RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1, RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1 (genetic_marker) Malus x domestica

Marker Overview

Name

RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1

dbSNP ID

SNP Array ID

480K SNP array for apple:	AX-105182860
IRSC 9K SNP array for apple:	RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1
20K SNP array for apple:	RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1
50K SNP array for apple:	AX-105182860

Type

SNP

SNP Alleles

A/C

Probe 1

RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1.probe: CTAACACACCCATTTGAGCTACATGCCCTTGAACACATTATTGGGAAGTG

5' Flanking Sequence

GTCAAAAGATTCTAACACACCCATTTGAGCTACATGCCCTTGAACACATTATTGGGAAGT G

3' Flanking Sequence

CTTAGTTAAAGGATCTGCAATCATCAAACCAGTCAATAAGAACTAAATTTCAATCTCCCA 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

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
MDC002816.507	contig	MDC002816.507:26120..26120 .	Malus x domestica Whole Genome v1.0 Assembly & Annotation	n/a
Chr02	chromosome	Chr02:37545891..37545891 +	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.
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_HCGA_F1	2	N/A	53.92	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
2	Apple_HC64_F1	2	N/A	74.21	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
3	Apple_HCMO_F1	2	N/A	51.35	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
4	Apple_HGMM_Consenus	2	N/A	78.86	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
5	Apple-BB-F1	2	N/A	80.47	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
6	Apple-NC-F1	2	N/A	87.46	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
7	Apple-NCZFBB-consensus	2	N/A	80.47	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
8	Apple-ZF-F1	2	N/A	84.46	SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
9	Apple-MM-F1	2	N/A	79.6	a475877453	View
10	Apple-Honeycrisp_Consensus-F1	2	N/A	62.61	RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View
11	Pear-PH-CG-2017	LG16	N/A	11.28	RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1	View

Sequence

>RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1 ID=RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1; Name=RosBREEDSNP_SNP_CA_40092827_Lg2_02535_MAF40_MDP0000258051_exon1; organism=Malus x domestica; type=genetic_marker; length=75bp
GAGCTACATGCCCTTGAACACATTATTGGGAAGTG[A/C]CTTAGTTAAA
GGATCTGCAATCATCAAACCAGTCA