IC4R008-Genome-2016-26984283

Project Title

Indica rice genome assembly, annotation and mining of blast disease resistance genes

Rice is a major staple food crop in the world. Over 80 % of rice cultivation area is under indica rice.Currently, 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.

The genome of indica rice cultivar, HR-12 was assembled using combination of short reads (PE and MP libraries) from Illumina and long reads from Pacific Biosciences.
HR-12 genome was sequenced using PacBio RS SMRT platform with 20x coverage.
We scaffolded HR-12 contigs by utilizing stranded RNA sequencing data, which reduced scaffold numbers from 61001 to 59692.
The gene prediction using MAKER-P in gap filled assembly of HR-12 genome yielded 56,284 protein-coding transcripts. We performed two-way comparison of genes from short read and gap filled assemblies, resulting into 31,933 genes with 100 % identity.

The researchers 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, the researchers 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 Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program.

Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP),National Centre for Biological Sciences (NCBS), Bengaluru 560065, India.
Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru 560065, India.
Pacific Biosciences, Boon Lay Way, Singapore 609964, Singapore.
Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences,Ohio State University, Columbus 43210, USA.
Manipal University, Manipal 576104, India.
Genomics Discovery Program, School of Conservation, Life Science and Health Sciences, TransDisciplinary University, Foundation of Revitalization of Local Health Traditions, Bengaluru 560064, India.