IWGC Conference

August 9, 2021 is the registration deadline to participate in the workshop survey and in preparation for training. Registrations after that deadline will still be able to participate in the meeting, but will miss out on the pre-meeting communication for the workshop and training.

International Weed Genomics Consortium
Conference Agenda

September 22-24, 2021
Sheraton Crown Plaza
Kansas City, MO

Hybrid conference – in-person and virtual attendance options

Registration website: https://conferencereg.colostate.edu/IWGC2021

  • Both virtual and in-person registration options are available
  • Full conference registration is $200 for students and $400 for professionals from academia, government, and industry; this full event registration includes attendance at all sessions on all 3 days, lunch and networking receptions on Days 1 and 2, and access to the online virtual conference platform
  • New: two day (Thursday and Friday) registration for $125 (both students and professionals); this 2 day registration includes the scientific program on day 2 and the workshop on day 3, along with lunch and networking reception on day 2, and access to the online virtual conference platform

Reserve your room at the Sheraton Crown Plaza.

Information for Early Career Travel Award Applications, due July 16, 2021

Submit poster abstracts by August 15, 2021


Day 1, September 22: Training Day
8 am – 12:30 pm: KeyGene training on CropPedia database

1 pm – 5:30 pm: Training workshops

Attendees will select 3 of the 5 workshops to attend

Workshops:

  1. Molecular Biology 101: Dana MacGregor
    1. In this 1.25-hour session, you will gain an understanding of the processes that plants use create, regulate, and modify the macromolecules that sustain life. Our focus will be on deoxyribonucleic acids (DNA), ribonucleic acid (RNA), and proteins – what they are, what they do, and how they can be changed and measured. You will not only learn how the  composition and structure of these macromolecules defines their functionalities, but how they interact with one another and the consequences of those interactions. This workshop will define but go beyond the “Central Dogma”, as we will examine the ways these macromolecules are modified and how those modifications can alter plant growth and behaviour. We will explain the different techniques that can be used to find changes in DNA, RNA, or proteins across different scales, and how to functionally validate the consequences of these changes. Examples from the weed science literature will demonstrate how these macromolecules can be changed naturally (through selection and adaptation) and intentionally (through modifications performed in the laboratory). Our examples will then illustrate how these modifications alter the plant’s ability to survive the challenges of the agri-ecosystem. At the end of the session you will have a better understanding of what DNA, RNA and proteins are, the different roles they play within a cell, how to change their form and how that leads to changes in function, and how those modifications change the responsiveness and/or behaviour plants; all of which will better enable you to consider how DNA, RNA and proteins allow weeds to be weedy.
  2. RNA-Seq pipelines: Darci Giacomini
    1. RNA sequencing (RNA-seq) has become the preferred method for analyzing gene expression and uncovering novel RNA splicing events in an organism. It uses next-generation sequencing to get a snapshot of the RNA molecules present at any one time and compare that RNA expression profile across time, treatments, or genotypes. In this module, we will learn the basics of RNA-seq analysis, including what to consider before embarking on an RNA-seq study, the best practices for setting up and executing a successful RNA-seq experiment, and what tools and workflows are available to get you analyzing on your own. During the session, we will walk through the analysis of an example RNA-seq data set in real time, using the Kallisto/Sleuth workflow to quickly and accurately quantify transcript abundance. Participants will gain practical experience in running command-line Linux based analysis on the cloud, (psuedo)aligning RNA-seq data to a reference transcriptome, performing differential expression analysis, and visualizing the results in RStudio. Experience with the command line and R is helpful but not required.
  1. Mapping herbicide resistance and quantitative traits: Brent Murphy and Jake Montgomery
    1. This workshop will center around utilizing genetic mapping approaches to identify genes or genomic regions associated with traits of interest. The session will be split into two sections, with the first half focusing on quantitative trait loci (QTL) mapping and the second on genome-wide association studies (GWAS). The first section will start with genotype variants already having been called and phenotypes already having been collected from a simulated segregating F2 population. We will use the qtl2 package in R to associate these two data sets and identify regions of the simulated genome that are causing our trait of interest. This first section will finish with some discussion on the benefits and limitations of QTL mapping. The second half of the session will focus on using the GAPIT package in R for GWAS. In this section, we will use a simulated dataset derived from Palmer amaranth to identify herbicide resistance mechanism presence and distribution throughout the United States. We will discuss file formatting, model selection, and analysis of data output produced by GAPIT, with a focus on how the genomic analysis can address important questions in weed science.
  2. Command Line 101: Nathan Hall
    1. Scientific computing, from HPCCs, to custom bioinformatics analysis  often requires the use of the command line in a unix environment. In this section participants will learn basics for navigating and interacting with their programs and data from the command line. In this hands on sessions we will securely access a virtual machine on Amazon Web Services, navigate through file system, and explore genomic data using basic commands.
  3. Population genomics for weeds: Sara Martin
    1. R can be a powerful and flexible tool for analyzing SNP data for population genomics. In this section participants will develop familiarity with these tools by using packages such as poppr, adegenet, and hierfstat. We will import data and perform analyses 1) calculating basic population statistics, 2) producing a principal component analysis of molecular variance, and 3) creating a neighbour joining tree.

6 pm: Welcome networking reception

Day 2, September 23: Scientific Presentations

TimeTopicSpeaker
8:00 – 8:30Introduction and Recognition of Grant Agencies and Sponsors   USDA-NIFA and FFARTodd Gaines
8:30 -10:00Keynote Session: The Problem and Tools/Resources 
8:30 – 9:00Examples and use cases from an industrial herbicide research perspectiveJens Lerchl, BASF & Fanny Gatzmann
9:00 – 9:30Applying State of the Art Genomics on Non-Model Plants: Not a Contradiction in TermsKatrien Devos, Univ. of Georgia
9:30 – 10:00TBDJeff Bennetzen, University of Georgia
10:00 – 12:00Poster session with coffee/snacksVolunteered poster submissions; even numbered poster authors in hour 1, odd number poster authors in hour 2
12:00 – 1:00Lunch 
1:00 – 3:00Invited Speaker Session 
1:00 – 1:20Planned IWGC genomes – species sequenced by IWGC, existing genomes hosted on website, expected outputs for each genomeSarah Morran, Colorado State University
1:20 – 1:40Getting into the Weeds: Reference Genome Assembly of Agronomically Important SpeciesVictor Llaca, Corteva
1:40 – 2:00Annotation of IWGC genomesEric Patterson, Michigan State University
2:00 – 2:20Parasitic Plant Genomes Provide Insights into AdaptationJim Westwood, Virginia Tech University
2:20 – 2:40Going Beyond a Reference Genome: Resequencing to Characterize Resistance EvolutionJulia Kreiner, University of Toronto
2:40 – 3:00Genomics and Molecular Cytogenetics to Understand the Evolution of Herbicide Resistance in Weedy and Invasive SpeciesMithila Jugulam, Kansas State University
3:00 – 3:30Coffee/Snacks break 
3:30 – 5:00Keynote Session – High-Tech Plant Genomics to Address Plant Biology 
3:30 – 4:00Population genomics and discovery of a new gene for shatteringElizabeth Kellogg, Danforth Center
4:00 – 4:30Leveraging population genomics to infer origins of weedy plants and weedy traits: the case of weedy riceAna Caicedo, University of Massachusetts – Amherst, NIFA-Sponsored
4:30 – 5:00Q&A Session
 
5:30 – 7:00Networking Reception 

Day 3, September 24: Research Priority and Roadmap Workshop

8:30 am – 12 pm: Facilitated discussions and capturing priorities

Workshop objective is to produce a white paper with community-supported directions and priorities for the next 5 years of weed genomics research