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
9Apple-ZF-F15N/A83.9SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
10Apple-consensus-Allard-2016LG5N/A6.03SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
11Apple-MM-F15N/A11b475878172View
12Apple-M27xM116-2016LG5N/A11RBbinsnp0252View
13Apple-Honeycrisp_Consensus-F15N/A5.74RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16View
Sequence
>RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16 ID=RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16; Name=RosBREEDSNP_SNP_AC_4171437_Lg5_01566_MAF20_MDP0000307862_exon16; organism=Malus x domestica; type=genetic_marker; length=75bp
AACTCCCAAATATGAACGCGACTCCCATTGACCAC[A/C]CCTGTGAGGC
ACAAACAGCCTCGCCGCACACATAA
Alignments
Feature NameTypeLocationAnalysis
MDC017626.57 contig MDC017626.57:12142..12142. Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr05 chromosome Chr05:45102157..45102157- Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
Chr05 chromosome Chr05:45102159..45102159. Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation