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Whole genome sequencing of ASD 16 and ADT 43 to identify predominant grain size and starch associated alleles in rice

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Abstract

Background

The rice cultivars ASD 16 and ADT 43 are the most popular high-yielding Indica rice cultivars in southern India. Despite their popularity very little is known about their genetic basis due to lack of studies on the complete genome. In the current study, efforts were made to identify alleles and SNP markers that differentiate the two contrasting rice genotypes, ASD 16 and ADT 43 for grain shape and starch content.

Methods and results

The complete genome of bold grain ASD 16 and slender grain ADT 43 were sequenced via Illumina’s paired-end sequencing and the reads obtained were mapped to the Oryza sativa Indica Group cultivar 93–11 reference genome. The grain size of rice is controlled by Quantitative Trait Loci (QTL) that has a robust effect on grain yield and quality. To gain insight into genes that controlling grain size and starch content, an in-silico analysis was performed by taking into account of 72 grain elongation and starch biosynthesis genes. The identified alleles were further validated in the whole genome sequencing data of 32 bold grain and 25 slender grain varieties that were retrieved from the 3 K rice genome project.

Conclusion

An “A to G” polymorphism leading to SER 74 PRO was identified at the CDS position 220 of the An-1 gene, encoding bHLH domain-containing protein that regulates awn formation and increase in grain length. The non-synonymous substitutions such as A545C variant leading PHE 182 CYS in ADP Glucose Pyrophosphorylase large subunit IV (AGPL4) and C3094G variant leading to VAL 1032 LEU in Starch synthase IIIb (OsSSIIIb) were also identified in the starch biosynthesis genes. These identified allelic variants may contribute to the crop improvement programs in rice.

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Data availability

ASD 16: The data from this study were submitted to NCBI under BioProject ID PRJNA666312 and BioSample ID SAMN16287940. The reads were submitted in compressed FastQ format at SRA database of NCBI with the accession number SRR12791393. ADT 43: Data were submitted to NCBI under BioProject ID PRJNA666316 and BioSample ID SAMN16288314. Quality reads were deposited in compressed FastQ format at SRA database of NCBI with the accession number SRR12777939.

Code availability

Not applicable.

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Acknowledgements

This research was carried out in the Bioinformatics Laboratory, Dept. of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University supported by the Biotechnology Information System (BTIS) program (No.BT/BI/04/015/89 Vol.III dated 13.03.2018 and BT/PR40235/BTIS/137/39/2022 dated 15.03.2022) of the Department of Biotechnology (DBT), Government of India, New Delhi.

Funding

The financial support of the Department of Biotechnology, Government of India through the program support for research and development in agricultural bioinformatics (BT/PR40235/BTIS/137/39/2022) is acknowledged.

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Author notes

  1. Jayakanthan Mannu and Abillasha Mohan Latha have equally contributed to this work.

Authors and Affiliations

  1. Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, 641 003, India

    Jayakanthan Mannu, Abillasha Mohan Latha, Shalini Rajagopal, Hari Dharani A. Lalitha & Gnanam Ramasamy

  2. Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India

    Raveendran Muthurajan, Arul Loganathan & Ramalingam Jegadeesan

  3. Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641 003, India

    Mohankumar Subbarayalu

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  1. Jayakanthan Mannu
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Contributions

JR, MJ, RG and SM: Designed and directed the project. MJ, JR and MR: Performed genome sequencing. MLA, HDL, RS, and MJ: Performed data analysis. MJ, MR, MLA and LA: Drafted the manuscript and designed the figures. All authors discussed the result and reviewed the manuscript.

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Correspondence to Ramalingam Jegadeesan.

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Mannu, J., Latha, A.M., Rajagopal, S. et al. Whole genome sequencing of ASD 16 and ADT 43 to identify predominant grain size and starch associated alleles in rice. Mol Biol Rep 49, 11743–11754 (2022). https://doi.org/10.1007/s11033-022-07935-8

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