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Dissecting the biochemical and molecular-genetic regulation of diverse metabolic pathways governing aroma formation in indigenous aromatic indica rice varieties

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Abstract

Background

Aromatic rice is characterized by its distinct flavor and fragrance, imparted by more than 200 volatile organic compounds. The desirable trait of aroma relies on the type of the variety, with some varieties exhibiting considerably higher aroma content. This prompted us to undergo an exhaustive study of the aroma-associated biochemical pathways and expression of related genes, encoding the enzymes involved in those pathways in indigenous aromatic rice cultivars.

Methods and results

The higher aroma level in aromatic rice varieties was attributed to higher transcript levels of PDH, P5CS, OAT, ODC, DAO and TPI, but lower P5CDH and BADH2, as revealed by comparative expression profiling of genes in 11 aromatic and four non-aromatic varieties. Some of the high-aroma containing varieties exhibited lower expression of SPDS and SPMS genes, concomitant with higher PAO expression. Protein immunoblot analyses showed lesser BADH2 protein accumulation in the aromatic varieties. The involvement of shikimate pathway in aroma formation was justified by higher levels of shikimic and ferulic acids due to higher expression of SK1, SK2 and ARD genes. The aromatic varieties exhibited higher expression of LOX3 and HPL, with higher corresponding enzyme activity, accompanied with lower accumulation of lipid hydroperoxides and higher level of total terpenoids, signifying the role of oxylipin pathway and terpene-related volatiles in aroma formation. The pattern of transcript level and metabolite accumulation followed the same trend in both vegetative (seedling) and reproductive (seed) tissues. Sequence analyses revealed several mutations in the upstream region and different exons and introns of BADH2 in the examined aromatic varieties. The allele specific marker system acted as fingerprint to distinguish the selected aromatic rice varieties. The cleaved amplified polymorphic sequence marker established the absence of any mutation in the 14th exon of BADH2 in the aromatic varieties.

Conclusion

The present work clearly highlighted the biochemical and molecular-genetic mechanism of differential aroma levels which could be attributed to differential regulation of metabolites and genes, belonging to 2-acetyl-1-pyrroline, shikimate, oxylipin and terpenoid metabolic pathways in the indigenous aromatic rice varieties.

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Acknowledgements

Financial assistance 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 would also like to acknowledge Chinsurah Rice Research Station, West Bengal, and Bidhan Chandra Krishi Viswa Vidyalaya (BCKV), West Bengal, for providing the seeds of all the aromatic as well as non-aromatic rice varieties used in this investigation. The authors also thank Dr. Saikat Paul for assisting in the initial phase of this work.

Funding

Financial assistance 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.

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Authors and Affiliations

  1. Department of Biotechnology, St. Xavier’s College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India

    Puja Ghosh & Aditya Banerjee

  2. Discipline of Life Sciences, School of Sciences, Indira Gandhi National Open University, Maidan Garhi, 110068, New Delhi, India

    Aryadeep Roychoudhury

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  1. Puja Ghosh
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Contributions

PG performed all the experiments and generated data. AB assisted in the amplification and purification of the exons and introns of BADH2 gene. AR designed all the experiments, supervised the overall work, drafted the manuscript and critically analyzed all the experimental results.

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Correspondence to Aryadeep Roychoudhury.

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Ghosh, P., Banerjee, A. & Roychoudhury, A. Dissecting the biochemical and molecular-genetic regulation of diverse metabolic pathways governing aroma formation in indigenous aromatic indica rice varieties. Mol Biol Rep 50, 2479–2500 (2023). https://doi.org/10.1007/s11033-022-08227-x

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