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

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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.


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.

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



Basal thermotolerance


Caseinolytic protease B1


Heat stress


Heat shock proteins


Heat shock factors


Heat shock protein 101




Long-term acquired thermotolerance


Presence/absence variations


Quantitative trait loci


Short-term acquired thermotolerance


Single nucleotide polymorphism


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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.

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Correspondence to Anil Grover.

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Communicated by Dorothea Bartels.

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Kumar, R., Tripathi, G., Goyal, I. et al. Insights into genomic variations in rice Hsp100 genes across diverse rice accessions. Planta 257, 91 (2023).

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