Genomic analysis of polycarpellary rice ( Oryza sativa L.) through whole genome resequencing
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ORIGINAL ARTICLE
Genomic analysis of polycarpellary rice (Oryza sativa L.) through whole genome resequencing Soumya Prakash Das1 • Rahul Singh Jasrotia2 • Debal Deb3 • Mir Asif Iquebal2 • Sarika Jaiswal2 Narottam Dey1
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Received: 20 March 2020 / Accepted: 3 September 2020 Ó Society for Plant Biochemistry and Biotechnology 2020
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 morphoanatomical 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. Chromosomewise 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. Keywords Rice Floral organ mutants Multiple seeded rice Whole genome sequencing SNP InDels
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13562-020-00602-8) contains supplementary material, which is available to authorized users.
Abbreviations BAM Binary alignment map CTX Inter chromosomal translocation DEL Deletion 2
Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
3
Centre for Interdisciplinary Studies, Basudha Biotechnology Laboratory for Conservation (Basudha Trust), 9 Old Calcutta Road, Barrackpore, Kolkata, West Bengal 700123, India
& Narottam Dey [email protected] Soumya Prakash Das [email protected] Rahul Singh Jasrotia [email protected] Debal Deb [email protected] Mir Asif Iquebal [email protected] Sarika Jaiswal [email protected] 1
Rice Biotechnology Laboratory, Department of Biotechnology, Visva-Bharati, Santiniketan, West Bengal 731235, India
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J. Plant Biochem. Biotechnol.
DL FON GB INS INV IRGSP ITX MADS
NCBI NGS OSH1 SAM SAM tool SNP SPAdes SRA Ts Tv UTR Vcf
Droopin
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