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Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm

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The association of natural genetic variations of salt-responsive candidate genes belonging to different gene families with salt-tolerance phenotype and their haplotype variation in different geographic regions.

Abstract

Soil salinity covers a large part of the arable land of the world and is a major factor for yield losses in salt-sensitive crops, such as rice. Different gene families that respond to salinity have been identified in rice, but limited success has been achieved in developing salt-tolerant cultivars. Therefore, 21 salt stress-responsive candidate genes belonging to different gene families were re-sequenced to analyse their genetic variation and association with salt tolerance. The average single nucleotide polymorphism (SNP) density was 16 SNPs per kbp amongst these genes. The identified nucleotide and haplotype diversity showed comparatively higher genetic variation in the transporter family genes. Linkage disequilibrium (LD) analysis showed significant associations of SNPs in BADH2, HsfC1B, MIPS1, MIPS2, MYB2, NHX1, NHX2, NHX3, P5CS1, P5CS2, PIP1, SIK1, SOS1, and SOS2 genes with the salt-tolerant phenotype. A combined analysis of SNPs in the 21 candidate genes and eight other HKT transporter genes produced two separate clusters of tolerant genotypes, carrying unique SNPs in the ion transporter and osmoticum-related genes. Haplotype network analysis showed all the major and few minor alleles distributed over distant geographic regions. Minor haplotypes may be recently evolved alleles which migrated to distant geographic regions and may represent recent expansion of Indian wild rice. The analysis of genetic variation in different gene families identified the relationship between adaptive variations and functional significance of the genes. Introgression of the identified alleles from wild relatives may enhance the salt tolerance and consequently rice production in the salinity-affected areas.

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Acknowledgments

The financial assistance from the Indian Council of Agricultural Research through National Professor B. P. Pal Chair project is gratefully acknowledged. We are thankful to the National Bureau of Plant Genetic Resources, New Delhi, India for providing seeds of 58 wild rice accessions.

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Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India

    Shefali Mishra, Balwant Singh, Vandna Rai & Nagendra Kumar Singh

  2. Sam Higginbottom Institute of Agriculture Technology and Sciences, Allahabad, 211007, India

    Shefali Mishra & Pragati Misra

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  1. Shefali Mishra
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  2. Balwant Singh
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  3. Pragati Misra
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  4. Vandna Rai
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  5. Nagendra Kumar Singh
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Correspondence to Nagendra Kumar Singh.

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Communicated by M. Prasad.

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Mishra, S., Singh, B., Misra, P. et al. Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm. Plant Cell Rep 35, 2295–2308 (2016). https://doi.org/10.1007/s00299-016-2035-6

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  • DOI: https://doi.org/10.1007/s00299-016-2035-6

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