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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
 
Creator Jain, Mukesh
Moharana, Kanhu Charan
Shankar, Rama
Kumari, Romika
Garg, Rohini
 
Subject Oryza sativa
stress response
single-nucleotide polymorphisms
insertions/deletions
gene function
 
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.
 
Date 2015-12-16T11:52:32Z
2015-12-16T11:52:32Z
2014
 
Type Article
 
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
 
Language en_US
 
Publisher John Wiley & Sons