Progress 05/01/20 to 03/29/21
Outputs
Target Audience:PARTICIPANTS: *Christian Cantos, MS, Graduate Student, Penn State University, Department of Biology, University Park, PA. Lab Head: Dr. SarahAssmann Jeongmin Choi, PhD, Postdoctoral Fellow, University of Cambridge, Department of Plant Sciences, Cambridge, UK. Lab Head: Dr. Uta Paszkowski *Anju Giri, PhD, Postdoctoral Fellow, Cornell University, Institute of Genomic Diversity, Ithaca, NY. Lab Head: Dr. Edward Buckler Yasmeen Haider, Graduate Student, Arcadia Biosciences, Research and Development, Davis, CA. Lab Head: Dr. Randy Schultz Sessen Iohannes, Graduate Student, Sant'Anna School of Advanced Studies, Agricultural Sciences and Biotechnology, Pisa, Italy. Lab Head: Mario Enrico Pe' Emmanuel Iwuala, MS, Graduate Student, University of Lagos, Botany, Lagos, Nigeria.Lab Head: Dr. Caroline Umebese *Sunil Kumar Kenchanmane Raju, PhD, Postdoctoral Fellow, Michigan State University, Plant Biology, East Lansing, MI. Lab Head: Dr. Chad Niederhuth Hyun-Sook Lee, PhD, Postdoctoral Fellow, Department of Agronomy, Chungnam National University, Daejeon, South Korea. Lab Head: Dr. Sang-Nag Ahn Cathal Meehan, Graduate Student, University of Warwick, School of Life Sciences, Coventry, UK. Lab Head: Dr. Jose Gutierrez-Marcos *Queen Obi, MS, Staff Scientist, International Institute of Tropical Agriculture, Bioscience Unit, Ibadan, Nigeria. Lab Head: Dr. Melaku Gedil *Jeremy Pardo, Graduate Student, Michigan State University, Plant Biology, East Lansing, MI. Lab Head: Dr. Robert VanBuren Pratishtha Poudel, MS, Graduate Student, Oklahoma State University, Plant and Soil Sciences, Stillwater, OK. Lab Head: Dr. Phillip Alderman Curtis Provencher, MS, Staff Scientist, Inari Agriculture, Digital, Cambridge, MA.Lab Head: Dr. Alex Wimbush Rency Raquid, Graduate Student, International Rice Research Institute, Strategic Innovation Platform, Los Baños, Laguna, Philippines. Lab Head: Dr. Jae Sung Lee Armin Patrick Scheben, PhD, Postdoctoral Fellow, Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY. Lab Head: Dr. Adam Siepel *Salome Suarez, MS, Graduate Student, Oklahoma State University, Entomology and Plant Pathology, Stillwater, OK. Lab Head: Dr. Stephen Marek 16 Participants (8 Female, 8 Male, 1 URM) * USDA Scholarship support Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?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 lectures. 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 surveyfilled out by students. The responses were unanimously very positive ("exceptional" or "very good"), with statements such as: "welcoming environment, helpful instructors"...."inclusion of several instructors pioneering in the field"..... "diversity of participants"...."really life changing stuff".... "meeting world class leaders in research"... "carefully chosen topics that gave a very broad overview of field". 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. This workshop was a great success, and we believe it will be game changing for the students' careers. 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 What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This one-week workshop in Cereal Genomics enabled participants to take advantage of emerging genetic tools and the completed cereal genome sequences of most of the major cereal crops. The workshop featured morning and evening lectures with afternoon lab exercises, including hands-on lab work and computer sessions in comparative anatomy, GWAS, Next Gen expression analysis, whole genome sequencing assembly, emerging model systems, genome editing and phenomics. The faculty (instructors and invited lecturers) were/are active researchers in cereal genetics and genomics who have made significant contributions to the field, ensuring that the latest techniques and ideas were presented. The course was structured to provide time for informal discussions and exchange with instructors. Topics Included: 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 SEMINARS: Edward Buckler, USDA-ARS, Ithaca, NY "Nucleotide level natural variation and genetic architecture" "QTL Mapping and Prediction" "Machine learning the central dogma of molecular biology" 'Learning from evolution and molecular biology for a new agriculture" Katrien Devos, University of Georgia, Augusta, GA "Genetic analysis of non-model plants: challenges and successes" Jorge Dubcovsky, University of California Davis, Davis, CA "Resources for Wheat Functional Genomics" Andrea Eveland, Donald Danforth Plant Science Center, St. Louis, MO "Extracting biological insights through multi-omics data integration" Elizabeth Kellogg, Donald Danforth Plant Science Center, St. Louis, MO "Introduction to the grass family" Sam Leiboff, University of California, Berkeley, Albany, CA "Hands-on RNAseq: from maize sequence to developmental inference" Devin O'Connor, Pairwise Plants, Research Triangle Park, NC "Enabling comparative biology with comparative genomics tools" Uta Paszkowski, University of Cambridge, UK "Molecular Genomics of arbuscular mycorrhizal symbiosis in cereals" Christopher Topp, Donald Danforth Plant Science Center, St. Louis, MO "Plant Phenomics" Bing Yang, University of Missouri, Columbia, MO "Reverse Genetics & Genome Editing"
Publications
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Progress 05/01/20 to 11/23/20
Outputs
Target Audience:PARTICIPANTS: *Christian Cantos, MS, Graduate Student, Penn State University, Department of Biology, University Park, PA. Lab Head: Dr. SarahAssmann Jeongmin Choi, PhD, Postdoctoral Fellow, University of Cambridge, Department of Plant Sciences, Cambridge, UK. Lab Head: Dr. Uta Paszkowski *Anju Giri, PhD, Postdoctoral Fellow, Cornell University, Institute of Genomic Diversity, Ithaca, NY. Lab Head: Dr. Edward Buckler Yasmeen Haider, Graduate Student, Arcadia Biosciences, Research and Development, Davis, CA. Lab Head: Dr. Randy Schultz Sessen Iohannes, Graduate Student, Sant'Anna School of Advanced Studies, Agricultural Sciences and Biotechnology, Pisa, Italy. Lab Head: Mario Enrico Pe' Emmanuel Iwuala, MS, Graduate Student, University of Lagos, Botany, Lagos, Nigeria.Lab Head: Dr. Caroline Umebese *Sunil Kumar Kenchanmane Raju, PhD, Postdoctoral Fellow, Michigan State University, Plant Biology, East Lansing, MI. Lab Head: Dr. Chad Niederhuth Hyun-Sook Lee, PhD, Postdoctoral Fellow, Department of Agronomy, Chungnam National University, Daejeon, South Korea. Lab Head: Dr. Sang-Nag Ahn Cathal Meehan, Graduate Student, University of Warwick, School of Life Sciences, Coventry, UK. Lab Head: Dr. Jose Gutierrez-Marcos *Queen Obi, MS, Staff Scientist, International Institute of Tropical Agriculture, Bioscience Unit, Ibadan, Nigeria. Lab Head: Dr. Melaku Gedil *Jeremy Pardo, Graduate Student, Michigan State University, Plant Biology, East Lansing, MI. Lab Head: Dr. Robert VanBuren Pratishtha Poudel, MS, Graduate Student, Oklahoma State University, Plant and Soil Sciences, Stillwater, OK. Lab Head: Dr. Phillip Alderman Curtis Provencher, MS, Staff Scientist, Inari Agriculture, Digital, Cambridge, MA.Lab Head: Dr. Alex Wimbush Rency Raquid, Graduate Student, International Rice Research Institute, Strategic Innovation Platform, Los Baños, Laguna, Philippines. Lab Head: Dr. Jae Sung Lee Armin Patrick Scheben, PhD, Postdoctoral Fellow, Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY. Lab Head: Dr. Adam Siepel *Salome Suarez, MS, Graduate Student, Oklahoma State University, Entomology and Plant Pathology, Stillwater, OK. Lab Head: Dr. Stephen Marek 16 Participants (8 Female, 8 Male, 1 URM) * USDA Scholarship support Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?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 lectures. 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 surveyfilled out by students. The responses were unanimously very positive ("exceptional" or "very good"), with statements such as: "welcoming environment, helpful instructors"...."inclusion of several instructors pioneering in the field"..... "diversity of participants"...."really life changing stuff".... "meeting world class leaders in research"... "carefully chosen topics that gave a very broad overview of field". 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. This workshop was a great success, and we believe it will be game changing for the students' careers. 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 What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
This one-week workshop in Cereal Genomics enabled participants to take advantage of emerging genetic tools and the completed cereal genome sequences of most of the major cereal crops. The workshop featured morning and evening lectures with afternoon lab exercises, including hands-on lab work and computer sessions in comparative anatomy, GWAS, Next Gen expression analysis, whole genome sequencing assembly, emerging model systems, genome editing and phenomics. The faculty (instructors and invited lecturers) were/are active researchers in cereal genetics and genomics who have made significant contributions to the field, ensuring that the latest techniques and ideas were presented. The course was structured to provide time for informal discussions and exchange with instructors. Topics Included: 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 SEMINARS: Edward Buckler, USDA-ARS, Ithaca, NY "Nucleotide level natural variation and genetic architecture" "QTL Mapping and Prediction" "Machine learning the central dogma of molecular biology" 'Learning from evolution and molecular biology for a new agriculture" Katrien Devos, University of Georgia, Augusta, GA "Genetic analysis of non-model plants: challenges and successes" Jorge Dubcovsky, University of California Davis, Davis, CA "Resources for Wheat Functional Genomics" Andrea Eveland, Donald Danforth Plant Science Center, St. Louis, MO "Extracting biological insights through multi-omics data integration" Elizabeth Kellogg, Donald Danforth Plant Science Center, St. Louis, MO "Introduction to the grass family" Sam Leiboff, University of California, Berkeley, Albany, CA "Hands-on RNAseq: from maize sequence to developmental inference" Devin O'Connor, Pairwise Plants, Research Triangle Park, NC "Enabling comparative biology with comparative genomics tools" Uta Paszkowski, University of Cambridge, UK "Molecular Genomics of arbuscular mycorrhizal symbiosis in cereals" Christopher Topp, Donald Danforth Plant Science Center, St. Louis, MO "Plant Phenomics" Bing Yang, University of Missouri, Columbia, MO "Reverse Genetics & Genome Editing"
Publications
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