Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots

Wei Wang; Sunil Kumar Singh; Xiwen Li; Hui Sun; Yu Yang; Min Jiang; Hailing Zi; Renyi Liu; Huiming Zhang; Zhaoqing Chu

doi:10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots

PeerJ. 2019 Jun 13:7:e7102. doi: 10.7717/peerj.7102. eCollection 2019.

Authors

Wei Wang^#^{1

2}, Sunil Kumar Singh^#³, Xiwen Li^{1

2

4}, Hui Sun³, Yu Yang³, Min Jiang^{1

2}, Hailing Zi³, Renyi Liu⁵, Huiming Zhang³, Zhaoqing Chu^{1

2}

Affiliations

¹ Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
² Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.
³ Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
⁴ College of Life Sciences, Shanghai Normal University, Shanghai, China.
⁵ Center for Agroforestry Mega Data Science and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.

^# Contributed equally.

Abstract

Background: There have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon.

Results: Our Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice.

Conclusions: This study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation.

Keywords: Brachypodium distachyon; Defoliation; Grass; Nutrition; Transcriptome.

Grants and funding

This work was funded by grants from the Shanghai Landscaping Administrative Bureau (Grant Nos. G182405 and G192412). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.