CSIRO_D5chr05_54116139 (genetic_marker) Gossypium hirsutum

Marker Overview

Name

CSIRO_D5chr05_54116139

Alias

Chr05_54116139

dbSNP ID

N/A

SNP Array ID

TAMU_CottonSNP63K:

i19006Gh

Type

SNP

SNP Alleles

T/C

5' Flanking Sequence

CTTGCAACACATCTTGTGGTTCGCCAAATTCCATAACAGCTCGCACTTAGCTTGGCTTGC ATCTTGGATTGAATTCATATCTCTAAATGAGCTCGCATTT

3' Flanking Sequence

GTTGTTGAGCTCGTAGCTTCAATTGAGCTCACAAATGTAGAGCTCGCAAGCTTGTTTGAG CTCACATCTTCTAATGTTGAATTCGCCACTGCATGAATGG

Species

Gossypium hirsutum

Germplasm

Siokra 1-4
MCU-5 (PI 694627)

Source Type

restriction-site associated DNA
RNA-seq and restriction-site associated DNA

Restriction Enzyme

EcoRI; ApekI; SbfI

Publication

[view all]

Contact

Zhu, Qian-Hao
Wilson, Iain
Stelly, David M.

Comment

Data obtained 2014. SNP location is based on D5 JGI 221 position

Contact

Name

Details

Zhu, Qian-Hao

First name:	Qian-Hao
Last name:	Zhu
Title:	Research Scientist
Institution:	CSIRO
Address:	CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601,
Country:	Australia
Email:	Qianhao.Zhu@csiro.au
Phone:	61 2 62464903
Last update:	24-Aug-2014

Wilson, Iain

Description:	SNPs; Disease resistance
First name:	Iain
Last name:	Wilson
Title:	Senior Scientist
Institution:	CSIRO
Address:	Black Mountain Laboratories Clunies Ross Street, Black Mountain, ACT 2601
Country:	Australia
Email:	iain.wilson@csiro.au
Phone:	+61 (0)2 62465211
Last update:	28-Feb-2010

Stelly, David M.

Description:	Integrative structural genomics; Cytogenetics; Genetics; Cytogenomics; Radiation hybrid mapping; Chromosome manipulations. ; Wide-cross introgression.; QTL definition. ; Reproductive cytology, genetics and manipulations. ; Fiber cell initiation.
First name:	David
Last name:	Stelly
Title:	Professor
Institution:	Texas A&M University
Address:	370 Olsen Blvd. , Dept. Soil & Crop Sci., TAMU, College Station, TX 77843-2474
Country:	United States
Email:	stelly@tamu.edu
Phone:	+1 979 845 2745
Fax:	+1 979 845 0456
Last update:	19-Feb-2007

Libraries


Library Name	Type
TAMU_CottonSNP63K	SNP_chip

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
Chr05	chromosome	Chr05:54116139..54116139 .	Gossypium raimondii (D5) genome JGI_v2_a2.1	n/a
D5_03	chromosome	D5_03:10160764..10160964 -	Gossypium raimondii (D5) 'D5-4' genome NSF_v1	n/a
Dt_chr5	chromosome	Dt_chr5:21092095..21092295 +	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
scaffold3852_D02	supercontig	scaffold3852_D02:6027..6227 -	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
Ghir_D02	chromosome	Ghir_D02:59652781..59652981 +	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
Ghir_D02	chromosome	Ghir_D02:59608700..59608900 +	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
D02	chromosome	D02:60050952..60051152 +	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
D02	chromosome	D02:60010775..60010975 +	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
A12	chromosome	A12:70533510..70533710 -	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
D02	chromosome	D02:61039552..61039752 +	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
D02	chromosome	D02:58083514..58083714 +	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
D02	chromosome	D02:58042990..58043190 +	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
CM017624.1	chromosome	CM017624.1:59967462..59967662 +	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017624.1	chromosome	CM017624.1:60007837..60008037 +	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017650.1	chromosome	CM017650.1:61415640..61415840 +	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
D02	chromosome	D02:62010609..62010809 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
D02	chromosome	D02:61966504..61966704 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
Chr03	chromosome	Chr03:53084544..53084744 +	Gossypium raimondii (D5) 'Grai D502' genome HAU_v1	n/a
chr05	chromosome	chr05:41833838..41834038 +	Gossypium armourianum (D2-1) genome ISU_v1	n/a

Publications


Year	Publication
2014	Zhu QH, Spriggs A, Taylor JM, Llewellyn D, Wilson I. Transcriptome and Complexity-Reduced-DNA Based Identification of Intraspecies Single Nucleotide Polymorphisms in the Polyploid Gossypium hirsutum L. G3 (Bethesda, Md.). 2014 Aug 7.
2015	Hulse-Kemp AM, Lemm J, Plieske J, Ashrafi H, Buyyarapu R, Fang DD, Frelichowski J, Giband M, Hague S, Hinze LL, Kochan KJ, Riggs PK, Scheffler JA, Udall JA, Ulloa M, Wang SS, Zhu QH, Bag SK, Bhardwaj A, Burke JJ, Byers RL, Claverie M, Gore MA, Harker DB, Islam MS, Jenkins JN, Jones DC, Lacape JM, Llewellyn DJ, Percy RG, Pepper AE, Poland JA, Mohan Rai K, Sawant SV, Kumar Singh S, Spriggs A, Taylor JM, Wang F, Yourstone SM, Zheng X, Lawley CT, Ganal MW, Van Deynze A, Wilson IW, Stelly DM. Development of a 63K SNP Array for Cotton and High-Density Mapping of Intra- and Inter-Specific Populations of Gossypium spp. G3 (Bethesda, Md.). 2015 Apr 22.

Germplasm


Stock Name	Type
Siokra 1-4	accession
MCU-5 (PI 694627)	accession

Sequence

>CSIRO_D5chr05_54116139 ID=CSIRO_D5chr05_54116139; Name=CSIRO_D5chr05_54116139; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
CTTGCAACACATCTTGTGGTTCGCCAAATTCCATAACAGCTCGCACTTAG
CTTGGCTTGCATCTTGGATTGAATTCATATCTCTAAATGAGCTCGCATTT
[T/C]GTTGTTGAGCTCGTAGCTTCAATTGAGCTCACAAATGTAGAGCTC
GCAAGCTTGTTTGAGCTCACATCTTCTAATGTTGAATTCGCCACTGCATG
AATGG

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CSIRO_D5chr05_54116139 (genetic_marker) Gossypium hirsutum