In silico characterisation of novel rice transcripts differentially expressed in phosphorus dificient conditions suggests a role of these transcripts in multiple abiotic stresses

Yumnam, Julia S. and Rai, Mayank and Tyagi, Wricha (2017) In silico characterisation of novel rice transcripts differentially expressed in phosphorus dificient conditions suggests a role of these transcripts in multiple abiotic stresses. Acta Biologica Hungarica, 68 (4). pp. 398-411. ISSN 0236-5383

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Abstract

Phosphorus deficiency adversely affects crop productivity. The mechanism of tolerance in plants is not well understood. The current study successfully annotated a set of highly significant (Log₂ RPKM ≥3) nine novel sequences up-regulated in P deficient condition identified from a low P tolerant rice genotype. Sequence annotation identified two transcripts (Os01g37260 and Os02g11060) carrying known domains, F-box and WD, respectively. Multiple Expectation maximization for Motif Elicitation (MEME) revealed presence of conserved domains like D[LP][HY][CL]D[CM][DT]C[AP][DQ][IQ]C, [EH][DN]HN[HS] [ER][FY][EP]I[HN]H which might play a role in phosphorus deficiency tolerance. Analysis of the upstream regions indicated presence of stress responsive elements like E Box, ABRE, and MYBCORE suggesting regulation of the novel transcripts by DNA binding. Protein localization prediction tool suggests that these novel proteins might be targeted to nucleus, chloroplast and cell wall. Transcripts Os02g03640 and Os02g10250 revealed potential target sites for microRNA binding suggesting role of novel miRNAs in low phosphorus response. Our analysis suggests that an F-box protein, Os01g37260 (OSFBx14) might be a promising candidate gene playing a role in multiple abiotic stresses including P deficiency.

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