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Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance

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Three coding SNPs and one haplotype identified in the OsDREB1F gene have potential to be associated with drought tolerance in rice.

Abstract

Drought is a serious constraint to rice production worldwide, that can be addressed by deployment of drought tolerant genes. OsDREB1F, one of the most potent drought tolerance transcription activator genes, was re-sequenced for allele mining and association study in a set of 136 wild rice accessions and four cultivated rice. This analysis led to identify 22 SNPs with eight haplotypes based on allelic variations in the accessions used. The nucleotide variation-based neutrality tests suggested that the OsDREB1F gene has been subjected to purifying selection in the studied set of rice germplasm. Six different OsDREB1F protein variants were identified on the basis of translated amino acid residues amongst the orthologues. Five protein variants were truncated due to deletions in coding region and found susceptible to drought stress. Association study revealed that three coding SNPs of this gene were significantly associated with drought tolerance. One OsDREB1F variant in the activation domain of OsDREB1F gene which led to conversion of aspartate amino acid to glutamate was found to be associated with drought tolerance. Three-dimensional homology modeling assisted to understand the functional significance of this identified potential allele for drought tolerance in rice. The natural allelic variants mined in the OsDREB1F gene can be further used in translational genomics for improving the water use efficiency in rice.

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Acknowledgments

The financial assistance received from Indian Council for Agricultural Research funded “Network Project on Transgenic Crops” project is gratefully acknowledged. We are thankful to NBPGR gene bank for providing seeds of 26 O. nivara and 5 O. rufipogon accessions used in this study.

Conflict of interest

All the authors declare no conflict of interest.

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Authors and Affiliations

  1. National Research Center on Plant Biotechnology, IARI, New Delhi, 110012, India

    Bikram Pratap Singh, Pawan Kumar Jayaswal, Balwant Singh, Pankaj Kumar Singh, Vinod Kumar, Shefali Mishra, Nisha Singh, Kabita Panda & Nagendra Kumar Singh

  2. Banasthali University, Tonk, Rajasthan, India

    Bikram Pratap Singh

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  1. Bikram Pratap Singh
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  2. Pawan Kumar Jayaswal
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  7. Nisha Singh
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  9. Nagendra Kumar Singh
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Correspondence to Nagendra Kumar Singh.

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Communicated by M. Prasad.

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Singh, B.P., Jayaswal, P.K., Singh, B. et al. Natural allelic diversity in OsDREB1F gene in the Indian wild rice germplasm led to ascertain its association with drought tolerance. Plant Cell Rep 34, 993–1004 (2015). https://doi.org/10.1007/s00299-015-1760-6

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  • DOI: https://doi.org/10.1007/s00299-015-1760-6

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