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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).

12 years, 3 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-2…

12 years, 3 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/>

12 years, 8 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

12 years, 8 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

12 years, 8 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

12 years, 9 months

CottonGen and ICGI Mailing List Clarification

by Main, Doreen

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

13 years, 3 months

Re: [CottonGen] [ICGI] A survey about using cotton genome resources

by Andrew Paterson

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

13 years, 3 months

A survey about using cotton genome resources

by Yu, Jing

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

13 years, 3 months

The draft G. raimondii sequence data is now in CottonGen

by Yu, Jing

Dear Cotton Researchers, The CottonGen team is pleased to announce the availability of the draft G. raimondii (D genome) presented in the Wang et al., 2012 Nature Genetics publication, graciously provided by Drs. Shuxun Yu, Jun Wang and Yu-Xian Zhu to CottonGen. The assembly includes their pseudomolecules, predicted genes, non-coding RNA and repeats. In addition, the CottonGen team has aligned to the genome several commonly used resources such as CottonGen RFLP, SSR, and SNP markers, NCBI cotton dbSNP, CottonGen unigenes, PlantGDB unigenes, Josh Udall's 454-derived transcript contigs, NCBI cotton dbEST, NCBI cotton mRNA and protein sequences from various plant genomes. Additionally, the gene models have been annotated with Gene Ontology (GO), InterPro (IPR) domains and KEGG pathways and orthologs. The assembly and all ancillary annotations and alignments are available for exploration with GBrowse on the CottonGen website and are available for sequence comparison on our BLAST servers. All files are available for download on the CottonGen G. raimondii genome page or from our FTP repository. In the near future we will be adding a page for each gene providing all functional and structural details. Another announcement will be sent when these additional resources are available. Here are some quick links: Draft G. raimondii genome page http://www.cottongen.org/species/Gossypium_raimondii/bgi-cgp_genome_v1.0 GBrowse Viewer: http://www.cottongen.org/gb/gbrowse/CGP_Dgenome/ FTP downloads: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_raimondii/CGP-BGI_G.raimondii_D… NCBI BLAST (returns results to screen): http://www.cottongen.org/tools/blast Batch BLAST (returns results parsed in an excel file): http://www.cottongen.org/tools/batch_blast The CottonGen team

13 years, 8 months

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