Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance
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Title |
Genome-wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance
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Creator |
Jain, Mukesh
Moharana, Kanhu Charan Shankar, Rama Kumari, Romika Garg, Rohini |
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Subject |
Oryza sativa
stress response single-nucleotide polymorphisms insertions/deletions gene function |
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Description |
Accepted date: 12 September 2013
Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole- genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice. This work was financially supported by the Department of Biotechnology, Government of India, and core grant from the National Institute of Plant Genome Research. RS acknowl- edges grant of research fellowship from the Department of Biotechnology. RG acknowledges INSPIRE Faculty Award from the Department of Science & Technology and Innovative Young Biotechnologist Award from the Department of Biotechnology, Government of India. We are thankful to Dr S. Parida, NIPGR, for helpful discussion and Prof. S. Jackson for proofreading of the MS. We are also thankful to Ms. A. Bhattacharjee for genomic DNA extraction and Mr. M. Verma for generating Circos diagrams. |
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Date |
2015-12-16T11:52:32Z
2015-12-16T11:52:32Z 2014 |
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Type |
Article
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Identifier |
Plant Biotechnol. Journal, 12(2): 253-264
1467-7652 http://172.16.0.77:8080/jspui/handle/123456789/416 http://onlinelibrary.wiley.com/doi/10.1111/pbi.12133/abstract 10.1111/pbi.12133 |
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Language |
en_US
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Publisher |
John Wiley & Sons
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