Difference between revisions of "IC4R008-Genome-2016-26984283"
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*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. | *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. | ||
==Plant Culture & Treatment== | ==Plant Culture & Treatment== | ||
| + | *The genome of indica rice cultivar, HR-12 was assembled using combination of short reads (PE and MP libraries) from Illumina and long reads (Additional file 2) from Pacific Biosciences (Additional file 3). | ||
==Research Findings== | ==Research Findings== | ||
Revision as of 09:08, 26 June 2016
Contents
Project Title
- Indica rice genome assembly, annotation and mining of blast disease resistance genes
The Background of This Project
- 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.
Plant Culture & Treatment
- The genome of indica rice cultivar, HR-12 was assembled using combination of short reads (PE and MP libraries) from Illumina and long reads (Additional file 2) from Pacific Biosciences (Additional file 3).
Research Findings
- 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, 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.
Labs working on this Project
- 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.
Corresponding Author
- malalig@ccamp.res.in & malalig@frlht.org
