Research Article: Gene Expression Profiles Deciphering Rice Phenotypic Variation between Nipponbare (Japonica) and 93-11 (Indica) during Oxidative Stress

Date Published: January 8, 2010

Publisher: Public Library of Science

Author(s): Fengxia Liu, Wenying Xu, Qiang Wei, Zhenghai Zhang, Zhuo Xing, Lubin Tan, Chao Di, Dongxia Yao, Chunchao Wang, Yuanjun Tan, Hong Yan, Yi Ling, Chuanqing Sun, Yongbiao Xue, Zhen Su, Shin-Han Shiu. http://doi.org/10.1371/journal.pone.0008632

Abstract: Rice is a very important food staple that feeds more than half the world’s population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core Intersectional Probesets (CIPs). These CIPs were analyzed by gene ontology (GO) and highlighted with enrichment GO terms related to toxin and oxidative stress responses as well as other responses. These GO term-enriched genes of the CIPs include glutathine S-transferases (GSTs), P450, plant defense genes, and secondary metabolism related genes such as chalcone synthase (CHS). Further insertion/deletion (InDel) and regulatory element analyses for these identified CIPs suggested that there may be some eQTL hotspots related to oxidative stress in the rice genome, such as GST genes encoded on chromosome 10. In addition, we identified a group of marker genes individuating the japonica and indica subspecies. In summary, we developed a new strategy combining biological experiments and data mining to study the possible molecular mechanism of phenotypic variation during oxidative stress between Nipponbare and 93-11. This study will aid in the analysis of the molecular basis of quantitative traits.

Partial Text: Rice (Oryza sativa) is the major food staple for about half of the world’s population, and it also is a model monocot plant for molecular and genetic studies. Oryza sativa L. ssp indica (Hsien) and Oryza sativa L. ssp japonica (Keng) are two major Asian cultivated rice (Oryza sativa L.) subspecies [1], [2], [3]. These two subspecies have been distinguished based on morphological characters and geographical distribution for 2,000 years. Indica and Japonica rice originated from different ancestors and they diverged about 0.2∼0.44 million years ago [4], [5]. From Khush’s report, indica was probably domesticated in eastern India and japonica somewhere in South China [6]. These variations affect genomic structure and may cause intra-specific phenotypic adaptations. For example, there exists variance of seed maturity, seed quality, stress and defense tolerance between the two subspecies. Genome-wide comparative analyses were conducted on DNA sequences derived from indica and japonica rice [5], [6], [7], [8], [9], [10], [11], [12], [13]. In recent years, sequence variance analysis between the two rice subspecies have become well-established due to the publicly available rice genome, including the genome sequences of the japonica variety Nipponbare and indica variety 93-11 [14], [15], [16], [17], and a genetic map for 150 rice recombinant inbred lines constructed by the recently introduced next-generation sequencing technology [18]. In order to further elucidate genetic differences between rice subspecies, an approach using Gene Ontology (GO) analysis together with genomic variation analysis was conducted by different research groups [19], [20]. Several GO terms were highlighted with significant enrichment, including production of defense-related compounds, cell wall components, cell signaling proteins, and transcription factors. The GO analysis results indicated that there was positive selection either by natural means or by human interests during indica–japonica differentiation. However, the underlying regulatory mechanisms of rice phenotypic variation during development or during stress conditions between the two subspecies are largely unknown.

Genetic variation among different rice varieties may lead to alternative gene expression, which may influence phenotypic variation. Nipponbare seedlings showed strong oxidative stress resistance to methyl viologen (MV) treatment compared to 93-11. In order to elucidate the molecular mechanisms of phenotypic divergence in oxidative stress response observed between Nipponbare (japonica variety) and 93-11 (indica variety), we conducted a microarray analysis and real-time RT-PCR validation to identify genes differentially expressed in response to MV treatment in the two rice cultivars. We identified Core Intersectional Probeset, and further employed multiple enrichment analysis to understand the genetic basis of oxidative stress resistance.

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http://doi.org/10.1371/journal.pone.0008632

 

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