J Integr Plant Biol ›› 2018, Vol. 60 ›› Issue (7): 578-590.DOI: 10.1111/jipb.12645

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Transcriptional and temporal response of Populus stems to gravi‐stimulation

Matthew Zinkgraf1,2†, Suzanne Gerttula1,2, Shutang Zhao3, Vladimir Filkov2 and Andrew Groover1,4*   

  1. 1USDA Forest Service, Pacific Southwest Research Station, 1731 Research Park Drive, Davis, CA 95618, USA
    2Department of Computer Science, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
    3State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
    4Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA 95618, USA
  • Received:2018-01-26 Accepted:2018-02-24 Published:2018-07-01
  • About author:Current address: Biology Department, Western Washington University, 516 High Street, Bellingham, WA 98225, USA
    *Correspondence: Email: Andrew Groover (agroover@fs.fed.us)

Abstract:

Plants modify development in response to external stimuli, to produce new growth that is appropriate for environmental conditions. For example, gravi‐stimulation of leaning branches in angiosperm trees results in modifications of wood development, to produce tension wood that pulls leaning stems upright. Here, we use gravi‐stimulation and tension wood response to dissect the temporal changes in gene expression underlying wood formation in Populus stems. Using time‐series analysis of seven time points over a 14‐d experiment, we identified 8,919 genes that were differentially expressed between tension wood (upper) and opposite wood (lower) sides of leaning stems. Clustering of differentially expressed genes showed four major transcriptional responses, including gene clusters whose transcript levels were associated with two types of tissue‐specific impulse responses that peaked at about 24–48 h, and gene clusters with sustained changes in transcript levels that persisted until the end of the 14‐d experiment. Functional enrichment analysis of those clusters suggests they reflect temporal changes in pathways associated with hormone regulation, protein localization, cell wall biosynthesis and epigenetic processes. Time‐series analysis of gene expression is an underutilized approach for dissecting complex developmental responses in plants, and can reveal gene clusters and mechanisms influencing development.

Analysis of gene expression data from time series studies can provide novel insights into gene networks and developmental processes. Here, we used a time series approach to understand how poplar trees change wood formation in response to gravistimulation.
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