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Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes

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Abstract

Background

With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited.

Methods and results

In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation.

Conclusions

The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.

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Data availability

All the supporting data of the article has been provided in the supplementary files.

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Funding

LRV gratefully acknowledge ICAR for funding the Extramural Project (F.No.:CS/18 (8)/2015-O&P dated 12–082016). This research was supported by the Department of Biotechnology (DBT), Govt. of India (Sanction Order: No. BT/PR5493/AGIII/103/848/2012) awarded to LRV. VS and KVS is supported by IISER Tirupati institutional postdoctoral research fellowship. E.R. acknowledges IISER Tirupati for research support. Aparna to Bayer fellowship.

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Authors and Affiliations

  1. Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India

    Aparna Eragam & Lakshminarayana R. Vemireddy

  2. Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India

    Aparna Eragam, Vishnu Shukla, Vijaya Sudhakararao Kola & Eswarayya Ramireddy

  3. Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India

    P. Latha & Srividhya Akkareddy

  4. Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India

    Madhavi L. Kommana

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  1. Aparna Eragam
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  2. Vishnu Shukla
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  3. Vijaya Sudhakararao Kola
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  4. P. Latha
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  5. Srividhya Akkareddy
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  6. Madhavi L. Kommana
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  7. Eswarayya Ramireddy
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  8. Lakshminarayana R. Vemireddy
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Contributions

LRV and ER: conceived the experiment and prepared the manuscript. AE, VS, VS, LP, and SA: conducted the experiment. MLK: assisted in field work and VS: has carried out data analysis.

Corresponding authors

Correspondence to Eswarayya Ramireddy or Lakshminarayana R. Vemireddy.

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This is an observational study. The Research Ethics Committee of the University has confirmed that no ethical approval is required.

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Eragam, A., Shukla, V., Kola, V.S. et al. Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes. Mol Biol Rep 49, 7649–7663 (2022). https://doi.org/10.1007/s11033-022-07581-0

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