Drought and salinity are two major environmental factors determining plant productivity that due to their high magnitude of impact and wide distribution. The regulatory circuits include stress sensors, signaling pathways comprising a network of protein-protein reactions, transcription factors and promoters, and finally the output proteins or metabolites. Plant receptor-like kinases (RLKs) are transmembrane proteins family, are predicted to be major components of the signaling pathways that allow plants to respond to diverse environmental and development condition. Subfamily of Catharanthus roseus RLK1-like kinases (CrRLK1Ls) is a novel type of RLK, was identified in Arabidopsis with 17 members carrying a putative extracellular carbonhydrate-binding malectin-like domain. To study the function of CrRLK1Ls subfamily in rice which is a most widely consumed staple food, we produced the phylogenomic data with the integration of microarray-based anatomical and stress expression profiling data to the context of rice CrRLK1Ls family phylogenic tree. The expression profiling data are based on a large number of public microarray data such as 1150 Affymetrix arrays and 209 Agilent 44K arrays. Chromosomal localization of CrRLK1Ls reveals that three of 16 genes were tandem duplicated. Subsequently, we identified 7 genes that showed circadian regulation pattern and three genes of them simultaneously response to drought stress: two were down-regulated and one was up-regulated. Functional gene network development mediated by these stress responsible genes might be an useful foundation to explain the molecular mechanism of stress response mediated by this gene family.

Drought and salinity are two major environmental factors determining plant productivity that due to their high magnitude of impact and wide distribution. The regulatory circuits include stress sensors, signaling pathways comprising a network of protein-protein reactions, transcription factors and promoters, and finally the output proteins or metabolites. Plant receptor-like kinases (RLKs) are transmembrane proteins family, are predicted to be major components of the signaling pathways that allow plants to respond to diverse environmental and development condition. Subfamily of Catharanthus roseus RLK1-like kinases (CrRLK1Ls) is a novel type of RLK, was identified in Arabidopsis with 17 members carrying a putative extracellular carbonhydrate-binding malectin-like domain. To study the function of CrRLK1Ls subfamily in rice which is a most widely consumed staple food, we produced the phylogenomic data with the integration of microarray-based anatomical and stress expression profiling data to the context of rice CrRLK1Ls family phylogenic tree. The expression profiling data are based on a large number of public microarray data such as 1150 Affymetrix arrays and 209 Agilent 44K arrays. Chromosomal localization of CrRLK1Ls reveals that three of 16 genes were tandem duplicated. Subsequently, we identified 7 genes that showed circadian regulation pattern and three genes of them simultaneously response to drought stress: two were downregulated and one was up-regulated. Functional gene network development mediated by these stress responsible genes might be an useful foundation to explain the molecular mechanism of stress response mediated by this gene family.

ATP-binding cassette (ABC) proteins comprise a large superfamily and play as key in the physiology and development of plants but it is highly likely that more functions for members of this interesting family are still in dark. Thus systematic analysis for this family will be helpful to design effective experimental plans for functional analysis of each of ABC family in rice. To do this, we performed phylogenomic analysis of integrating anatomy and stress meta-profiling data based on a large collection of rice affymetrix array data which provide useful clues to study functions of ABC transporter family in rice in term of anatomy and stress response. Then, we processed Significance analysis for Microarray to identify ABC transporters involved in water stress such as drought and salt. Subsequently, we identified 23 genes showing significant upregulation or downregulation by both drought and salt. Finally, we developed the interaction network mediated by six of them and then integrated diverse data such as co-expression patterns, putative functions and sub-cellular localization to the network and the network was further refined based on coexpression patterns in response to drought and salt stresses. Our analysis will provide molecular basis to study diverse biological phenomena mediated by ABC family in rice, a major model crop plant.

Global warming and climate changing nowadays are known as one of the most harmful factors concerning the yield of worldwide crop plants. To adapt with new challenges, a well-known strategy of plants is water-balance control. Aquaporins are a gene family of integral membrane proteins which play a central role in water transport regulation. By searching diverse databases, we expanded the number of rice aquaporin family from 33 to 37 genes. After that, the phylogenomic data integrating anatomical expression patterns consisting of 1150 affymetrix arrays and 209 Agilent 44K arrays, and stress responsible expression patterns were constructed and analyzed. The systemic overview of gene expression for rice aquaporin family is used to evaluate functional redundancy within this family and identify suitable target genes in response to water stress. Functional gene network mediated by water stress relating aquaporin genes also suggested a useful platform for further researches.

Global warming and climate changing nowadays are known as one of the most harmful factors concerning the yield of worldwide crop plants. To adapt with new challenges, a well-known strategy of plants is water-balance control. Aquaporins are a gene family of integral membrane proteins which play a central role in water transport regulation. By searching diverse databases, we expanded the number of rice aquaporin family from 33 to 37 genes. After that, the phylogenomic data integrating anatomical expression patterns consisting of 1150 affymetrix arrays and 209 Agilent 44K arrays, and stress responsible expression patterns were constructed and analyzed. The systemic overview of gene expression for rice aquaporin family is used to evaluate functional redundancy within this family and identify suitable target genes in response to water stress. Functional gene network mediated by water stress relating aquaporin genes also suggested a useful platform for further researches.