Abstract
Vetiver [Vetiveria zizanioides (L.) Roberty] is a perennial C-4 grass traditionally valued for its aromatic roots/root essential oil. Owing to its deep penetrating web-forming roots, the grass is now widely used across the globe for phytoremediation and the conservation of soil and water. This study has used the transcriptome data of vetiver roots in its two distinct geographic morphotypes (North Indian type A and South Indian type B) for reference gene(s) identification. Further, validation of reference genes using various abiotic stresses such as heat, cold, salt, and drought was carried out. The de novo assembly based on differential genes analysis gave 1,36,824 genes (PRJNA292937). Statistical tests like RefFinder, NormFinder, BestKeeper, geNorm, and Delta-Ct software were applied on 346 selected contigs. Eleven selected genes viz., GAPs, UBE2W, RP, OSCam2, MUB, RPS, Core histone 1, Core histone 2, SAMS, GRCWSP, PLDCP along with Actin were used for qRT-PCR analysis. Finally, the study identified the five best reference genes GAPs, OsCam2, MUB, Core histone 1, and SAMS along with Actin. The two optimal reference genes SAMS and Core histone 1 were identified with the help of qbase + software. The findings of the present analyses have value in the identification of suitable reference gene(s) in transcriptomic and molecular data analysis concerning various phenotypes related to abiotic stress and developmental aspects, as well as a quality control measure in gene expression experiments. Identifying reference genes in vetiver appears important as it allows for accurate normalization of gene expression data in qRT-PCR experiments.
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The target vetiver genotypes used in this study could be availed through UCL.
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10 July 2023
A Correction to this paper has been published: https://doi.org/10.1007/s12298-023-01330-8
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Acknowledgements
The authors acknowledge the logistic support received from Dr. A. K. Shasany, Director CSIR – National Botanical Research Institute, Lucknow India, and AcSIR for Ph. D. degree registration. DC is grateful for funding from project OLP-110. R. D. Tripathi is grateful to NASI Prayagraj for the award of the NASI-Senior Scientist Platinum Jubilee Fellowship (GAP-3495). UCL is supported by the INSA Senior Scientist scheme. Y. Indoliya is grateful to CSIR, New Delhi for the award of RAship. This work is a part of the AcSIR Ph.D. program of ASC. CSIR-NBRI allotted the manuscript number CSIR-NBRI_MS/2023/04/16.
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DC, RDT, PSC, UCL and ASC designed and drafted the work. ASC carried out the bioinformatics analysis. MT and YI performed quantitative expression analysis (qRT-PCR). RDT, SKM, DC and PSC participated in the supervision of the study. YI helped in the writing of the manuscript. UCL facilitated to arrange the live material of the two contrasting Vetiver morphotypes used in this study. SKM corporated in the functional execution of the experiments. RDT and DC helped in the editing of the manuscript. All the authors read and approved the final manuscript.
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Chauhan, A.S., Tiwari, M., Indoliya, Y. et al. Identification and validation of reference genes in vetiver (Chrysopogon zizanioides) root transcriptome. Physiol Mol Biol Plants 29, 613–627 (2023). https://doi.org/10.1007/s12298-023-01315-7
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DOI: https://doi.org/10.1007/s12298-023-01315-7