CSIRO_D5chr02_41983978 (genetic_marker) Gossypium hirsutum

Marker Overview

Name

CSIRO_D5chr02_41983978

Alias

Chr02_41983978

dbSNP ID

N/A

SNP Array ID

TAMU_CottonSNP63K:

i18446Gh

Type

SNP

SNP Alleles

C/T

5' Flanking Sequence

CAATATAAAATTAATCTTATAACTAAATAATGTAACACAATACAATTAACCTGATGTAAC AGATTCACAACAAATAGGGGAGTTCAGTATAAACGAATAA

3' Flanking Sequence

ATAGTAATTTCAACATTTATAATGCTATTCAATTTAGTAACATTCACATAGAATTCACGT TTCAATATCATGTACCTTATTGAATCATCATATACCATTT

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
Chr02	chromosome	Chr02:41983978..41983978 .	Gossypium raimondii (D5) genome JGI_v2_a2.1	n/a
CM018215.1	chromosome	CM018215.1:41933729..41933927 -	Gossypium barbadense (AD2) '3-79' genome HGS_v1.1	n/a
D5_01	chromosome	D5_01:36094423..36094623 +	Gossypium raimondii (D5) 'D5-4' genome NSF_v1	n/a
Dt_chr2	chromosome	Dt_chr2:21449984..21450185 +	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
D01	chromosome	D01:39989410..39989611 -	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
Ghir_D01	chromosome	Ghir_D01:41666772..41666973 -	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
D01	chromosome	D01:43616620..43616821 -	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
D01	chromosome	D01:43060294..43060495 -	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
D01	chromosome	D01:40565785..40565986 -	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
Gbar_D01	chromosome	Gbar_D01:42130542..42130740 -	Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1	n/a
D01	chromosome	D01:42953517..42953715 -	Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1	n/a
CM017623.1	chromosome	CM017623.1:42889437..42889638 -	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017649.1	chromosome	CM017649.1:43872086..43872286 -	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
CM017701.1	chromosome	CM017701.1:42307278..42307476 -	Gossypium darwinii (AD5) genome HGS_v1.1	n/a
D01	chromosome	D01:43491614..43491815 -	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
Chr01	chromosome	Chr01:31624798..31624998 +	Gossypium raimondii (D5) 'Grai D502' genome HAU_v1	n/a
Chr02	chromosome	Chr02:40687215..40687415 +	Gossypium thurberi (D1-5) genome CRI_v1	n/a
chr02	chromosome	chr02:30687757..30687957 +	Gossypium armourianum (D2-1) genome ISU_v1	n/a
Chr_02	chromosome	Chr_02:27808522..27808721 +	Gossypium harknessii (D2-2) 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_D5chr02_41983978 ID=CSIRO_D5chr02_41983978; Name=CSIRO_D5chr02_41983978; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
CAATATAAAATTAATCTTATAACTAAATAATGTAACACAATACAATTAAC
CTGATGTAACAGATTCACAACAAATAGGGGAGTTCAGTATAAACGAATAA
[C/T]ATAGTAATTTCAACATTTATAATGCTATTCAATTTAGTAACATTC
ACATAGAATTCACGTTTCAATATCATGTACCTTATTGAATCATCATATAC
CATTT

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CSIRO_D5chr02_41983978 (genetic_marker) Gossypium hirsutum