RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1, RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1 (genetic_marker) Malus x domestica

Marker Overview

Name

RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1

dbSNP ID

SNP Array ID

480K SNP array for apple:	AX-115182849
IRSC 9K SNP array for apple:	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1
20K SNP array for apple:	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1
50K SNP array for apple:	AX-105216739

Type

SNP

SNP Alleles

A/G

Probe 1

RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1.probe: GCAGGAATAGGGGTTCTTAATGCAGCACGGAAAACAATGGCAAGGATGTT

5' Flanking Sequence

CCTTGGCATCAACCACCCAGAATTGCCTGCCTGCACTCTGAAATGCATCTTCATTGTTTC C

3' Flanking Sequence

AACATCCTTGCCATTGTTTTCCGTGCTGCATTAAGAACCCCTATTCCTGCACTGTAAAAA T

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
50K SNP array for apple	SNP_chip

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.
2013	Troggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin. PloS one. 2013; 8(6):e67407.
2020	Rymenants 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 Name	Linkage Group	Bin	Position	Locus	MapViewer
1	Apple-M432-2013	2	N/A	58.5	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1	View
2	Apple-M432-2013-physical-Malus-domestica	2	N/A	27298641	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1	View
3	Apple-RosBREED-3.9K-2019	2	N/A	46.72	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1	View
4	Apple-Honeycrisp_Consensus-F1	2	N/A	46.72	RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1	View

Sequence

>RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1 ID=RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1; Name=RosBREEDSNP_SNP_TC_27298641_Lg2_02271_MAF40_952256_exon1; organism=Malus x domestica; type=genetic_marker; length=75bp
CTGCCTGCACTCTGAAATGCATCTTCATTGTTTCC[C/T]AACATCCTTG
CCATTGTTTTCCGTGCTGCATTAAG

Alignments

Feature Name	Type	Location	Analysis
MDC009725.232	contig	MDC009725.232:16454..16454.	Malus x domestica Whole Genome v1.0 Assembly & Annotation
Chr02	chromosome	Chr02:26683848..26683848-	Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation