Summary
Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project – undergraduates phenotyping Arabidopsis knockouts – has generated phenotype data for thousands of non‐lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness‐related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild‐type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.
We present a curriculum description, an initial student outcome investigation, and sample scientific results for a representative Course-Based Undergraduate Research Experience (CURE) that is part of the “Undergraduates Phenotyping
Arabidopsis
Knockouts” (unPAK) network. CUREs in the unPAK network characterize quantitative phenotypes of the model plant
Arabidopsis
from across environments to uncover connections between genotype and phenotype. Students in unPAK CUREs grow plants in a replicated block design and make quantitative measurements throughout the semester. This CURE enables students to answer plant science questions that draw from fields such as environmental science, genetics, ecology, and evolution. Findings indicate that this experience provides students with opportunities to make relevant scientific discoveries. Eighty percent of student datasets produced from the CURE met criteria for inclusion in the project database, indicative of student learning in data collection and analysis of quantitative plant traits. Student datasets uncovered novel effects of mutation on plant form. In addition, students’ science self-efficacy increased as a result of course participation, and faculty feedback on course implementation was positive. We present unPAK as a new network that supports CUREs and research experiences focused on collecting biological data made publicly available to the scientific community. The unPAK CUREs can be tailored to address instructor interests or pedagogical needs while involving students in research investigating quantitative plant phenotypes.
Undergraduates phenotyping
Arabidopsis
knockouts (unPAK) is a biology research network that has provided undergraduate research experiences (URE) since 2010. In 2019, unPAK expanded to include a summer URE that engaged undergraduate researchers from across the network in an intensive collaborative program.
Over a decade ago, faculty researchers at primarily undergraduate institutions embarked on a project motivated as much by questions about plant genomics as by commitment to undergraduate mentoring. The project gained funding from NSF and also an acronym: UNPAK, Undergraduates Phenotyping Arabidopsis Knockouts. The project aims to test ideas about how often mutation results in detectable change in plant traits important in both ecology and agriculture, relying on the premier model species in plant science, much like the lab mouse in biomedicine. UNPAK has two major tenets. First, it harnesses the hands, eyes and brains of undergraduates across many campuses to amass and analyze its data and analyses. Second, it connects faculty and students on these campuses to build and share social, cultural and human capital, essential for scientists at all stages to continue to advance and flourish. Social science colleagues have joined UNPAK to assess this second tenet and to examine its influence as student motivations and access to resources before and after graduation, and the project’s impact on faculty careers. More basically, UNPAK fosters friendships and solidarity, the underpinning of social groups that are working toward the intertwined goals of sustainability and social justice.
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