NEW STREAM - STARTS SPRING 2022!

Full Stream Name: X-Plants: Mutant Plants for Studying Gene Function

Research Educators: Robert Heckman & Nolan Bentley

Principal Investigator: Tom Juenger

Credit Options: Spring & Fall

Stream Overview

The X-Plants stream focuses on the use of a newly created population of mutant Hall’s panicgrass (Panicum hallii) and genomics analyses in order to study the biology of perennial grasses with an emphasis on their utility as biofuels, role in sustainable carbon sequestration, and ecological restoration. 

Students interested in computational biology, molecular biology, ecology, physiology and / or plant science are invited to join this new stream to design and implement analyses to characterize the mutated genes induced in the population. Students will gain experience utilizing high-impact data analysis skills as they learn and utilize R-programming (no prior programming experience required) and whole-genome sequencing based data sets to investigate this population. Students will also learn plant biology, PCR design, genomics, field observations, and many other valuable experiences throughout the course of their research. 

In this stream students will examine a new mutant P. hallii population developed in collaboration with the Department of Energy Joint Genome Institute (JGI). This population has been irradiated with fast neutrons in order to generate genetically stable mutations for studying gene function and grass biology. It includes over 1,000 lines that have been extensively characterized with whole-genome next-generation sequencing by JGI to generate a database of SNP and indel mutations induced across their genomes. This database will be used as a forward- and  reverse-genetics tool in order to generate testable hypotheses regarding the impact of gene disruption.

The ultimate goal for this stream is for students to utilize computational biology and data analysis tools to generate hypotheses regarding the potential impacts of the mutant alleles, design experiments to test for these hypothetical effects, and implement these tests using molecular biology techniques and/or by growing and observing mutant plants in greenhouse or field conditions.

Students in X-Plants will learn the following methods:

• How to manipulate and interpret large variant datasets.
• Utilize genome assembly and annotation resources.
• Annotate gene models and understand the basics of functional gene analysis.
• Experimental design and statistical analysis (utilizing R when possible).
• Plant propagation; growing and maintaining plants in field or greenhouse settings.
• Plant ecophysiological and morphological measurements.