Please use this identifier to cite or link to this item: https://doi.org/10.1093/gbe/evt152
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dc.titleGenome-wide survey on genomic variation, expression divergence, and evolution in two contrasting rice genotypes under high salinity stress
dc.contributor.authorJiang, S.-Y.
dc.contributor.authorMa, A.
dc.contributor.authorRamamoorthy, R.
dc.contributor.authorRamachandran, S.
dc.date.accessioned2014-12-12T07:49:02Z
dc.date.available2014-12-12T07:49:02Z
dc.date.issued2013
dc.identifier.citationJiang, S.-Y., Ma, A., Ramamoorthy, R., Ramachandran, S. (2013). Genome-wide survey on genomic variation, expression divergence, and evolution in two contrasting rice genotypes under high salinity stress. Genome Biology and Evolution 5 (11) : 2032-2050. ScholarBank@NUS Repository. https://doi.org/10.1093/gbe/evt152
dc.identifier.issn17596653
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/116368
dc.description.abstractExpression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1-10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hAT elements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions. © The Author(s) 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
dc.sourceScopus
dc.subjectCustom microarray
dc.subjectGene set enrichment analysis
dc.subjectPromoter motif
dc.subjectSingle nucleotide polymorphism
dc.subjectTandem and segmental duplication
dc.subjectTransposition
dc.typeArticle
dc.contributor.departmentINSTITUTE OF MOLECULAR AGROBIOLOGY
dc.description.doi10.1093/gbe/evt152
dc.description.sourcetitleGenome Biology and Evolution
dc.description.volume5
dc.description.issue11
dc.description.page2032-2050
dc.identifier.isiut000328410600002
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