Skip to main content
Log in

Insights into genomic variations in rice Hsp100 genes across diverse rice accessions

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

Abstract

Main conclusion

The Hsp101 gene is present across all sequenced rice genomes. However, as against Japonica rice, Hsp101 protein of most indica and aus rice contain insertion of glutamic acid at 907th position.

Abstract

The understanding of the heat stress response of rice plants is important for worldwide food security. We examined the presence/absence variations (PAVs) of heat shock proteins (Hsps)/heat shock transcription factor (Hsf) genes in cultivated rice accessions. While 53 Hsps/Hsfs genes showed variable extent of PAVs, 194 genes were the core genes present in all the rice accessions. ClpB1/Hsp101 gene, which is critically important for thermotolerance in plants, showed 100% distribution across the rice types. Within the ClpB1 gene sequence, 40 variation sites consisting of nucleotide polymorphisms (SNPs) and short insertion/deletions (InDels) were discerned. An InDel in ClpB1 leading to an in-frame insertion of 3 nucleotides (TCC) thereby an additional amino acid (glutamic acid) at 907th amino acid position was noted in most of the indica and aus as against japonica rice types. Three rice types namely Moroberekan (japonica), IR64 (indica) and N22 (aus) were further analyzed to address the question of ClpB1 genomic variations and its protein levels with the heat tolerance phenotype. The growth profiling analysis in the post heat stress (HS) period showed that N22 seedlings were most tolerant, IR64 moderately tolerant and Moroberekan highly sensitive. Importantly, the ClpB1 protein sequences of these three rice types showed distinct differences in terms of SNPs. As the ClpB1 protein levels accumulated post HS were generally higher in Moroberekan than N22 seedlings in our study, it is proposed that some additional gene loci in conjunction with ClpB1 regulate the overall rice heat stress response.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Data availability

Data generated is included in the manuscript and the supplementary data.

Abbreviations

BT:

Basal thermotolerance

ClpB1:

Caseinolytic protease B1

HS:

Heat stress

Hsps:

Heat shock proteins

Hsfs:

Heat shock factors

Hsp101:

Heat shock protein 101

InDels:

Insertion/deletions

LAT:

Long-term acquired thermotolerance

PAVs:

Presence/absence variations

QTL:

Quantitative trait loci

SAT:

Short-term acquired thermotolerance

SNP:

Single nucleotide polymorphism

References

Download references

Acknowledgements

RK acknowledges the University Grants Commission (UGC), Government of India for the research fellowship, GT and RS are thankful to Department of Biotechnology (DBT), Government of India and IG to the Council of Scientific & Industrial Research (CSIR), Government of India for the fellowship awards, NKS acknowledges Centre for Advanced Research and Innovation on Plant Stress and Developmental Biology, DBT, Government of India. AG acknowledges J.C. Bose Fellowship, (SR/S2/JCB-28/2011) SERB, Government of India and National Agricultural Science Foundation (NASF), ICAR (NASF/ABP-7014/2018-19), Government of India for the financial support. The award of FIST and PURSE grants from Department of Science and Technology (DST), Government of India to our Department are gratefully acknowledged.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Anil Grover.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by Dorothea Bartels.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kumar, R., Tripathi, G., Goyal, I. et al. Insights into genomic variations in rice Hsp100 genes across diverse rice accessions. Planta 257, 91 (2023). https://doi.org/10.1007/s00425-023-04123-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00425-023-04123-1

Keywords

Navigation