Rice Genome

 

ABSTRACT


Background: Rice is a major staple

foodcrop in the world. Over 80% of rice

cultivation area is under indica rice. Cur-

-rently, genomic resources are lacking for

indica as compared to japonica rice. In

this study, we generated deep

-sequencing data (Illumina and Pacific

Biosciences sequencing) for one of the

indica rice cultivars, HR-12 from India.


                                                 Dr.Mahesh H B with sequenced  HR-12 Rice Variety

Results: We assembled over 86% (389 Mb) of rice genome and annotated 56,284 protein-coding genes from HR-12 genome using Illumina and PacBio sequencing. Comprehensive comparative analyses between indica and japonica subspecies genomes revealed a large number of indica specific variants including SSRs, SNPs and InDels. To mine disease resistance genes, we sequenced few indica rice cultivars that are reported to be highly resistant (Tetep and Tadukan) and susceptible (HR-12 and Co-39) against blast fungal isolates in many countries including India. Whole genome sequencing of rice genotypes revealed high rate of mutations in defense related genes (NB-ARC, LRR and PK domains) in resistant cultivars as compared to susceptible. This study has identified R-genes Pita and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program.

Conclusions: This is the first report of whole genome sequencing approach to characterize Indian rice germplasm. The genomic resources from our work will have a greater impact in understanding global rice diversity, genetics and molecular breeding.

Full article: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2523-7