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1.  Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling 
PLoS Genetics  2015;11(4):e1004953.
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
Author Summary
Because plants depend on light for photosynthesis, neighboring plant shade can be detrimental to survival. Many plants sense and respond to neighbor shade to compete for light. Although shade causes responses throughout the plant (collectively known as the shade avoidance syndrome or SAS), most SAS studies have been limited to single-gene analyses in seedlings. Here we move beyond these analyses by taking a multi-gene, multi-trait study of SAS across developmental stages. Recently, whole-genome studies examining large mutant collections have been exploited to determine the pathways and their interactions that combine to determine complex phenotypes. This type of analysis (phenotypic profiling) typically uses thousands of mutants and robotic phenotyping for assaying many characters in the multitude of mutant lines. In this paper, we develop a directed alternative that allows us to take a similar approach to understanding SAS. To reduce the number of mutants required for such an approach, we used a logical selection procedure to define mutants of interest by over-representation analysis of shade-responsive genes. We found at least three different subgroups of shade responses, and that each subgroup had both shared and separate pathways. Also, we found eighteen novel genes involved in SAS. Therefore, our method is useful for multi-dimensional phenotypic profiling without expensive robots.
doi:10.1371/journal.pgen.1004953
PMCID: PMC4398415  PMID: 25874869
2.  Protein abundances are more conserved than mRNA abundances across diverse taxa 
Proteomics  2010;10(23):4209-4212.
Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression datasets from seven different species: two bacteria, yeast, nematode, fly, human, and plant. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge.
doi:10.1002/pmic.201000327
PMCID: PMC3113407  PMID: 21089048

Results 1-2 (2)