Analysis of genomic variations using DNA sequencing technologies has imparted significance to crop genetics and breeding. In the present study, a photo sensitive genic male sterile

(PGMS) line of a Japonica rice has been sequenced by Genotyping by Sequencing (GBS) method of next generation sequencing (NGS) for detecting genome wide single nucleotide polymorphisms (SNPs). The optimized protocol of GBS revealed 57.2% of uniquely mapped short reads onto the Nipponbare reference rice genome. The uniquely mapped reads of 200bp were further imputed in TASSAL-GBS software for identification of total 1894 genome-wide SNPs. The identified SNPs within the PGMS genome was scattered unevenly across and within the 12 chromosomes of rice. The annotation of identified SNPs confirmed the presence of 963 SNPs within the intragenic spaces along with 140 and 765 SNPs in the intron and exon regions, respectively. Also, the presence of 498 non-synonymous SNPs in the sequenced genome inferred significance for future breeding applications. The outcome of our study implied that 1004S could be elite breeding germplasm for enhancing the genetic diversity of two-line hybrid rice system. Moreover, the identified SNPs concluded to be potential resource for molecular breeding and genome-wide variations on hybrid performance.

Key words; GBS, PGMS, SNP discovery, annotation, diversity.