1:00 pm EST Agricultural Genomics: The Rise of Genomes
Doreen Ware, Ph.D., Molecular Biologist, USDA Agricultural Research Service and Adjunct Professor, Cold Spring Harbor Laboratory, New York
Breeding for 2050 and beyond will require designing plants for new environments and preparing them for new diseases, while they are still offshore. Key to this effort will be access to high-quality genomes and annotations for agricultural species and their pests. The genomes of many plants have been sequenced over the past decade, but these are usually limited to one reference assembly. The available genomes are often fragmented and missing complex repeat regions—and so lack sufficient high-level representation of genes and functional variation within a species. We are now entering an era where genome assemblies are reaching a theoretical maximum of contiguity and completeness—at ~0.1% the cost of 10 years ago. This provides an unprecedented opportunity to access genomic information to dissect complex agronomic traits and to provide insights into species evolution.
2:00 pm EST Emerging Trends in Agricultural Diagnostics
Zach Bateson, Ph.D., Research Scientist, National Agricultural Genotyping Center, Fargo, ND
Pests and pathogens account for up to 30% of the annual losses in food crops worldwide. All agricultural commodities are negatively impacted by pests, either directly in the field or indirectly through the supply chain. Molecular diagnostics to identify and manage threats in agriculture lag behind diagnostic applications in the medical sciences, despite deep connections between agriculture and human health. In this webinar, I describe the diagnostic biotechnology used at the National Agricultural Genotyping Center (NAGC) and how diagnostic data provide insights into emerging threats across the agricultural community. Specifically, I discuss research underway at the NAGC that helps: 1) identify drivers of colony losses impacting the honeybee industry, 2) quickly detect herbicide resistant weeds, and 3) measure environmental pathogen densities to develop predictive models for crop diseases. While the research is diverse in scope, the diagnostic methods take advantage of a commonality across all pests and pathogens—the genetic code.
3:00 pm EST Clones, Carbon and Climate Change: The Epigenetics of Oil Production
Rob Martienssen, Ph.D, Professor, Cold Spring Harbor Laboratory, NY
The African oil palm is the most efficient oil bearing crop, but demand for edible oils and biofuels, combined with sustainability concerns over dwindling rainforest reserves, has led to intense pressure to improve oil palm yield. The fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield—and has largely halted efforts to clone elite hybrids for oil production. Using epigenome wide association studies, we found that loss of methylation of a LINE retrotransposon related to rice Karma predicts mantled fruit. Identifying “bad Karma” in cloned plantlets allows growers to cull mantled palms before they reach the field. Since many palms in a given plantation are low-yielding, the broad introduction of high-performing clones promises to reduce the land needed to meet world requirements for palm oil.
About the speakers
Doreen Ware (left) is recognized as a leader in plant genomics and bioinformatics. Over the last several years her laboratory has contributed to collaborative projects supporting genomics-enabled science with a focus on understanding plant genome architecture and its impact on complex traits—including grain yield, response to nitrogen, and disease resistance. Dr. Ware’s group has contributed to the development of reference genome resources for rice, maize, sorghum and grape, as well as Cyberinfrastructure projects to support access and integration of genome-scale data. Dr. Ware serves in several leadership positions within the plant science community and was acting Chief Scientific Information Officer for USDA Agricultural Research Service (ARS) from 2014-2017.
Trained as a population geneticist, Zack Bateson (center) has used bioinformatics and molecular diagnostics for the last 15 years to investigate issues in conservation genetics and agriculture. Dr. Bateson is currently lead research scientist at the National Agricultural Genotyping Center (NAGC), a not-for-profit, ISO-accredited testing facility. At NAGC, he and colleagues develop molecular-based tests to rapidly identify pathogens and pests that threaten crops and livestock around the United States. NAGC is also the primary testing facility for the National Predictive Modeling Tool Initiative, a new USDA ARS collaborative project that aims to help farmers predict disease outbreaks. Dr. Bateson is a part-time instructor at North Dakota State University in Fargo.
Rob Martienssen (right) studies epigenetic mechanisms that shape and regulate the genome, and their impact on transposable elements, first discovered by Barbara McClintock at Cold Spring Harbor Laboratory. These mechanisms underlie clonal propagation of oil palm, with implications for rain forest conservation, and of aquatic plants, including the humble duckweed, that are being engineered in the Martienssen lab for biofuel production and carbon sequestration. The link between epigenetics and RNA interference was named “Breakthrough of the Year” by Science magazine in 2002. Dr. Martienssen joined the faculty at Cold Spring Harbor in 1989. He is a Fellow of the Royal Society and a Howard Hughes Medical Institute Investigator. He was awarded the McClintock Prize in 2018 and the Darwin Medal in 2020.