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Candidate gene based association analysis of salt tolerance in traditional and improved varieties of rice (Oryza sativa L.)

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Abstract

Rice is a staple food for more than half of the world population but the productivity of rice plant is attenuated in salt-stressed environment. Here 69 diverse rice varieties were evaluated for their salt tolerance capacity. Tolerant and susceptible genotypes were differentiated based on their standard evaluation score and thirteen other physiological parameters. A genome wide 48-SNP markers chip was used to analyze genetic diversity and population structure of the genotypes. Thirteen different salt-responsive candidate genes belonging to different functional categories including transporters, metabolic pathways, intermediate genes and transcription factors were amplified and re-sequenced using Ion Torrent PGM platform. Total 155 SNPs were identified in the selected 13 genes. A candidate gene based association analysis found seven-marker trait associations with five salt tolerance traits. From the 13 genes analyzed, DUF 6 was associated with Na+/K+ ratio, root biomass and root dry weight; SOS 1 with Na+ concentration in leaves and HKT 2;4 with shoot dry weight. This study will be helpful in the development of functional markers associated with salt stress tolerance in rice.

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Abbreviations

HKT:

High-affinity potassium transporter

SOS:

Salt overly sensitive

CCC:

Cation chloride co-transporter

SHMT:

Serine hydroxymethyltransferase

DREB:

Dehydration responsive element binding

MLM:

Mixed linear model

SDW:

Shoot dry weight

CDS:

Coding DNA sequence

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Acknowledgements

Authors are grateful for the financial assistance from Indian Council for Agricultural Research under ‘‘Network Project on Transgenic Crops’’. DS is also grateful to fellowship support from the Council of Scientific and Industrial Research, New Delhi.

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Authors and Affiliations

  1. ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 11 0012, India

    Deepika Singh, Balwant Singh, Shefali Mishra & Nagendra Kumar Singh

  2. Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 11 0012, India

    Ashok Kumar Singh

Authors
  1. Deepika Singh
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  2. Balwant Singh
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  3. Shefali Mishra
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  4. Ashok Kumar Singh
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  5. Nagendra Kumar Singh
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Contributions

DS: design and conduct of experiments, data analysis manuscript preparation BS: collection of landraces, conduct of experiments and manuscript drafting; SM: sequencing, data analysis NKS: planning and supervision of the experiments, and manuscript editing and finalization.

Corresponding author

Correspondence to Nagendra Kumar Singh.

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Singh, D., Singh, B., Mishra, S. et al. Candidate gene based association analysis of salt tolerance in traditional and improved varieties of rice (Oryza sativa L.). J. Plant Biochem. Biotechnol. 28, 76–83 (2019). https://doi.org/10.1007/s13562-018-0464-8

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  • DOI: https://doi.org/10.1007/s13562-018-0464-8

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