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Genomic analysis of polycarpellary rice (Oryza sativa L.) through whole genome resequencing

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Abstract

There is a natural floral organ mutant of rice (var. Jugal) where the florets, popularly known as spikelet bear multiple carpels and produce multiple kernels in most of its grain. In our earlier work a detailed study has been done on its morpho-anatomical structure with allelic diversity and expression study of the major genetic loci associated with floral organ development. In present study high throughput whole genome sequencing was done which generated about of 3.7 million base pair genomic data for downstream analysis. The reads were about 101 bases long and mapped to the Oryza sativa var. Nipponbare as reference genome. Genome wide variant analysis detected 1,096,419 variants which included 943,033 SNPs and 153,386 InDels. A total of 24,920 non-synonymous SNPs were identified for 11,529 identified genes. Chromosome-wise distribution of uniquely mapped reads onto reference genome showed that maximum reads were mapped to 1st chromosome and least to 9th chromosome. 10th chromosome showed highest density of variations (about 325.6 per 100 kb genome sequence). Detailed sequence analysis of 23 floral organ developmental genes detected 419 potent variants where DL (Drooping Leaf) and OSH1 (Oryza sativa Homeobox1) genes showed highest number (32) of variants; whereas, MADS21 (Minichromosome Agamous Deficient Serum Factor 21) gene have lowest number (5) of variants. The information generated in this study will enrich the genomics of floral organ development in indica rice and cereal crops in general.

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Abbreviations

BAM:

Binary alignment map

CTX:

Inter chromosomal translocation

DEL:

Deletion

DL :

Drooping leaf

FON:

Floral organ mutant

GB:

Gigabyte

INS:

Insertion

INV:

Inversion

IRGSP:

International Rice Genome Project

ITX:

Intra chromosomal translocation

MADS :

M for minichromosome maintenance factor, a for agamous, d for deficient s for serum response factor

NCBI:

National Center for Biotechnology Information

NGS:

Next generation sequencing

OSH1 :

Oryza sativa Homeobox1

SAM:

Sequence alignment map

SAM tool:

Sequence alignment map tool

SNP:

Single nucleotide polymorphism

SPAdes:

Sequential pattern discovery using equivalence classes

SRA:

Sequence alignment map

Ts:

Transition

Tv:

Transversion

UTR:

Untranslated region

Vcf:

Variant call format

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Acknowledgements

The work was financially supported by SERB, Department of Science and Technology, Government of India in form of a research project (Ref. No. SB/YS/LS-187/2013).

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Authors and Affiliations

  1. Rice Biotechnology Laboratory, Department of Biotechnology, Visva-Bharati, Santiniketan, West Bengal, 731235, India

    Soumya Prakash Das & Narottam Dey

  2. Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India

    Rahul Singh Jasrotia, Mir Asif Iquebal & Sarika Jaiswal

  3. Centre for Interdisciplinary Studies, Basudha Biotechnology Laboratory for Conservation (Basudha Trust), 9 Old Calcutta Road, Barrackpore, Kolkata, West Bengal, 700123, India

    Debal Deb

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  1. Soumya Prakash Das
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  2. Rahul Singh Jasrotia
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  3. Debal Deb
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Das, S.P., Jasrotia, R.S., Deb, D. et al. Genomic analysis of polycarpellary rice (Oryza sativa L.) through whole genome resequencing. J. Plant Biochem. Biotechnol. 30, 364–372 (2021). https://doi.org/10.1007/s13562-020-00602-8

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