ArticleBMC genomics2016
Indica rice genome assembly, annotation and mining of blast disease resistance genes.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
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- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia.Communications biology · 2024Article
- Challenges and Perspectives for Integrating Quinoa into the Agri-Food System.Plants (Basel, Switzerland) · 2023Review
- Whole-genome identification and expression profiling of growth-regulating factor (GRF) and GRF-interacting factor (GIF) gene families in Panax ginseng.BMC genomics · 2023Article
- Stacking Multiple Genes Improves Resistance toGenes · 2023Article
- A chromosome-level genome assembly of an early matured aromaticFrontiers in plant science · 2023Article
- Comparative analysis of repeat content in plant genomes, large and small.Frontiers in plant science · 2023Article
- Chromosome-level genome assembly and population genetic analysis of a near-threatened rosewood species (Frontiers in plant science · 2023Article
- Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.Genome research · 2022Article
- Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution.Botanical studies · 2022Article
- Microwave Cooking Enriches the Nanoscale and Short/Long-Range Orders of the ResultingFoods (Basel, Switzerland) · 2022Article
- The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains.Computational and structural biotechnology journal · 2022Article
- Colorimetric loop-mediated isothermal amplification assay for detection and ecological monitoring ofFrontiers in plant science · 2022Article
- Optimisation of a rapid and efficient transformation protocol for fungal blast-susceptible indica rice cultivars HR-12 and CO-39.Plant biotechnology (Tokyo, Japan) · 2021Article
- A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment.Journal of advanced research · 2021Article
- Molecular virulence determinants ofMycology · 2021Review
- Genome, Transcriptome, and Germplasm Sequencing Uncovers Functional Variation in the Warm-Season Grain Legume HorsegramFrontiers in plant science · 2021Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRice 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.
resultsWe 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 Pi-ta and Pi54 from durable indica resistant cultivars; Tetep and Tadukan, which can be used in marker assisted selection in rice breeding program.
conclusionsThis 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.
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