Potential iPlant Education Projects
Dave Micklos, Cold Spring Harbor Laboratory
The Annotation Pipeline will be a general tool/workspace/discovery environment.
However, there was consensus at the Genome Annotation Meeting that iPlant should get
behind some organized projects that provide frameworks for sustained involvement of
students, teachers, and researchers. Although all understand that iPlant's brief is not data
generation, these projects do entail data collection. This is in line with faculty's desire for
projects that link wet lab and discovery tools.
1. Chloroplast evolution and phylogenetics offers an ideal educational project for
iPTOL. The endosymbiois of chloroplasts (and mitochondria) show the evolutionary
synthesis of the key attributes of plant life. Chloroplast genes are widely used in
developing plant phylogenies, and the chloroplast genome itself is an interesting case
of genome reduction and lateral gene transfer (to the nucleus). The chloroplast
genome provides sequence comparison projects at several levels of complexity. At
an entry level, students would generate DNA sequence from the large subunit gene of
ribulose-bisphosphate carboxylase (rbcl), which is a widely-used in plant
phylogenetics. Using methods analogous to the DNALC's human mitochondrial
sequencing project, students would isolate plant DNA and generate PCR products
from selected plants. The amplicons would then be sequenced locally or sent to a
central sequencing service provided by one or more iPlant collaborators. The
sequences would be placed in a database for communal access. Students would then
use their own rbcl sequences as a starting point in a study of plant phylogenetics,
using alignment and tree-drawing tools available at the iPlant Annotation Pipeline. At
an advanced level, entire chloroplast genomes would be appropriate targets for next
generation sequencing, with classes preparing linker libraries and Illumina
sequencing provided by a shared facility. Then, students would assemble their
genome by scaffolding it against a complete chloroplast genome and use comparative
methods to study genome evolution.
2. Maize Genomics and Genetics We need to develop a project to illustrate how
genome resources are brought to bear on the plant genotype-to-phenotype problem.
There are a number of reasons to focus educational resource development on maize,
among the several plants with complete genome sequences available. Aside from its
strong genetics and agricultural/industrial importance, maize is a uniquely American
(North and South) success story that illustrates the connection between cultivation
and culture. Maize also presents an excellent model of domestication as humaninduced plant evolution. An iPlant maize education project could build upon,
organize, and polish many smaller educational efforts conducted under NSF's Plant
Genome Initiative. Experiments ranging from classical genetics to the molecular basis
of Round-up resistance offer entry points for middle and high school students, while
the large community of education-interested researchers can vet genomic data
generated/annotated by college students.
3. Phenology of a Common Plant iPlant should promulgate at least one project
targeted toward elementary students and citizen scientists. A plant project analogous
to the Audubon Christmas Bird Count could provide useful geographical and trend
data on plant phenology. Data on plant emergence and flowering time – along with
climatic information – are perfectly compatible with a GoogleEarth display. By
distributing work over thousands of classrooms, this project could create a large set of
phenological, temporal, climatic, and geographical data. Comparing these data would
allow students to understand the range of phenotypic variation within plant species
and the effect of latitude and other variables on plant growth. Comparison with
historical data sets could potentially show differential effects of global climate change
at different latitudes. Ideally the project would select several "sentinel" plants with
wide geographical ranges. Selected plants should flower in the spring, allowing
broadest participation by school classes.
4. Arabidopsis and Brassica. Arabidopsis has well developed genome and phenotype
resources and an enthusiastic research community. The fast-cycling Brassica, a.k.a.
Wisconsin Fast Plants, is probably the most widely used plant system in precollege
education, but it currently has virtually no genetic resources. If these two plants were
one, they would be the perfect teaching system. However, although they are both in
the Brassica family, they are sufficiently different that Arabidopsis genomic
resources cannot be applied to Fast Plants. Furthermore, Arabidopsis lacks the
compelling commercial or cultural links of maize. Erin Dolan, at Virginia Tech, has
probably the best distributed genotype-phenotype education project in Arabidopsis.
Her Partnership for Education in Plants (PREP) has students screen for phenotypic
changes in mutagenized Arabidopsis seeds and share their data with research
scientists. Plans are being laid to sequence Fast Plants by 454 and Illumina methods.
Useable sequence is not anticipated for at least a year, and it is not clear how well
these short reads can be aligned to the Arabidopsis sequence. I doubt that iPlant has
enough resources for two genome-based teaching models, so I would recommend that
we wait to see what comes out of the Fast Plants sequencing effort while we move
forward with maize genomics.