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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2523-7) contains supplementary material, which is available to authorized users.
Highlights
Rice is a major staple food crop in the world
Values of rice nuclear DNA was estimated by comparing rice nuclear peak on the linear scale with the peak for Pisum sativum included as an internal standard
All three assemblers resulted comparatively lower contig N50 (Additional file 4), which might result due to inherent disadvantages of short read assemblies, such as poor repeat resolution [3, 28], missing exons and genes and genes split between scaffolds [29]
Summary
Rice is a major staple food crop in the world. Genomic resources are lacking for indica as compared to japonica rice. We generated deep-sequencing data (Illumina and Pacific Biosciences sequencing) for one of the indica rice cultivars, HR-12 from India. Rice (Oryza sativa L.) is a staple food for more than half of the world’s population. India is the second most rice producer in the world and 65 % of its population depends on rice as a staple food. Rice is a model cereal crop with small genome size, short generation time, diploid (2n = 24) and amenable for genetic manipulation. Due to its global importance, several genomes of rice cultigen including japonica (Nipponbare [1]), indica (93-11 [2] and IR64 [3]) and aus (Kasalath [4]) have been sequenced. Gold standard assembly and annotation are available for japonica
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