RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1, RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1 (genetic_marker) Malus x domestica

Marker Overview

Name

RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1

dbSNP ID

SNP Array ID

480K SNP array for apple:	AX-115182278
IRSC 9K SNP array for apple:	RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1
20K SNP array for apple:	RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1

Type

SNP

SNP Alleles

T/C

Probe 1

RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1.probe: TTGAAGATTCTCGGATGCTTTCTTGCGGTTATCTTGATTTGGGAAATACC

5' Flanking Sequence

CTGAACGGGGTTACTCACCCAATAAGAATGATAATGGATGAAAGACTAATTCAAACACTC C

3' Flanking Sequence

GGTATTTCCCAAATCAAGATAACCGCAAGAAAGCATCCGAGAATCTTCAAAGCCATAACT G

Species

Malus x domestica

Publication

[view all]

Contact

Michela Troggio

Contact

Name

Details

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

Libraries


Library Name	Type
20K SNP array for apple	SNP_chip
480K SNP array for apple	SNP_chip
IRSC 9K SNP array for apple	SNP_chip

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
MDC001276.321	contig	MDC001276.321:6276..6276 .	Malus x domestica Whole Genome v1.0 Assembly & Annotation	n/a
Chr10	chromosome	Chr10:35921759..35921759 -	Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation	n/a
Chr05	chromosome	Chr05:42197120..42197120 -	Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation	n/a

Analyses

This genetic_marker is derived from or has results from the following analyses


Analysis Name	Date Performed
RosBREED SNP development	2011-01-01

Publications


Year	Publication
2014	Bianco 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.
2012	Antanaviciute 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.
2016	Bianco 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.

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	Apple-MM-F1	10	N/A	73.7	b475879902	View
2	Apple-Honeycrisp_Consensus-F1	10	N/A	62.09	RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1	View

Sequence

>RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1 ID=RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1; Name=RosBREEDSNP_SNP_AG_30223751_Lg10_00734_MAF50_1646703_exon1; organism=Malus x domestica; type=genetic_marker; length=75bp
AATGATAATGGATGAAAGACTAATTCAAACACTCC[A/G]GGTATTTCCC
AAATCAAGATAACCGCAAGAAAGCA