Evaluation of “Transcript*Profiling of Nematode and Aphid Infectome in Soybean” (2012-7)
By: Matt Hunt (Secondary Reviewer)
Overall Score: Excellent
Summary of Objectives and Approaches:
This project seeks to determine if soybean cyst nematode (scn) and soybean aphid have
synergistic effects during mutual soybean infection. Both scn and soybean aphid have a significant
effect on soybean yields in the US every year. Although the both pathogens have been studied
extensively in terms of their effects on yields and their molecular interactions with soybean, less
research has focused on how the two pests can effect both one another and soybean. Overall this
project aims to show the effect both on yield and gene expression of the pests on soybean yield
individually and together.
The first objective for the project seeks to determine how growing soybean plants either alone,
infested with scn along, soybean aphids alone, or scn and soybean aphids together affects soybean
yield, aphid populations, and scn populations. To carry out this objective a split plot design of resistant
and susceptible soybean lines will be tested with no pathogens, each pathogen singly, and both
pathogens together will be planted with five biological replicates.
The second objective for the project has the goal of collecting and characterizing transcriptomic
data from soybean, scn, and soybean aphid grown in the field experiment from objective one, and
identifying potential effector proteins for further study. To accomplish this objective samples will be
collected from the plots described in objective one and RNA will be extracted that will be used for RNA
seq on an Illumina next-generation sequencing machine. These data will be used to identify coexpressed genes that would be used as targets for protein interaction studies.
Strengths of the scientific merit of the proposal:
The impact of soybean aphids and soybean cyst nematodes (scn) on soybean yields can be
extreme and can range from 50-70% yield loss from only one of the two pathogens. When both types of
infestations happen simultaneously, the losses can be even higher. This study seeks to examine the
possible interactive effects of scn and soybean aphid in terms of both the yield effects on soybean, as
well as growth of the pests, and the gene expression profiles of the three in all possible combinations.
The field experiments proposed appear to be sound in terms of design, planning, and analysis. Each
field experiment has a clearly testable hypothesis and achievable goals. According to the methods
presented the resulting data will be fairly straightforward to analyze and depending on the results, make
into publications. Collecting gene expression data from all three species from the same plots used for
the field experiments is very unique, and contributes to the strength of the study, as most molecular
studies use samples collected from more controlled conditions such as greenhouse or growth chamber.
Weaknesses of the scientific merit of the proposal:
One potential weakness of the field experiment would be the possibility that the field site
chosen already has a scn population, and therefore the amounts of scn tested would be higher than the
experiment originally anticipated. This could be solved by testing the soil from the proposed field site
first before planting. The other potentially problematic feature of collecting field samples for a
transcriptomic study, is the potential for high variability amongst and between samples. This variability
may affect the statistical modeling of the data, and hide some interesting trends in the increased noise
introduced by the field variability. Another potential issue the author would face, would be the difficulty
in identifying targets for protein interaction studies. Gene expression data does not always correlate
with protein expression or function. The author is relying on co-expression of genes to determine
potential interactions for protein testing. There may be many more false positives than true positives
from this type of association, which would lead to less true interactors than the author may plan for.
Strengths and weaknesses of broader impacts:
This proposed project has the potential to be a high impact study both for agronomic and
genetic reasons. Soybean aphids and scn can have extreme effects on soybean yields on American
farms, and new methods of control, either through cultural practices or new modes of resistance, are
needed. The relative impacts on yield that are caused by either pest alone or together has the potential
to inform the broader community about herbivore interactions. The gene expression data may identify
candidate effectors from either scn or soybean aphid, and how they affect gene expression in soybean.
However, it may be difficult to clearly identify these effectors from field grown tissue, as multiple
environmental factors may affect the growth of soybean and of the herbivore species. This variability
introduced from the environment may impact the statistical analysis for these experiments.
Summary:
This proposal has the potential to create high impact research in the area of herbivore biology.
The field tests are well designed, and the authors present clearly testable hypothesis for these
experiments. This study is unique in the proposal to study the gene expression levels of three species
simultaneously that interact as host and herbivores. The second objective will be challenging because of
potential field variability, but may yield insights into the most important factors in a synergistic
interaction between scn and soybean aphid when feeding on soybean tissue.