Invitation: CottonGen in the NRSP10 training workshop at PAG
by Main, Doreen
Hi Folks,
Please join us for the NRSP10 workshop at PAG which covers many aspects of using the database resources we develop that are implemented in CottonGen. The NRSP10 project is up for renewal and significantly funds work on CottonGen.
Workshop: Database Resources for Crop Genomics, Genetics and Breeding: NRSP10
When: Sunday January 13, 1.30 – 3.40 PM
Where: Meeting Room
Presentations
1.30: Overview of NRSP10 - Achievements and Future Plan (Dorrie Main)
1.45: Using the Online GenSAS Platform for Community Genome Annotation (Jodi Humman)
2.00: Tripal v3, the Collaborative Online Database Platform for Genomic, Genetic and Breeding
Databases
2.15: Using NRSP10 Data and Tools for Basic Research (Sook Jung)
2.30: Using NRSP10 Data and Tools for Translational Research (Cameron Peace)
2.45: Using NRSP10 Data and Tools for Breeding (Ksenija Gasic)
3.00: Global Performance Prediction Tool in Tripal BIMS (Craig Hardiner)
3.15: Open Discussion of NRSP10
Overview
NRSP10 is a USDA NIFA, industry and US Land Grant Universities funded project which provides standardized database and informatic resources for undeserved or specialty crops such as tree fruit, nuts, cotton and berries. It builds on existing database resources developed for Rosaceae (Genome Database for Rosaceae, www.rosaceae.org), Citrus (Citrus Genome Database, www.citrusgenomedb.org), Vaccinium (Genome Database for Vaccinium, www.vaccinium.org), Cool Season Food Legumes (Cool Season Food Legume Genome Database, www.csfl.org) and Cotton (CottonGen, www.cottongen.org). Developed using Tripal, an open-source, resource-efficient, modular, well supported software platform, these community databases provide centralized access to integrated genomic, genetic and breeding data and analysis tools for 24 crops representing a combined annual production value of over $25B. In this training workshop, we present progress in NRSP10 through a series of presentations by users and discuss the next 5 year plan for this project.
Cheers
Dorrie
Dorrie Main, PhD
Professor of Bioinformatics
Department of Horticulture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774 (office)
Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu>
URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>
1 year, 8 months
CottonGen Newsletter
by Main, Doreen
Hi Folks,
Please find attached the first biannual newsletter reporting new data and functionality in CottonGen.
If you have any questions or feedback please send them through the contact link on the CottonGen website.
Best regards
The CottonGen Team
Dorrie Main, PhD
Associate Professor of Bioinformatics
Department of Horticulture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774 (office)
Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu>
URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>
4 years, 4 months
Request for cotton germplasm
by Yu, Jing
Tahir Mehmood sent a message using the contact form at https://www.cottongen.org/contact
I'm a student of PMAS Arid agriculture University Rawalpindi, Pakistan. I'm
working on drought tolerant cotton for pothohar region and non irrigated
areas as well.
I need cotton germplasm for my research so pleas guide me that how i shall
get cotton germplam from your forum of research?
5 years, 1 month
requesting seed of cotton var. deltapine 61
by Yu, Jing
Dear Colleagues,
If you happen to know any information that helps R. JAGADEESWARAN (described in his email at below), please contact him at iari.nema(a)gmail.com
Thank you.
The cottongen team
________________________________________
From: cottongen-admin(a)cottongen.org [cottongen-admin(a)cottongen.org] on behalf of iari.nema(a)gmail.com [iari.nema(a)gmail.com]
Sent: Thursday, August 07, 2014 3:56 AM
To: Cheng, Chun-Huai; Main, Doreen; Yu, Jing
Subject: [Research Questions] requesting seed of cotton var. deltapine 61
R. JAGADEESWARAN sent a message using the contact form at
http://www.cottongen.org/contact.
respected sir/ madam
i am working as nematologist involved in development of resistant source in
pulse crops against root knot nematode in Indian institute of pulses
research, kanpur, india. deltapine 61 is an important variety of cotton
recommended to be used as differential host to identify host races in root
knot nematode, meloidogyne spp. i humbly request you to guide me how can i
get the seed of deltapine 61. sir/madam, i am assuring you this is only for
reearch purpose. thanks
6 years, 1 month
Post-Doctoral Research Associate Position at USDA-ARS, Stoneville MS, USA
by Yu, Jing
Job Description:
The Crop Genetics Research Unit in Stoneville, Mississippi seeks a Research Plant Molecular Biologist/Geneticist for a three-year post-doctoral appointment. The incumbent will join a multidisciplinary team conducting research to develop improved upland cotton germplasm with reniform nematode resistance. The incumbent will conduct molecular genetic investigations aimed at dissecting the genetic control of reniform nematode resistance in cotton. The assignment is to use molecular, genomic or genetic approaches to: 1) study expression, regulation and function of genes associated with reniform nematode resistance; 2) characterize spatial, temporal, and genotypic variation in gene expression and mechanisms leading to this variation; and 3) discover and validate DNA markers associated with resistance for marker-assisted selection to enhance the introgression of resistance into upland cotton.
How to Apply:
Send application materials to Dr. John Erpelding, USDA-ARS-CRGU, P.O. Box 345, Stoneville, MS 38776 or john.erpelding(a)ars.usda.gov. USDA-ARS is an equal opportunity provider and employer.
Qualifications:
The position requires a Ph.D. in plant molecular biology, plant genetics, plant physiology, plant biochemistry, plant pathology or related field. Knowledge of current methods used in plant molecular biology, including techniques used in DNA marker discovery and gene expression analysis are highly desirable. Knowledge or experience using statistical software for genomics-based analysis is needed. Although a US citizen is preferred, non-US citizens are welcome to apply. For more details about this position, please contact Dr. John Erpelding (Tel: 662 686 5220) or Dr. David Fang (david.fang(a)ars.usda.gov, Tel: 662 686 5401 or 504 655 0068).
6 years, 5 months
Postdoctoral Position, Cornell University, Ithaca NY, USA - immediately available
by Yu, Jing
A postdoctoral associate position in Quantitative Genetics and Genomics is immediately available in the Gore lab (http://plbrgen.cals.cornell.edu/people/michael-gore) in the Department of Plant Breeding and Genetics at Cornell University. This position is supported by a Cotton Incorporated Fellowship. The successful candidate will collaborate closely with a diverse team of scientists on an NSF funded project titled "A field-based high-throughput phenotyping platform for plant genetics." Specifically, the candidate will develop and apply statistical and computational approaches to identify quantitative trait loci controlling agronomic, fiber quality, and physiological traits in cotton. In addition, there will be opportunities for collaborative research on the development of novel high-throughput phenotyping approaches for cotton with USDA-ARS scientists located at the U.S. Arid-Land Agricultural Research Center in Maricopa, Arizona, and Kansas State University in Manhattan, Kansas (http://fieldphenomics.org/).
How to Apply
A letter of interest in the position, C.V., and contact information for three references should be emailed to Michael Gore at: mag87(a)cornell.edu
Contact
Michael Gore
Associate Professor
Department of Plant Breeding and Genetics Cornell University
310 Bradfield Hall
Ithaca, NY 14853
E-mail: mag87(a)cornell.edu
Vox: (607) 255-5492
Fax: (607) 255-6683
http://plbrgen.cals.cornell.edu/cals/pbg/people/faculty.cfm?netId=mag87
For more information please see
http://www.cottongen.org/sites/default/files/cottongen_jobs/Post_Dr_Assoc...
6 years, 5 months
Employment posting on CottonGen
by Main, Doreen
Hi Folks,
If you have employment opportunities relevant to the Cotton Genomics, Genetics and Breeding community, please feel free to send them to us and we will post them under our new Employment section.
Thanks
The CottonGen Team
Dorrie Main, PhD
Associate Professor of Bioinformatics
Department of Horticulture
Washington State University
45 Johnson Hall
Pullman, WA 99164-6414
Tel: 509-335-2774 (office)
Email: dorrie(a)wsu.edu<mailto:dorrie@wsu.edu>
URL: www.bioinfo.wsu.edu<http://www.bioinfo.wsu.edu/>
6 years, 10 months
CottonGen's article in Nucleic Acids Research
by Yu, Jing
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
6 years, 10 months
Reminders for the CottonGen Community
by Stelly, David
Greetings,
(This message is the same as one just distributed to ICGI members via the ICGI listserv, and so if you receive it as well as the CottonGen listserv, I apologize for the duplication.)
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, ICGI
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
6 years, 11 months
Cotton SNP Chip Information
by Stelly, David
Dear CottonGen 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
ICGI Co-Chair
6 years, 11 months