GDR-LIST

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332 discussions

GDR Training Workshop at PAG 2017

by Main, Doreen

Hi Folks, This year at PAG we will have a GDR workshop focusing on users of GDR providing training on various aspects of GDR. The 2 hr workshop (#4316) will be held between 4 to 6 PM on Saturday January 14 in the California Room and afterwards we can go and socialize somewhere :-) The topics and presenters are as follows: 04.00 PM Using GDR: An Overview<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Sook Jung 04:20 PM Use of Strawberry Genomic Resources in GDR<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Richard J. Harrison 04:40 PM Using the New Apple Genome Assembly v4.0 Data in GDR<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Riccardo Velasco, 05:00 PM The GDR Is a Critical Resource for Developing and Refining Trait-Predictive DNA Tests<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Cameron Peace 05:20 PM Using the Field Book App and BIMS in GDR for Peach Breeding<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Ksenija Gasic, 05:40 PM - Open Discussion on GDR<https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxv… > - Michael Coe If you are able to attend, would appreciate if you could add your name to the doodle poll that was emailed to you separately. Please forward to any students or other program members who may not be part of this list. Cheers Dorrie and Sook 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/>

8 years, 11 months

GDR Training Workshop at PAG

by Dorrie Main (via Doodle)

Hi there, Dorrie Main (dorrie(a)wsu.edu) invites you to participate in the Doodle poll "GDR Training Workshop at PAG." 04.00 PM Using GDR: An Overview - Sook Jung 04:20 PM Use of Strawberry Genomic Resources in GDR - Richard J. Harrison 04:40 PM Using the New Apple Genome Assembly v4.0 Data in GDR - Riccardo Velasco, 05:00 PM The GDR Is a Critical Resource for Developing and Refining Trait-Predictive DNA Tests - Cameron Peace 05:20 PM Using Field Book App and Bims in GDR for Peach Breeding - Ksenija Gasic, 05:40 PM - Open Discussion on GDR - Michael Coe Participate now https://doodle.com/poll/93epu5inh276ffnd?tmail=poll_invitecontact_participa… What is Doodle? Doodle is a web service that helps Dorrie Main to find a suitable date for meeting with a group of people. Learn more about how Doodle works. (https://doodle.com/features?tlink=checkOutLink&tmail=poll_invitecontact_par…) ---------------------------------------------------------------------- You have received this e-mail because "Dorrie Main" has invited you to participate in the Doodle poll "GDR Training Workshop at PAG." ---- Doodle is also available for iOS and Android. ---- Doodle AG, Werdstrasse 21, 8021 Zürich

8 years, 11 months

Post doc position “Evolution of genomes in the genus Rosa” at the Research Institute in Horticulture and Seeds (Angers, France)

by Sook Jung

Call for applications for a 17 months Postdoctoral Fellowship on “Evolution of genomes in the genus Rosa” at the Research Institute in Horticulture and Seeds (Angers, France) A 17-months postdoctoral researcher position is available at the University of Angers (France). The project is a collaboration between the "Research Institute of Horticulture and Seeds" in Angers, astride two teams “Genetics and Diversity of Ornamentals” (GDO, http://www6.angers-nantes.inra.fr/irhs_eng/Research/GDO) and “Bioinformatics” (BioInfo, http://www6.angers-nantes.inra.fr/irhs_eng/Research/BioInfo), and the group of Pr Thomas Debener from the “Institute for Plant Genetics” at the Leibniz University of Hannover (Germany; http://www.genetik.uni-hannover.de/index.html?&L=1). The project will be a bio-informatic analysis of the evolution of genomes in the genus Rosa, at two levels: (i) the research of structural variants (SVs), and (ii) the study of the evolution of resistance gene families (see details below). Applications are open for candidates who did not have spent more than 12 months in France within the last 3 years immediately prior to the expected date of recruitment. The net salary (after taxes) is 2409.58 €/month. The opportunity to apply for AgreenSkills programmes (https://www.agreenskills.eu/) may allow to increase this salary. The beginning of the contract is expected for February or March 2017. The postdoctoral researcher will be based in Angers, regularly cited as the most pleasant city to live in France, and at proximity to the Loire Valley. Travels are planned between Angers and Hanover. Summary of the project: The rose bush is the most economically important ornamental plant and the model plant for many studies about ornamental traits (flowering, fragrance, disease resistance). The rose bush, constituting the genus Rosa, has a complex evolutionary history with interspecific hybridization events and polyploidizations. Little information about these events is presently available, mainly hypotheses drawn from sparse molecular markers. Recently, as part of an international consortium, co-coordinated by the GDO team, the first version of the genome sequence of a variety of rose (Rosa chinensis cv. ‘Old Blush’) has been obtained. In this genomic context, we propose to study the evolutionary history of the genus Rosa by resequencing different species of the genus Rosa. The objective is to understand the evolution of genomes in the genus Rosa, and especially to focus on the processes that led to the creation of wild species, including polyploid ones, which are at the base of cultivated modern roses. From short reads (paired-end) obtained from different representative Rosa species involved in cultivated rose breeding, (i) the research of structural variants (SVs as insertions, deletions, duplications, inversion, translocations …), and (ii) the study of the evolution of resistance gene families will be conducted. Mission of the postdoctoral fellow: The production of raw reads will be done before the postdoc arrival. The hired postdoc with a strong background in bioinformatics or genome analysis will make a survey of the best methods to analyze structural variations in rose genomes. He/she will then be in charge of the computer bio-analyses to research the structural variants and to study gene family evolution. Expected skills: The desired applicant is expected to be a bioinformatician or a bioanalyst with an expertise in genome assembly and genetics. Expertise in the detection of genomic rearrangements, identification of homologous relations within gene family and/or gene family evolution study would be appreciated. Programming skills for one or several languages are needed. Social skills are also important for the success of interactions. Applications should be sent by email to jeremy.clotault(a)univ-angers.fr, fabrice.foucher(a)inra.fr, debener(a)genetik.uni-hannover.de and include a letter of motivation, a CV, and names and contact information of three referees. The dead line for application is January 3rd, 2017.

9 years

FW: RosEXEC 2017 membership election

by Ksenija Gasic

Dear Rosaceae community members, This is a final reminder to please cast your vote for RosEXEC membership. Thank you to all of those that already voted and apology for repeated emails. Voting is ending on November 4th. Thank you, Ksenija Gasic RosEXEC, Chair Elect and Membership Subcommittee Chair in 2016 From: Ksenija Gasic Sent: Monday, October 17, 2016 3:26 PM To: 'gdr-list(a)bioinfo.edu.edu' <gdr-list(a)bioinfo.edu.edu<mailto:gdr-list@bioinfo.edu.edu>>; 'rosexec-list(a)bioinfo.wsu.edu' <rosexec-list(a)bioinfo.wsu.edu<mailto:rosexec-list@bioinfo.wsu.edu>> Subject: RosEXEC 2017 membership election Dear Rosaceae Community Members: We are ready to vote on the 2017 candidates for RosEXEC. Voting begins October 17 and ends October 31st. Please go to the following web site on GDR to fill out your electronic ballot. You can learn more about any candidates' background and vision for RosEXEC contribution by clicking on their name. http://tinyurl.com/RosEXEC-voting2017 or https://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_m… The community will elect five new U.S. members and two new International members to a 3-year term. U.S.-based members vote for both U.S. candidates and International candidates. International community members vote for International candidates only. This year's slate is diverse. We encourage you to consider voting to create a leadership group that will appropriately represent the amazing diversity of the Rosaceae community. Current RosEXEC membership can be found at https://www.rosaceae.org/rosexec_2016 As a reminder, the mission of RosEXEC is to: * Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community * Define research priorities based on input from the industry and research community * Facilitate scientific interaction and foster dynamic research teams * Promote research priorities * Coordinate educational efforts from the research community to the industry and the public. Thanks again to the following U.S. and International members rotating off for their service to our community: U.S. International Gina Fernandez Michael Dossett Briana Gross Riccardo Velasco Duke Lane Gregory Reighard Gayle Volk Regards, Ksenija Gasic RosEXEC, Chair Elect and Membership Subcommittee Chair in 2016

9 years, 1 month

GDR Biannual Newsletter: Oct 2016

by Main, Doreen

Hi Folks, Please find attached the second 2016 GDR biannual newsletter highlighting work completed and work in progress. Please feel free to provide feedback or suggestions for improvement to GDR. Please note we will be holding an user-taught GDR workshop at PAG on Saturday, January 14th from 4 to 6.10 PM. As always, we thank you for your support of GDR . Cheers Dorrie, Sook and the GDR team 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/>

9 years, 1 month

Re: [GDR] RosEXEC 2017 membership election

by Ksenija Gasic

Dear Rosaceae community members, This is a friendly reminder to please take the time to vote for RosEXEC membership. To make sure you have enough time to do it voting has been extended till November 4th. Thank you, Ksenija Gasic RosEXEC, Chair Elect and Membership Subcommittee Chair in 2016 From: Ksenija Gasic Sent: Monday, October 17, 2016 3:26 PM To: 'gdr-list(a)bioinfo.edu.edu' <gdr-list(a)bioinfo.edu.edu>; 'rosexec-list(a)bioinfo.wsu.edu' <rosexec-list(a)bioinfo.wsu.edu> Subject: RosEXEC 2017 membership election Dear Rosaceae Community Members: We are ready to vote on the 2017 candidates for RosEXEC. Voting begins October 17 and ends October 31st. Please go to the following web site on GDR to fill out your electronic ballot. You can learn more about any candidates' background and vision for RosEXEC contribution by clicking on their name. http://tinyurl.com/RosEXEC-voting2017 or https://www.rosaceae.org/bio/content/?title=&url=/cgi-bin/gdr/gdr_rosexec_m… The community will elect five new U.S. members and two new International members to a 3-year term. U.S.-based members vote for both U.S. candidates and International candidates. International community members vote for International candidates only. This year's slate is diverse. We encourage you to consider voting to create a leadership group that will appropriately represent the amazing diversity of the Rosaceae community. Current RosEXEC membership can be found at https://www.rosaceae.org/rosexec_2016 As a reminder, the mission of RosEXEC is to: * Serve as a communication and coordination focal point for the U.S. Rosaceae genomics, genetics and breeding community * Define research priorities based on input from the industry and research community * Facilitate scientific interaction and foster dynamic research teams * Promote research priorities * Coordinate educational efforts from the research community to the industry and the public. Thanks again to the following U.S. and International members rotating off for their service to our community: U.S. International Gina Fernandez Michael Dossett Briana Gross Riccardo Velasco Duke Lane Gregory Reighard Gayle Volk Regards, Ksenija Gasic RosEXEC, Chair Elect and Membership Subcommittee Chair in 2016

9 years, 1 month

Post-Doc position in Fruit Tree Architecture at Michigan State University

by Courtney Hollender

Dear All, I am seeking a post-doc to work on a project focused on fruit tree architecture. The ad is below. Please forward to anyone you think may be interested. Thank you for your help. Sincerely, Courtney Hollender, PhD Assistant Professor Department of Horticulture Plant and Soil Science Building 1066 Bogue Street, Room A342-C Michigan State University East Lansing, MI 48824-1325 office: (517) 353-0446 — Post-Doctoral Scientist Position in Plant Architecture Available at Michigan State University The Hollender Lab in the Department of Horticulture at Michigan State University is seeking a post-doctoral scientist for a project on plant architecture. The goal of this project is to identify molecular and genetic mechanisms underlying aspects of shoot architecture, including branch orientation, and apply this knowledge to tree fruit agriculture. This project is part of an on-going program in deciduous fruit tree breeding. The research project relies on molecular biology, genetics, and genomics techniques and utilizes both model plant systems and fruit trees (eg. apple, cherry, and plum). Requirements include a PhD, a strong background in plant molecular biology and genetics, excellent written and oral communication skills, and an interest in transitioning the research to the field (orchard). A background in plant development or experience with bioinformatics (e.g. genomic and transcriptomic sequencing analysis) is preferred. No prior experience with trees or other crops is necessary, but enthusiasm for horticulture and tree fruit agriculture is required. Candidates should email a single PDF file containing their CV, contact information for three references, and a cover letter describing their interests in plant biology and future goals to Dr. Courtney Hollender (chollend(a)msu.edu <mailto:chollend@msu.edu>). Please write “Tree Architecture Post-Doc” in the subject line. The position is available as early as December 2016.

9 years, 1 month

Postdoctoral Employment Opportunity at Cornell.

by Main, Doreen

Cornell University – College of Agriculture and Life Sciences School of Integrative Plant Science – Section of Plant Pathology and Plant Microbe Biology New York State Agricultural Experiment Station, Geneva, New York Post-Doctoral Associate Position We are seeking a highly motivated postdoctoral researcher with an interest in interdisciplinary research into understanding disease resistance mechanisms in rosaceous fruit trees. The primary responsibility of this position is to identify loci, pathways, and candidate genes underlying disease resistance in rosaceous fruit trees using a combination of omics and quantitative genetic approaches. The responsibilities of the candidate are: 1) to conduct research to understand resistance/susceptibility mechanisms in rosaceous fruit trees; 2) identify QTLs, candidate genes, and underlying disease resistance pathways using omics and bioinformatics approaches; 3) support development of research proposals; and 4) present at international conferences and publish peer-reviewed journal articles. Specific Work Responsibilities: Specific focus of this position will be Genetics of Disease Resistance in Apples (85%): QTL and association mapping to dissect genetic basis of apple diseases Bioinformatics to mine high-throughput omics data for candidate gene identification Design molecular biology and transcriptomics experiments to identify and validate candidate genes Research Communication (10%): Excellent presenter at scientific meetings, seminars, workshops and to develop both web-based and traditional tools for outreach and research extension. Proposal Development (5%): Motivated and creative thinker to support development of research proposals for basic and applied plant genetics and molecular biology. Required Qualifications: Must possess a PhD in plant molecular biology, plant genetics/breeding, plant pathology, or a related field. Must have demonstrated experience with work in molecular biology laboratory, greenhouse and field for plant pathology, molecular markers and quantitative genetics. Must have first-author publications in peer-reviewed journals. Ambitious and self-motivated. Preferred Qualifications: Experience and interest in application of CRISPR/CAS based genome editing is desirable. Candidate should have excellent writing and oral communication skills, and a record of publications in highly respected peer-reviewed journals. Candidate should be able to multi-task and have good time management and attention to detail to meet tight deadlines, and work independently to initiate communications and collaborative research. Creativity and pro-activeness are assets, as well as enthusiasm to work and interact in an international scientific environment. Excellent student supervision/mentoring skills are beneficial. Interested candidates should send letter of motivation, Curriculum Vitae, and names and contact information for three references to: Awais Khan, Ph.D., Associate Professor, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, New York State Agricultural Experiment Station Cornell University 221 Barton Lab, 630 West North Street Geneva, NY 14456 USA Email: awais.khan(a)cornell.edu<mailto:awais.khan@cornell.edu> 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/>

9 years, 2 months

Research Associate, Molecular Fruit Breeding Program at Sun World

by Ksenija Gasic

[cid:image005.jpg@01D217FB.6D4738E0] Research Associate, Molecular Fruit Breeding Program at Sun World Innovations Variety Development Center About the Role: Sun World Innovations, a division of Sun World International LLC (www.sun-world.com<http://www.sun-world.com/>), is seeking applicants for a Research Associate position for its molecular fruit breeding program at the renowned Sun World Innovations Variety Development Center located near Bakersfield, California. The Research Associate will work with breeders, research associates and others at the Variety Development Center in the areas of marker assisted selection and other molecular capabilities, as well as post harvest evaluations within the breeding programs to aid in the identification and development of new table grape and stone fruit varieties. Responsibilities include management of the molecular and post harvest labs as well as coordination of greenhouse seedling organization and field seedling phenotyping, as related to Molecular Lab work. The Research Associate will also be involved in other duties in the breeding programs as needed. At Sun World, all jobs include broad responsibilities for continually improving the processes and tools used to develop new fruit varieties. Specific skills required include previous experience with large-scale DNA extraction, PCR/qPCR, and allele calling. Background in association analysis, QTL analysis, and candidate gene work for marker development are preferred. Additionally, experience with fruit post-harvest lab operation is preferred but not required. About the Company: Sun World International LLC is one of California's top table grape grower-marketers and operates the world's preeminent fruit breeding and licensing enterprise with more than 1,600 licensed growers on five continents. The company's variety development center focuses on development of new seedless table grape, peach, nectarine, plum, apricot, and cherry varieties. Sun World's company culture is to create a supportive work environment that nurtures open and friendly communication, provides targeted focus and direction, and encourages collaboration and team interaction. Sun World is committed to providing opportunities for individuals to grow along with the company, as well as cultivate their personal well-being. The successful candidate will have the following skills, experience and attributes: * M.S. degree and/or 2+ years' hands-on experience in plant molecular biology, molecular plant breeding, molecular plant pathology, or a related field. Demonstrated experience in plant molecular biology techniques is required. * Expertise with techniques required for marker-assisted breeding (i.e. DNA extraction, PCR/qPCR, and allele calling on a large scale) and other molecular techniques that support a molecular breeding program. * Excellent laboratory and greenhouse organizational skills with attention to detail. * Expertise using, maintaining, and troubleshooting equipment, and protocols used in a molecular biology lab. * Ability to perform molecular biology research with commercial kits and classical protocols that require preparation of diverse reagents and materials. * Strong passion for working with fruit; self-motivated, dedicated, and willing to work and balance a diverse set of yearly tasks. * A positive team member, excellent communicator, and willing collaborator across diverse scientific disciplines. Interested candidates should submit a letter of interest, CV and summary of scientific work to: [cid:image006.jpg@01D217FB.6D4738E0]Sun World International LLC, Human Resources Department 5701 Truxtun Avenue, Suite 200, Bakersfield, CA 93308 twoods(a)sun-world.com<mailto:twoods@sun-world.com>, 661-631-4100

9 years, 2 months

RosEXEC membership nomination

by Ksenija Gasic

Dear All, RosEXEC (the U.S. Rosaceae Genomics, Genetics, and Breeding Executive Committee,) is ready for another round of elections to renew membership for 2017. As a reminder, RosEXEC helps coordinate research initiatives in the U.S. Rosaceae Genomics, Genetics, and Breeding community (www.rosaceae.org/community/us_rosexec<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rosaceae.org_commun…>). We need nominations! We are looking to add five new U.S. members (three-year terms) and two new international liaisons (two-year terms). If you are willing to join or know of someone else who would be great for RosEXEC participation, please email me at kgasic(a)clemson.edu<mailto:kgasic@clemson.edu>the following info for each nominated candidate prior to Monday 10th October<x-apple-data-detectors://7>: * name * CV (short version) * brief statement (100-word max) on proposed contributions to the RosEXEC mission Just names are good enough to get us moving – although if you are nominating someone else, it’s best if you have checked their interest first. I can contact them soon after to obtain the CV and brief statement. Past service: Five U.S. people will be rotating off as of Jan 2017, after three-year terms: Gina Fernandez, Briana Gross, Duke Lane, Greg Reighard and Gayle Volk, who served as Chair in 2015. Two international liaisons will also be rotating off after two-year terms: Michael Dossett and Riccardo Velasco. Thanks to all of these RosEXEC members for their service! As a reward, these people get a one-year respite (unless voted in as the 2017 Secretary) and so are not eligible for immediate re-election. However, those who rotated off in prior years are allowed to rejoin. Current members continuing into 2017 are, Cameron Peace (Chair -> Past Chair) Ksenija Gasic (Vice chair -> Chair), Mercy Olmstead (Secretary -> Vice Chair), Richard Bell, Jill Bushakra, Chunxian Chen, Amy Iezzoni, Kenong Xu, Bob Curtis, Steve Knapp, Jim McFerson, Vance Whitaker, Eric van de Weg (Intl), David Chagne (Intl), and Dorrie Main (ex officio). Diversity is important to any committee – we aim to represent (1) roughly equally the various Rosaceae crop production and research regions of the U.S., (2) at least a couple members each of university, government / USDA-ARS, and industry, (3) rosoid, pome, and stone fruit research focuses, roughly equally, and (4) various parts of the rest of the research world. Current members continuing into 2017 add up to: U.S. regions: 3 south, 3 east, and 6 west – slightly skewed towards west Institutions: 7 university, 2 government, 1 industry – need more industry and govt Crop groups: 3.0 rosoid, 2.8 pome, and 6.3 stone – need more rosoid and pome International: 1 NZ/Aus, 1 Europe – need Asia, S. Africa, Down Under, S. America The only mandate for new 2017 membership is that one U.S. member must be industry. Details above are just a guide for areas most needing representation. Another area that would be particularly useful to have represented is bioinformatics (in Rosaceae), given RosEXEC’s recently acquired new role as steering committee for the GDR. Our next in-person, open meeting will be within the Plant & Animal Genome (PAG) Conference in San Diego, CA on Sunday January 15, 2017 from 8-10 am<x-apple-data-detectors://12>. All welcome! Specific details will be distributed closer to the event. Timeline: Nominations to me by Monday 10th October<x-apple-data-detectors://13> Voting will be carried out 17 -31 October<x-apple-data-detectors://14> (U.S. researchers may cast votes) New members will be announced by mid-November Secretary nominations and election (internal RosEXEC process) by Christmas/the PAG meeting Regards, Ksenija RosEXEC Vice Chair and Membership Subcommittee Chair in 2016

9 years, 3 months

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GDR-LIST