Progress 11/01/16 to 10/31/17
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The students were trained in modern genomics techniques relevant to plant breeding and crop improvement. The small format of the workshop made it easy for students to network with the instructors, and discussions continued throughout mealtimes and after the lecture, at the bar. Students gained in depth understanding of bioinformatics methods, and all data from the workshop, and workflows are permanently stored on Cyverse. Effectiveness of the workshop was assessed using a survey, filled out by for students. The responses were unanimously very positive ("exceptional" or "very good"), with statements such as: "The organizers should be congratulated on a brilliant, well organized and intense course, .... wonderful course, wonderful instructors... diversity of students was beneficial for discussions,.... I learned so much, and the experience was invaluable,.... I learned many tools that will greatly benefit my work, .... The workshop was a truly an amazing experience that has already benefited my research". From past experience, we find that students who have attended these workshops gain confidence and self-motivation, and a close bond with other students and instructors, important for future careers and networking. We believe that this workshop was a great success, and are planning a follow-up workshop in 2019. How have the results been disseminated to communities of interest?The workshop materials are freely available through Cyverse, for anyone who has a (free) CyVerse account in the Discovery Environment), URL: /iplant/home/shared/iplant_training/cereal_genomics_CSHL2016 What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
A highly successful Workshop on Cereal Genomics was held at Cold Spring Harbor Laboratory from October 19 - October 25, 2016. The lead instructors were Sarah Hake, University of California, Berkeley, Albany, CA, David Jackson, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY and Doreen Ware, USDA/ARS and Cold Spring Harbor Laboratory. The workshop trained 17 participants (graduate students or post docs, and we had balanced representation, with 8 Males and 9 Females, including 2 underrepresented minorities. Fourteen of the students were from the US, and 3 from overseas (Australia, China). Nine of the US students benefitted from USDA Scholarship Funding. The workshop covered the following topics, with lectures and hands on bioinformatics classes led by invited instructors, listed below. Instruction included a range of cereals, including maize, rice, wheat, sorghum, orphan cereal crops, brachypodium and setaria. Comparative anatomy and phylogeny; Cereal genomes, assembly, annotation and synteny; Genetics and databases; Quantitative trait locus mapping and genome wide association studies; Genome wide expression analyses; Reverse genetics and genome editing; Phenomics PARTICIPANTS: *Martin Alexander, Ph.D., Graduate Student, University of California, Berkeley, CA. Lab Head: Dr. Sarah Hake *Demeke Bayable, MSc, Graduate Student, Purdue University, West Lafayette, IN. Lab Head: Dr. Tesfaye Mengiste Andrew Bowerman, Ph.D., Post Doctoral Fellow, The Australian National University, AUSTRALIA. Lab Head: Dr. Barry Pogson Jennifer Brophy, Ph.D., Post Doctoral Fellow, Massachusetts Institute of Technology, Cambridge, MA. Lab Head: Dr. Christopher Voigt *Katherine Guthrie, Graduate Student, University of Missouri Columbia, MO. Lab Head: Dr. Paula McSteen *Brianna Haining, Graduate Student, University of California, Berkeley, CA. Lab Head: Dr. Sarah C. Hake *Harry Klein, Ph.D., Graduate Student, University of Massachusetts, Amherst, MA. Lab Head:Dr. Madelaine E. Bartlett *Stephanie Klein, Graduate Student, The Pennsylvania State University, University Park, PA. Lab Head: Dr. Jonathan Lynch Katie Liberatore, Ph.D., Post Doctoral Fellow, United States Department of Agriculture- Agricultural Research Service, St. Paul, MN. Lab Head: Dr. Shahryar Kianian Haijun Liu, Graduate Student, Huazhong Agricultural University, CHINA. Lab Head: Dr. Yan Jianbing *Elly Poretsky, Graduate Student, University of California, San Diego, CA. Lab Head: Dr. Alisa Huffaker Candace Seeve, Ph.D., Post Doctoral Fellow, United States Department of Agriculture- Agricultural Research Service, Columbia, MO. Lab Head: Dr. Melvin Oliver Xiaomeng Shen, Graduate Student, HuaZhong Agriculture Universiy, CHINA. Lab Head: Dr. Qifa Zhang *Ashley Smith, Graduate Student, University of Wisconsin, Milwaukee, WI. Lab Head: Dr. Dazhong Zhao Karyn Willyerd, Ph.D., Post Doctoral Fellow, Oklahoma State University, Stillwater, OK. Lab Head: Dr. Charles Chen *Kameron Wittmeyer, Ph.D., Graduate Student, Pennsylvania State University, University Park, PA. Lab Head: Dr. Surinder Chopra Chuanmei Zhu, Ph.D., Post Doctoral Fellow, Donald Danforth Plant Science Center, St. Louis, MO. Lab Head: Dr. Elizabeth Kellogg * USDA Scholarship support. Invited instructors: Edward Buckler, United States Department of Agriculture- Agricultural Research Service , Ithaca, NY "Breeding 4.0: Sorting through the adaptive and deleterious variants across the maize genome" Uta Paszkowski, University of Cambridge, Cambridge, United Kingdom "Genetics and genomics of endosymbiosis: fundamental science and translation" Devin Connor, University of Cambridge, Cambridge, United Kingdom "Brachypodium tools and their application to comparative developmental biology" Zhanguo Xin, United States Department of Agriculture- Agricultural Research Service, Lubbock, TX "Pedigree Mutant Library as a resource for forward and reverse genetics in sorghum" Patrick Brown, University of Illinois, Urbana, IL "Using sorghum to understand and improve stress resilience in cereals" Katrien Devos, University of Georgia, Augusta, GA "Use of genotyping-by-sequencing in the genomic analyses of non-model plants: from inbreeding diploids to outcrossing polyploids" Christopher Topp, Danforth Plan Science Center, Saint Louis, MO "Reality is a perception: using phenomics to explore the hidden world of plant phenotypes" Caixia Gao, Institute of Genomics and Developmental Biology, Beijing, China "Genome editing in wheat and corn" Matthew Hudson, University of Illinois, Urbana, IL "Extracting biological insight from gene expression data" "RNAseq methods and data analysis in complex genomes: dealing with uncertainty, alternative splicing" Andrea Eveland, Danforth Plant Science Center, Saint Louis, MO "Extracting biological insight from gene expression data" Lisa Harper, University of California Berkeley, Berkeley, CA "Cereals and their Genomes" Elizabeth Kellogg, University of Missouri Saint Louis, Saint Louis, MO "Introduction to the grasses and major sub-groups" "Evolution of ecologically dominant grasses" Doreen Ware, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY "Genome Assembly"
Publications
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