期刊
PLANT BIOTECHNOLOGY JOURNAL
卷 12, 期 2, 页码 253-264出版社
WILEY
DOI: 10.1111/pbi.12133
关键词
Oryza sativa; stress response; single-nucleotide polymorphisms; insertions; deletions; gene function
资金
- Department of Biotechnology, Government of India
- National Institute of Plant Genome Research
- Department of Biotechnology. RG acknowledges INSPIRE Faculty Award
- Department of Science & Technology and Innovative Young Biotechnologist Award
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 1784583 nonredundant single-nucleotide polymorphisms (SNPs) and 154275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401683 and 662509 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.
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