RosBREED_SNP_GT_248882_Lg16, RosBREED_SNP_GT_248882_Lg16 (genetic_marker) Malus x domestica

Marker Overview

Name

RosBREED_SNP_GT_248882_Lg16

dbSNP ID

SNP Array ID

480K SNP array for apple:	AX-115190609
IRSC 9K SNP array for apple:	RosBREED_SNP_GT_248882_Lg16
20K SNP array for apple:	RosBREED_SNP_GT_248882_Lg16

Type

SNP

SNP Alleles

T/G

Probe 1

RosBREED_SNP_GT_248882_Lg16.probe: CATCCAGACCATCCTTAATCTCCCTCGTCGCCGCCCTTCTCATCATCTTG

5' Flanking Sequence

ATTGAGTTTAGTTTGCTTTGCCTTTTACTATAAATACACTGCGGTGTCGGATGTTTCCAT CACTCAAATTCCACTAAACAAAACAACCATGCCTCTAATCGCATCCAGACCATCCTTAAT CTCCCTCGTCGCCGCCCTTCTCATCATCTTG

3' Flanking Sequence

TGGCCCCAATCCCATCGCTGACCCATGCCGGAAAGCCCCACCTCATCAATTTCCGATCCC CCAACCTCTTCCCCGAAGGCCTCGCCTACGACTCATCCGCCCAGCACTTCATTGTCGGCT CCATCCGCCAACGCACCATCCACTCTGTGTC

Species

Malus x domestica

Publication

[view all]

Contact

Michela Troggio

Comment

Previously given SSID ss475884124 is incorrect (Edge-Garza et al. TGG, 2021)

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
MDC002955.279	contig	MDC002955.279:37920..37920 .	Malus x domestica Whole Genome v1.0 Assembly & Annotation	n/a
Chr16	chromosome	Chr16:2030279..2030279 +	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.
2021	Edge-Garza DA, Villamil-Castro M, Main D, Hardner C. Correction of database SNP accession numbers misassigned to SNPs of the 8K IRSC apple SNP array. 2021 Tree Genetics & Genomes 17:17
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.

Sequence

>RosBREED_SNP_GT_248882_Lg16 ID=RosBREED_SNP_GT_248882_Lg16; Name=RosBREED_SNP_GT_248882_Lg16; organism=Malus x domestica; type=genetic_marker; length=75bp
TAATCTCCCTCGTCGCCGCCCTTCTCATCATCTTG[G/T]TGGCCCCAAT
CCCATCGCTGACCCATGCCGGAAAG