Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress

PLoS One. 2017 May 1;12(5):e0176399. doi: 10.1371/journal.pone.0176399. eCollection 2017.

Abstract

Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution. Overall, 65 DHNs were identified by a genome-wide survey of 11 rice species, and 3 DHNs were found to be highly conserved. The correlation of a conserved pattern of DHNs with domestication and diversification of wild to cultivated rice was validated by synonymous substitution rates, indicating that Oryza rufipogon and Oryza sativa ssp. japonica follow an adaptive evolutionary pattern; whereas Oryza nivara and Oryza sativa ssp. indica demonstrate a conserved evolutionary pattern. A comprehensive analysis of tissue-specific expression of DHN genes in japonica and their expression profiles in normal and PEG (poly ethylene glycol)-induced dehydration stress exhibited a spatiotemporal expression pattern. Their interaction network reflects the cross-talk between gene expression and the physiological processes mediating adaptation to dehydration stress. The results obtained strongly indicated the importance of DHNs, as they are conserved during the course of domestication.

MeSH terms

  • Chromosome Duplication
  • Chromosomes, Plant
  • Conserved Sequence
  • Crops, Agricultural / genetics
  • Crops, Agricultural / metabolism
  • Databases, Genetic
  • Dehydration / genetics
  • Dehydration / metabolism
  • Domestication
  • Evolution, Molecular
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / physiology
  • Models, Molecular
  • Oryza / genetics*
  • Oryza / metabolism*
  • Peptide PHI
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism*
  • Plant Roots / metabolism
  • Polyethylene Glycols
  • Protein Conformation
  • Real-Time Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Homology, Amino Acid

Substances

  • Peptide PHI
  • Plant Proteins
  • dehydrin proteins, plant
  • Polyethylene Glycols

Grants and funding

This research was supported by the Science and Engineering Research Board, New Delhi, India (project file no. SB/YS/LS-74/2014) and also by the network project (BSC-204) funded by the Council of Scientific and Industrial Research, New Delhi. The authors are also thankful to Director, CSIR-National Botanical Research Institute, Lucknow, for the facilities and the financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.