Journal of Integrative Plant Biology 2007, 49 (6): 729−730

Rice Research: Past, Present and Future

Rice (Oryza sativa L.) is a major crop in the world and provides the staple food for over half of the world’spopulation. From thousands of years of cultivation and breeding to recent genomics, rice has been the focus ofagriculture and plant research. China is the home of both the high-yielding hybrid rice and the largest numberof rice consumers. The Chinese government has strongly supported rice breeding and research, with antici-pated further enhancement of such support in the near future. In this special issue of JIPB on rice research, atotal of twenty-two articles discuss recent advances covering a variety of topics, from domestication andbreeding to population genetics, from genomics to proteomics, from hormonal signaling to stress responses,and from evolutionary studies to functional analysis of gene families.

Rice domestication, breeding and genetics have laid a great foundation for modern rice research. Sang andGe discuss the current understanding of rice domestication, including the questions that still remain, and Tangand Shi provide a look at rice domestication from the perspective of population genetics. Jiang et al. report thegreat progress in rice genetics that has been made in recent years in China, including the molecular identifica-tion of genes that are important for key traits, such as male sterility, disease resistance, and tillering. Moreover,Li et al. review the analyses of a number of male sterile and restorer lines and their use in the generation ofhybrid rice varieties, which have greatly increased rice production. Also, Cheng et al. describe the accomplish-ments of breeding super hybrid rice using DNA markers, resulting in greater biomass and yield, and discusspossible future challenges and gains in this technology. In addition, Tan et al. summarize the efforts beingmade in the development of rice lines by introgression from the wild rice Oryza rufipogon into the cultivated riceO. sativa, with the aim of QTLs (quantitative trait loci) affecting yields. These articles both provide historicaloverviews and highlight current efforts in rice breeding.

Successful rice cultivation is intimately linked with hormonal signaling and appropriate responses to bioticand abiotic stresses, including bacterial and fungal disease, and salt and drought stresses. Fan et al. reviewthe advances in the understanding of signal transduction for the hormone gibberellin (GA), which controls plantheight and seed germination; both important traits in agriculture. Specifically, recent molecular analyses haveresulted in the identification of a GA receptor as a key regulator of ubiquitin-dependent proteolysis, as well asother mediators of GA signaling as components or targets of the ubiquitination pathway. In addition, Gao et al.present a summary of the current understanding of mechanisms conferring tolerance to abiotic stresses,whereas Xu et al. report molecular and biochemical analyses of members of the Xa3/Xa26 gene family confer-ring disease resistance to bacterial blight and/or fungal blast diseases in rice. Moreover, Hong et al. describeexpression results suggesting that the BWMK1 gene is responsive to both stress and hormone signaling,potentially acting to integrate multiple signals. Kong et al. report the molecular analyses of a newly identifiedrice receptor-like cytoplasmic protein kinase that is specifically expressed in the pollen.

If rice breeding and genetic endeavors have generated genetic materials that paved the way for recent ad-vances in studying specific genes that are important for many developmental and physiological traits, then thesequencing of the rice genome and the subsequent functional genomics and proteomics efforts have yieldedgreat volumes of global molecular and biochemical information on many thousands of genes and proteins.Such information has already greatly benefited rice research and allows researchers to investigate specificprocesses or pathways with a global perspective of the genome and great comprehensiveness hitherto notpossible. This will undoubtedly propel rice to become an ever more popular model organism for plant research.

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In this issue, several articles showcase the varying approaches investigators have taken to characterize ricegenomes and proteome. Tang et al. describe a method to use BAC clones, a resource made available by therice genome projects, as probes to identify rice chromosomes using fluorescence in situ hybridization. Also,Fan et al. demonstrate the power of a microarray-based method to uncover potentially new genes, usingArabidopsis and rice as examples, again using a functional genomics resource to address the fundamentalevolutionary problem of gene origins. Weedy rice is a pest in the USA and Olsen et al. provide a brief overviewof an ongoing effort to use evolutionary genomics to determine the origin of the weedy red rice and its relation-ship to other cultivated and wild varieties. The well-known hybrid rice requires male sterile lines, which arealtered in their mitochondrial genomes. Liu et al. present a molecular analysis of fertile and sterile mitochon-drial genomes and the identification of regions of structural and expression differences, allowing future func-tional studies of these regions as potential sterility genes. Furthermore, Chen et al. show a proteomic study ofplasma membrane-associated proteins induced by the treatment of chitooligosaccharide elicitors that arerelevant to disease responses and the identification of the polyprotein-like protein.

The rice genome project indicated that many genes are members of gene families, as is the case in Arabidopsis.The available information on gene families presents both opportunities and challenges. To facilitate functionalstudies of gene family members, it is important to understand the evolutionary relationships between, and theexpression patterns among the members. MADS-box genes play critical roles in plant development. Xu andKong report phylogenetic analyses of floral MADS-box genes in rice and other grasses and provide evidencefor the origin of novel regulatory genes by duplication and divergence. Another family important for plant devel-opment is the TCP family, controlling cell division, floral organ symmetry and branch formation. Yao et al.present a genome-wide phylogenetic analysis of the TCP genes in Arabidopsis and rice and describe theirexpression patterns, providing clues to functional relationships among family members. The WRKY genefamily encoding transcription factors contains members that are implicated in stress responses. Ross et al.carried out an extensive study of members of the WRKY family in rice and present their genome-wide results,as well as an overview of their functions in stress and hormonal responses. An area of exciting and rapidprogress is the regulation of gene expression by small RNAs, as reviewed by Sunkar and Zhu for rice and otherplants. In addition, Sun et al. report an analysis of a family of F-box proteins with Kelch repeats, includingphylogeny, genome organization and expression. They showed that while some of the subfamilies remainedquite stable during the evolution of flowering plants, one subfamily has greatly expanded in the Brassicaseaesince they diverged from poplar. Finally, Rohila and Yang reviewed recent progress in the studies of rice genesencoding mitogen activating protein (MAP) kinases, particularly their functions in mediating stress responses.

This selection of articles covers a wide range of topics and is indicative of the rapid advances in many areasof rice research in recent years. Undoubtedly, the future of rice research is very exciting, promising to revealmany more secretes about plant biology to promote agriculture and to ultimately benefit human society.

Hong Ma Pennsylvania State University, University Park, USAKang Chong Institute of Botany, the Chinese Academy of Sciences, Beijing, ChinaXing-Wang Deng Yale University, New Haven, USA