Journal of Plant Growth Regulation

, Volume 38, Issue 2, pp 539–556 | Cite as

Comparative Analysis of the Expression of Candidate Genes Governing Salt Tolerance and Yield Attributes in Two Contrasting Rice Genotypes, Encountering Salt Stress During Grain Development

  • Saikat Paul
  • Aryadeep RoychoudhuryEmail author


The rice grain filling process is of inordinate importance as it is directly associated with productivity and rice quality. Salt stress occurring during early grain development hinders seed development, resulting in yield penalty. To dissect transcriptional responses and to identify promising candidate genes, comparative expression profiling of key stress-responsive and yield-related genes was performed in developing (10 DAP, 20 DAP, and 30 DAP) and matured grains of salt-sensitive (IR-64) and salt-tolerant (Nonabokra) rice cultivars under salt stress (250 mM NaCl) along with the analyses of grain yield parameters. The phenotypic values of most of the tested yield attributes were significantly reduced under salt stress and the effect of stress was more pronounced in IR-64. Gene expression through semi-quantitative reverse transcriptase-polymerase chain reaction followed by statistical analyses identified that members of the TFs and LEA family (that is, TRAB-1, RITA-1, RISBZ1, WRKY-21, and Osem), osmolytes and polyamine metabolic genes (BADH1 and SAMDC) as well as the yield-related gene GIF1, were significantly induced by salt stress. Statistical analyses further revealed a significant correlation between the expression of these genes and grain yield under salt stress. In IR-64, the TRAB-1, RITA-1, and Osem transcripts were more up regulated during the early to mid-phase of seed development, suggesting an adaptive response of the sensitive cultivar to salt stress. The TFs along with BADH1, SAMDC, and GIF1 transcripts were mostly up regulated in Nonabokra during the early phase, and the level was maintained even after the mid-phase under stress. The heat map analysis also revealed the differential expression of genes between the two cultivars throughout the seed developmental stages. Our result indicated a possible interplay between ABA-inducible TFs and grain filling-related genes, allowing Nonabokra to maintain the grain filling process under stress condition. This is also evident by comparatively lower reduction of grain weight and filled-grain number in Nonabokra under stress. The role of different TFs in ABA-signaling in matured grains is clear by the accumulation of transcripts, especially in dry and ABA-imbibed seeds. Overall, our data established the correlation of grain yield with tolerance or susceptibility, accompanied by the expression of effector or regulatory genes.


Rice IR-64 Nonabokra Developing grains Salt stress Gene expression Transcription factor Productivity Developing grain Microarray ANOVA Semi-quantitative RT-PCR 



Financial assistance from Science and Engineering Research Board (SERB), Government of India through the research grant (SR/FT/LS-65/2010) and from Council of Scientific and Industrial Research (CSIR), Government of India, through the research grant [38(1387)/14/EMR-II] to Dr. Aryadeep Roychoudhury is gratefully acknowledged. The authors are thankful to University Grants Commission (UGC), Government of India, for providing Senior Research Fellowship to Saikat Paul.

Supplementary material

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Supplementary material 5 (DOC 51 KB)


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Authors and Affiliations

  1. 1.Post Graduate Department of BiotechnologySt. Xavier’s College (Autonomous)KolkataIndia

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