Greetings to All ICGI members!
We hope everyone is doing well.
You are cordially invited to attend the 2014 biennial meeting of the International Cotton Genome Initiative (ICGI), to be held from 25-28 September 2014 in Wuhan, Hubei, China, hosted by Huazhong Agricultural University. A formal announcement for 2014 ICGI Research Conference will be send soon after the conference home page set with full detailed information of the meeting.
We look forward to seeing you at the 2014 ICGI meeting.
Sincerely,
Prof. Dr.Tianzhen Zhang
ICGI Chair
Dear Colleagues,
We are pleased to inform you that Oxford Journals has published CottonGen's article in Nucleic Acids Research.
The open-access link to the online article is: http://nar.oxfordjournals.org/cgi/content/full/gkt1064?
ijkey=fcXHnQiFBc9po6s&keytype=ref
The full citation for the article is: Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D (2013) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research 2013; doi: 10.1093/nar/gkt1064
Thank you for your support and contribution to CottonGen. We will continue to enhance CottonGen with new data and functionality to make it better serve the cotton community. As always we welcome your feedback and comments.
Best Regards,
The CottonGen Team
Greetings ICGI Members,
Please recognize approaching deadlines and upcoming events:
Nov. 1, 2013 PAG Discounted Registration rate deadline -- PAG Meeting (Jan.11-15)
Nov. 1 2013 PAG Poster Abstract Submission (submit through PAG website; presenters must register)
Nov. 8, 2013 PAG Deadline for 2014 PAG Cotton Workshop Abstract Submissions (invited speakers only; submit through PAG website)
Nov. 15, 2013 Discounted rate deadline for the "Cotton SNP Chip" (see information, see "News" at http://www.cottongen.org and previous email (copied below))
Dec. 13, 2013 Discounted Registration rate deadline -- Beltwide Cotton Conference ( Jan 6-8)-
Jan. 6-8, 2014 Beltwide Cotton Conference (New Orleans, Louisiana, USA Jan 6-8)-
Jan. 11-15, 2014 Plant and Aniimal Genome (PAG) Meeting (San Diego, California, USA, Jan.11-15)
Jan. 12, 4pm Cotton Genome Workshop, at PAG Meeting
Sept. 25, 2014 Biennial meeting of ICGI, Wuhan, Hubei, China (more information is forthcoming)
Best wishes,
David Stelly
Co-Chair
COPY OF PREVIOUS EMAIL:
=============================================
A Cotton SNP Consortium is about to produce a Cotton SNP Chip with up to 70,000 public SNPs in the "Fixed Content" (on all Chips), including up to 50k intraspecific and 20k interspecific; up to 65k will involve the primary gene pool. In addition, up to 20,000 additional SNPs can be added to the sector known as "Add-on" content, which can vary from one batch of chips to another. The initial period for purchase is expected to end mid-November.
Please note that while most if not all of the multi-national participants in the Consortium are members of ICGI, neither the Consortium or Chip is ICGI-organized or sponsored.
If you are interested in obtaining additional information about the Chip, please contact me at the following EMAIL ADDRESS and SUBJECT LINE:
David M. Stelly <stelly(a)tamu.edu> SUBJECT LINE: "Cotton SNP Chip Information Request"
Some time after sending your email, you should receive an acknowledgment email in return.
Thanks,
David Stelly
Co-Chair
Greetings to All ICGI members!!!
We hope everyone is doing well.
The 2014 PAG meeting is approaching!! The COTTON GENOME INITIATIVE workshop will be Sunday, January 12, 2014, 4:00-6:10pm in Pacific Salon 2.
This email is primarily about Workshop Speakers, but before discussing that, please note these abstract deadlines:
Deadline for workshop abstracts = November 8, 2013.
Deadline for poster abstracts = October 15, 2013
SPEAKERS FOR the 2014 PAG "COTTON GENOME INITIATIVE" WORKSHOP !!!
At this time, we solicit volunteers and nominations for "Cotton Genome Initiative" Workshop Speakers -- -- Please, follow the different instructions below for volunteering yourself or nominating a possible speaker.
----------------------------------------------------
Instructions for submitting your volunteered topic and draft abstract:
By the end of October 15, send an email with the following SUBJECT LINE:
2014 PAG Cotton Genome Workshop candidate abstract
to these two email addresses:
stelly(a)tamu.edu, cotton(a)njau.edu.cn
In your email, please include the following components:
1. Presenter (Your name): Family_name, First_name
Institutional affiliation: ______
2. Email address(es), separated by a comma.
3. List of co-authors (draft)
4. Abstract (draft) -- follow guidelines for PAG, please
5. Prioritize the ICGI workgroups your work relates most closely (top)
Bioinformatics
Evolutionary & Comparative Genomics
Functional Genomics
Germplasm & Genetic Stocks
Structural Genomics
If you do not get a response acknowledging reception of the submission, please inquire! Note that the Subject Line is important -- we will use it to identify submissions, so we recommend you use COPY/PASTE to fill in the Subject Line of your email.
We will attempt to make speaker selections by the end of Oct. 22.
----------------------------------------------------
Instructions for nominating a prospective speaker:
By the end of October 10,
[1] confer with the person you think would be an appropriate speaker about availability, their desire to speak (~20 minutes) at the Workshop (be sure to mention Sunday Jan. 12 4-6pm, so that they arrive in time), prospective topic title, and willingness if selected (~ Oct. 22) to provide an abstract to PAG before the deadline (Nov. 8). It would be important to inform that individual that PAG provides no support for travel or any other expenses for Workshop speakers, except as mentioned below.
[2] if the person confirms their interest, send an email containing with the following SUBJECT LINE:
2014 PAG Cotton Genome Workshop speaker nomination
to these two email addresses:
stelly(a)tamu.edu, cotton(a)njau.edu.cn
In your email, please explain why this person and topic might be a superb speaker in the Cotton Genome workshop.
If you do not get a response acknowledging reception of the submission, please inquire! Note that the Subject Line is important -- we will use it to identify submissions, so we recommend you use COPY/PASTE to fill in the Subject Line of your email.
--------------------------------------------
ADDITIONAL INFORMATION FROM PAG TO PROSPECTIVE WORKSHOP SPEAKERS:
Once speakers are added to a workshop, each speaker will be sent an automated email with instructions how to login and post their individual workshop abstract. This form will include an option and instructions for submitting a poster abstract as well. All speakers must register for the conference. Prior to the November 1 deadline, the rates for workshop speakers are the same as attendees. The rates have been reduced by $50 for full conference attendees and $25 for students and weekend only attendees versus 2013. After the November 1 deadline, the rates will increase but workshop speakers are protected from paying the increase however, they will need to use one of the discount codes below to get the lower rate.
--------------------------------------------
ANTICIPATED TIMELINE FOR CHOOSING WORKSHOP SPEAKERS
After collecting input from everyone, we'll share the data and consult with workgroup leaders (chair and co-chairs) as best we can to help guide us identifying an attractive set of topics for the 2014 PAG Cotton Genome Initiative Workshop. Again, we will attempt to arrive at decisions by the end of Oct. 22, so that everyone has plenty of time to perfect and submit their abstracts, and if not chose, to submit a poster instead. (Please note however, that space for posters is limited, so it might be wise to submit poster abstracts well before Oct. 23.)
Thanks,
Workshop Organizers:
David Stelly and Tianzhen Zhang
ICGI Co-Chair and Chair
Dear ICGI Members,
A Cotton SNP Consortium is about to produce a Cotton SNP Chip with up to 70,000 public SNPs in the "Fixed Content" (on all Chips), including up to 50k intraspecific and 20k interspecific; up to 65k will involve the primary gene pool. In addition, up to 20,000 additional SNPs can be added to the sector known as "Add-on" content, which can vary from one batch of chips to another. The initial period for purchase is expected to end mid-November.
Please note that while most if not all of the multi-national participants in the Consortium are members of ICGI, neither the Consortium or Chip is ICGI-organized or sponsored.
If you are interested in obtaining additional information about the Chip, please contact me at the following EMAIL ADDRESS and SUBJECT LINE:
David M. Stelly <stelly(a)tamu.edu> SUBJECT LINE: "Cotton SNP Chip Information Request"
Some time after sending your email, you should receive an acknowledgment email in return.
Thanks,
David Stelly
Co-Chair
Greetings to All ICGI members!!!
We hope everyone is doing well.
2014 ICGI Res Conference will be held on Sept 25 to 28, 2014 in Wuhan, Hubei, China. So, please arrange your time and attend this exciting conference. Full details of the meeting, registration information, and hotel information, visa and program etc will be available after ICGI Steering Committee meeting in San Diego in next January.
Prof. Dr.Tianzhen Zhang
Chair, ICGI
Natl Key Lab of Crop Genetics and Germplasm Enhancement
College of Agriculture, Nanjing Agricultural University
Nanjing 210095, Jiangsu Province, China
Tel./Fax: +86 25 84395307
E.mail: cotton(a)njau.edu.cn, tzzhangnj(a)163.com
Dear ICGI members,
Please find attached a spreadsheet detailing the election results. For the Germplasm and Genetic Stocks workgroup, there was a tie. Since our bylaws do not address this, the steering committee has voted unanimously … and the two candidates who are tied have agreed … that we will have two co-chairs (along with the chair) of this workgroup for the next two years, who will then serve for another two years as joint chairs.
At risk of sounding like the Academy Awards …
To all who voted, thank you for exercising this important right and responsibility.
To all who ran for office, thank you for offering to serve ICGI.
To newly elected co-chairs David Stelly, David Fang, Daniel Peterson, Sukumar Saha, Xianlong Zhang, Dorrie Main, and me, congratulations, and keep up the good work.
To the outgoing chairs, thank you for your 4 years (or more) of service.
To all members, thank you for the privilege of allowing me to serve as Chair for the past two years, a time that was of singular importance in my own cotton research. As the new co-chair of Comparative and Evolutionary Genomics, I look forward to joining Richard Percy as another former chair who continues to serve via workgroups, in support of Tianzhen Zhang who succeeds me as Chair, and yet another former chair David Stelly who will re-assume the Chair in 2015.
________________
Andrew Paterson
Regents Professor and Head,
Plant Genome Mapping Laboratory (Dept #398)
University of Georgia
111 Riverbend Road, Rm 228
Athens GA 30605
(for UPS deliveries the zip code is 30605)
Phone 1-706-583-0162; Fax 1-706-583-0160; Email paterson(a)plantbio.uga.edu
Web site: http://www.plantgenome.uga.edu/
Program Coordinators:
Anne A. Ogden, 706-583-0166, ogden(a)uga.edu
Melissa D. Brock, 706-583-0161, mbrock(a)uga.edu
---------- Forwarded message ----------
From: Andrew Paterson <paterson at plantbio.uga.edu>
Date: Tue, Mar 19, 2013 at 10:44 AM
Subject: [ICGI] Election extended to 3 April
To: icgi-list at cottongen.org
Dear ICGI members,
Tomorrow (March 20) will be the end of the 30 day period for the ICGI 2013 election. At present, only about 30% (108 of 349) of members have voted, so that it is very unlikely that we will reach 50% by the end of tomorrow.
Per our bylaws, we will therefore extend the election for two weeks, to the end of the day on April 3. Also per our bylaws, balloting will close after April 3, regardless of the % of the membership that has voted.
Please exercise your most important right and responsibility -- vote!
Thanks,
Andrew Paterson, Chair
________________
Andrew Paterson
Regents Professor and Head,
Plant Genome Mapping Laboratory (Dept #398)
University of Georgia
111 Riverbend Road, Rm 228
Athens GA 30605
(for UPS deliveries the zip code is 30605)
Phone 1-706-583-0162; Fax 1-706-583-0160; Email paterson at plantbio.uga.edu
Web site: http://www.plantgenome.uga.edu/
Program Coordinators:
Anne A. Ogden, 706-583-0166, ogden at uga.edu
Melissa D. Brock, 706-583-0161, mbrock at uga.edu
Dear Cotton Community Members,
Please accept our apology for the email you received yesterday containing unsupported statements about a fellow member of CottonGen and ICGI. To rectify this situation we include below a clarification offered to us by Dr. Paterson. In the future, any communication requests from members to the CottonGen/ICGI mailing lists will be sent to the steering committees for approval before posting.
Sincerely,
Dorrie Main
CottonGen Principal Investigator
Note from Dr. Andrew Paterson in reply to Dr. Thea Wilkins second email regarding access to genomic resources.
Having noted yesterday the merit of Dr. Wilkins libraries, ICGI members also may wish to consider that non-profit distribution centers including Texas A&M, CUGI/AGI, and PGML have BACs from the same genotypes used by Dr WIlkins. While these BACs would lack the value added by Dr Wilkins sequencing, they may be much less costly to obtain than those from a private vendor.
Dr. Wilkins unsupported comments about my BAC distribution record are incorrect. My policies were formulated under an NSF grant on which Dr. Wilkins was the PI. These policies and my record have been regularly reviewed and found satisfactory by my research sponsors. We have had an online ordering system (http://www.plantgenome.uga.edu/catalog/index.php?cPath=1) for many years, and requests are filled promptly. All who have requested BACs from me have received them. Likewise, our probe sequences were deposited in Genbank soon after their completion, and genome sequences that I have overseen were publicly released nearly a year (for cotton, and nearly 2 years for sorghum) in advance of publication.
Best wishes to all.
Andrew Paterson, Chair, ICGI and
Regents Professor, University of Georgia.
Dorrie Main, Ph.D.
Associate Professor of Bioinformatics
Department of Horticulture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774
Email: dorrie(a)wsu.edu
URL: www.bioinfo.wsu.edu
Some may wish to be aware that there are other public BAC libraries available (on a cost-recovery basis) for the same genotypes, although they are not the specific libraries that were used in Thea's sequencing.
On Mar 26, 2013, at 1:05 PM, "Yu, Jing" <jing.yu(a)wsu.edu> wrote:
> Dear Cotton Researchers,
>
> Dr. Thea WIlkins would like to release all of her genome resources through Amplicon Express (for lists the type and cost of services, please visit http://ampliconexpress.com), as they maintain excellent QC and provide a range of services. However, she needs know if there is sufficient interest by the community for Amplicon to provide such services.
>
> The resources are 6 BAC libraries of excellent quality with >125 kb inserts as follows
> ~8X MboI G. Arboreum AKA8401 library anchored by Andy Paterson
> ~6X BamHI G. arboreum AKA 8401 library used to generate sequence-based physical map
> ~6X EcoRI G. arboreum AKA 8401 library used to generate sequence-based physical map
>> 5X Gossypiodes Kirkii BAC library generated for making sequence-based physical map
>> 5X G. Kirkii library generated for making a sequence-based physical map
> 5X G. hirsutum TM1 BAC library
>
> Please let us know if you are interested in using these resources via services provided by Amplicon Express within the next two weeks. If there is not enough interest, these important resources, which are not currently available to the community, will be lost to the community forever.
>
> Please reply to this email with either a “yes” or “no” (please use reply and not reply all).
>
> Thank you for your help.
>
> Dr. Jing Yu
> CottonGen Curator
> _______________________________________________
> Main Bioinformatics Laboratory
> ICGI-LIST mailing list
> ICGI-LIST(a)cottongen.org
>
>
>
________________
Andrew Paterson
Regents Professor and Head,
Plant Genome Mapping Laboratory (Dept #398)
University of Georgia
111 Riverbend Road, Rm 228
Athens GA 30605
(for UPS deliveries the zip code is 30605)
Phone 1-706-583-0162; Fax 1-706-583-0160; Email paterson(a)plantbio.uga.edu
Web site: http://www.plantgenome.uga.edu/
Program Coordinators:
Anne A. Ogden, 706-583-0166, ogden(a)uga.edu
Melissa D. Brock, 706-583-0161, mbrock(a)uga.edu
