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

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Title Genomic analysis of polycarpellary rice (Oryza sativa L.) through whole genome resequencing
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Creator Soumya Prakash Das
Rahul Singh Jasrotia
Debal Deb
Mir Asif Iquebal
Sarika Jaiswal
Narottam Dey
 
Subject Rice
Floral organ mutants
Multiple seeded rice
Whole genome sequencing
SNP
InDels
 
Description Not Available
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.
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Date 2022-03-19T09:43:26Z
2022-03-19T09:43:26Z
2020-11-05
 
Type Research Paper
 
Identifier 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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http://krishi.icar.gov.in/jspui/handle/123456789/70371
 
Language English
 
Relation Not Available;
 
Publisher Not Available