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抯 population. From thousands of years of cultivation and breeding to recent genomics, rice has been the focus of agriculture and plant research. China is the home of both the high-yielding hybrid rice and the largest number of rice consumers. The Chinese government has strongly supported rice breeding and research, with anticipated further enhancement of such support in the near future. In this special issue of JIPB on rice research, a total of twenty-two articles discuss recent advances covering a variety of topics, from domestication and breeding 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 and Ge discuss the current understanding of rice domestication, including the questions that still remain, and Tang and Shi provide a look at rice domestication from the perspective of population genetics. Jiang et al. report the great progress in rice genetics that has been made in recent years in China, including the molecular identification 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 of hybrid rice varieties, which have greatly increased rice production. Also, Cheng et al. describe the accomplishments of breeding super hybrid rice using DNA markers, resulting in greater biomass and yield, and discuss possible future challenges and gains in this technology. In addition, Tan et al. summarize the efforts being made in the development of rice lines by introgression from the wild rice Oryza rufipogon into the cultivated rice O. sativa, with the aim of QTLs (quantitative trait loci) affecting yields. These articles both provide historical overviews and highlight current efforts in rice breeding.
Successful rice cultivation is intimately linked with hormonal signaling and appropriate responses to biotic and abiotic stresses, including bacterial and fungal disease, and salt and drought stresses. Fan et al. review the advances in the understanding of signal transduction for the hormone gibberellin (GA), which controls plant height and seed germination; both important traits in agriculture. Specifically, recent molecular analyses have resulted in the identification of a GA receptor as a key regulator of ubiquitin-dependent proteolysis, as well as other 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 conferring disease resistance to bacterial blight and/or fungal blast diseases in rice. Moreover, Hong et al. describe expression 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 identified rice 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 advances in studying specific genes that are important for many developmental and physiological traits, then the sequencing of the rice genome and the subsequent functional genomics and proteomics efforts have yielded great 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 specific processes or pathways with a global perspective of the genome and great comprehensiveness hitherto not possible. This will undoubtedly propel rice to become an ever more popular model organism for plant research. In this issue, several articles showcase the varying approaches investigators have taken to characterize rice genomes and proteome. Tang et al. describe a method to use BAC clones, a resource made available by the rice 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, using Arabidopsis and rice as examples, again using a functional genomics resource to address the fundamental evolutionary problem of gene origins. Weedy rice is a pest in the USA and Olsen et al. provide a brief overview of an ongoing effort to use evolutionary genomics to determine the origin of the weedy red rice and its relationship to other cultivated and wild varieties. The well-known hybrid rice requires male sterile lines, which are altered in their mitochondrial genomes. Liu et al. present a molecular analysis of fertile and sterile mitochondrial genomes and the identification of regions of structural and expression differences, allowing future functional studies of these regions as potential sterility genes. Furthermore, Chen et al. show a proteomic study of plasma membrane-associated proteins induced by the treatment of chitooligosaccharide elicitors that are relevant 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 functional studies of gene family members, it is important to understand the evolutionary relationships between, and the expression patterns among the members. MADS-box genes play critical roles in plant development. Xu and Kong report phylogenetic analyses of floral MADS-box genes in rice and other grasses and provide evidence for the origin of novel regulatory genes by duplication and divergence. Another family important for plant development 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 their expression patterns, providing clues to functional relationships among family members. The WRKY gene family 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 rapid progress is the regulation of gene expression by small RNAs, as reviewed by Sunkar and Zhu for rice and other plants. In addition, Sun et al. report an analysis of a family of F-box proteins with Kelch repeats, including phylogeny, genome organization and expression. They showed that while some of the subfamilies remained quite stable during the evolution of flowering plants, one subfamily has greatly expanded in the Brassicaseae since they diverged from poplar. Finally, Rohila and Yang reviewed recent progress in the studies of rice genes encoding 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 areas of rice research in recent years. Undoubtedly, the future of rice research is very exciting, promising to reveal many more secretes about plant biology to promote agriculture and to ultimately benefit human society.