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

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.