Special Issue: Rice Breeding and Functional Genomics   

June 2007, Volume 49 Issue 6, Pages 729-960.

Cover Caption:
Breeding and Funotional Genomics in Rice
Super hybrid rice is defined as the new type hybrids that combine the harmonious plant type with heterosis (as showed on the cover) through hybridization between indica and japonica. China has developed 34 super hybrids and produced 6.7 thousand million kg more rice in 1998-2005. See pages 805-810 for details.


Rice Research: Past, Present and Future  
Author: Hong Ma, Kang Chong and Xing-Wang Deng
Journal of Integrative Plant Biology 2007 49(6): 729-730
DOI: 10.1111/j.1744-7909.2007.00515.x
    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’s 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.
Abstract (Browse 6234)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Invited Expert Reviews
Gibberellin Signal Transduction in Rice  
Author: Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng
Journal of Integrative Plant Biology 2007 49(6): 731-741
DOI: 10.1111/j.1744-7909.2007.00511.x

In the past decade, significant knowledge has accumulated regarding gibberellin (GA) signal transduction in rice as a result of studies using multiple approaches, particularly molecular genetics. The present review highlights the recent developments in the identification of GA signaling pathway components, the discovery of GA-induced destruction of GA signaling repressor (DELLA protein), and the possible mechanism underlying the regulation of GA-responsive gene expression in rice.

Abstract (Browse 2237)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Understanding Abiotic Stress Tolerance Mechanisms: Recent Studies on Stress Response in Rice  
Author: Ji-Ping Gao, Dai-Yin Chao and Hong-Xuan Lin
Journal of Integrative Plant Biology 2007 49(6): 742-750
DOI: 10.1111/j.1744-7909.2007.00495.x

Abiotic stress is the main factor negatively affecting crop growth and productivity worldwide. The advances in physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to stresses. Rice plants are sensitive to various abiotic stresses. In this short review, we present recent progresses in adaptation of rice to salinity, water deficit and submergence. Many studies show that salt tolerance is tightly associated with the ability to maintain ion homeostasis under salinity. Na+ transporter SKC1 unloads Na+ from xylem, plasma membrane Na+/H+ antiporter SOS1 excludes sodium out of cytosol and tonoplast Na+/H+ antiporter NHX1 sequesters Na+ into the vacuole. Silicon deposition in exodermis and endodermis of rice root reduces sodium transport through the apoplastic pathway. A number of transcription factors regulate stress-inducible gene expression that leads to initiating stress responses and establishing plant stress tolerance. Overexpression of some transcription factors, including DREB/CBF and NAC, enhances salt, drought, and cold tolerance in rice. A variant of one of ERF family genes, Sub1A-1, confers immersion tolerance to lowland rice. These findings and their exploitation will hold promise for engineering breeding to protect crop plants from certain abiotic stresses.

Abstract (Browse 4545)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Rice Mitogen-activated Protein Kinase Gene Family and Its Role in Biotic and Abiotic Stress Response  
Author: Jai S. Rohila and Yinong Yang
Journal of Integrative Plant Biology 2007 49(6): 751-759
DOI: 10.1111/j.1744-7909.2007.00501.x

The mitogen-activated protein kinase (MAPK) cascade is an important signaling module that transduces extracellular stimuli into intracellular responses in eukaryotic organisms. An increasing body of evidence has shown that the MAPK-mediated cellular signaling is crucial to plant growth and development, as well as biotic and abiotic stress responses. To date, a total of 17 MAPK genes have been identified from the rice genome. Expression profiling, biochemical characterization and/or functional analysis were carried out with many members of the rice MAPK gene family, especially those associated with biotic and abiotic stress responses. In this review, the phylogenetic relationship and classification of rice MAPK genes are discussed to facilitate a simple nomenclature and standard annotation of the rice MAPK gene family. Functional data relating to biotic and abiotic stress responses are reviewed for each MAPK group and show that despite overlapping in functionality, there is a certain level of functional specificity among different rice MAP kinases. The future challenges are to functionally characterize each MAPK, to identify their downstream substrates and upstream kinases, and to genetically manipulate the MAPK signaling pathway in rice crops for the improvement of agronomically important traits.

Abstract (Browse 3191)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The Puzzle of Rice Domestication  
Author: Tao Sang and Song Ge
Journal of Integrative Plant Biology 2007 49(6): 760-768
DOI: 10.1111/j.1744-7909.2007.00510.x

The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snow-balling model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.

Abstract (Browse 3181)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Molecular Population Genetics of Rice Domestication  
Author: Tian Tang and Suhua Shi
Journal of Integrative Plant Biology 2007 49(6): 769-775
DOI: 10.1111/j.1744-7909.2007.00507.x

Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations? Another notable outcome of artificial selection is the reduction in the fitness of domesticated species when they live in the wild without human assistance. The complete sequences of the two subspecies of rice cultivars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous (N) than synonymous (S) substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica-japonica differentiation under rice domestication and subsequent improvement.

Abstract (Browse 2269)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Recent Progress on Rice Genetics in China  
Author: Hua Jiang, Long-Biao Guo and Qian Qian
Journal of Integrative Plant Biology 2007 49(6): 776-790
DOI: 10.1111/j.1744-7909.2007.00492.x

Through thousands of years of evolution and cultivation, tremendously rich genetic diversity has been accumulated in rice (Oryza sativa L.), developing a large germplasm pool from which people can select varieties with morphologies of interest and other important agronomic traits. With the development of modern genetics, scientists have paid more attention to the genetic value of these elite varieties and germplasms, and such rich rice resources provide a good foundation for genetic research in China. Approximately 100?00 accessions of radiation-, chemical- or insertion-induced mutagenesis have been generated since the 1980s, and great progress has been made on rice molecular genetics. So far at least 16 variant/mutant genes including MOC1, BC1, SKC1, and Rf genes have been isolated and characterized in China. These achievements greatly promote the research on functional genomics, understanding the mechanism of plant development and molecular design breeding of rice in China. Here we review the progress of three aspects of rice genetics in China: moving forward at the molecular level, genetic research on elite varieties and germplasms, and new gene screening and genetic analysis using mutants. The prospects of rice genetics are also discussed.

Abstract (Browse 2109)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Characterization and Use of Male Sterility in Hybrid Rice Breeding  
Author: Shaoqing Li, Daichang Yang and Yingguo Zhu
Journal of Integrative Plant Biology 2007 49(6): 791-804
DOI: 10.1111/j.1744-7909.2007.00513.x

The hybrid rice (Oryza sativa L.) breeding that was initiated in China in the 1970s led to a great improvement in rice productivity. In general, it increases the grain yield by over 20% to the inbred rice varieties, and now hybrid rice has been widely introduced into Africa, Southern Asia and America. These hybrid varieties are generated through either three-line hybrid and two-line hybrid systems; the former is derived from cytoplasmic male sterility (CMS) and the latter derived from genic male sterility (GMS). There are three major types of CMS (HL, BT and WA) and two types of GMS (photoperiod-sensitive (PGMS) and temperature-sensitive (TGMS)). The BT- and HL-type CMS genes are characterized as orf79 and orfH79, which are chimeric toxic genes derived from mitochondrial rearrangement. Rf3 for CMS-WA is located on chromosome 1, while Rf1, Rf4, Rf5 and Rf6 correspond to CMS-BT, CMS-WA and CMS-HL, located on chromosome 10. The Rf1 gene for BT-CMS has been cloned recently, and encodes a mitochondria-targeted PPR protein. PGMS is thought to be controlled by two recessive loci on chromosomes 7 and 12, whereas nine recessive alleles have been identified for TGMS and mapped on different chromosomes. Attention is still urgently needed to resolve the molecular complexity of male sterility to assist rice breeding.

Abstract (Browse 3580)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Super Hybrid Rice Breeding in China: Achievements and Prospects  
Author: Shi-Hua Cheng, Li-Yong Cao, Jie-Yun Zhuang, Shen-Guang Chen, Xiao-Deng Zhan, Ye-Yang Fan, De-Feng Zhu and Shao-Kai Min
Journal of Integrative Plant Biology 2007 49(6): 805-810
DOI: 10.1111/j.1744-7909.2007.00514.x

Hybrid rice has contributed greatly to the self-sufficiency of food supply in China. To meet the future demand for rice production, a national program on super rice breeding was established in China in 1996. The corresponding targets, breeding strategies and most significant advances are reviewed in this paper. New plant type models have been modified to adjust to various rice growing regions. In recognition of the importance of applying parents with intermediate subspecies differentiation in increasing F1 yield, medium type parental lines were selected from populations derived from inter-subspecies crosses with the assistance of DNA markers for subspecies differentiation. Results also indicate that a substantial increase of biomass is the basis for further enhancement of the grain yield potential, and amelioration of leaf characteristics is helpful in increasing the photosynthetic rate. Thirty-four super hybrid rice varieties have been released commercially, growing in a total area of 13.5 million hm2 and producing 6.7 thousand million kg more rice in 1998?005. Although remarkable progress has been made in super hybrid rice breeding in China, selections on the root system and integration of more biotechnological tools remain a great challenge.

Abstract (Browse 3157)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Evolutionary Genomics of Weedy Rice in the USA  
Author: Kenneth M. Olsen, Ana L. Caicedo and Yulin Jia
Journal of Integrative Plant Biology 2007 49(6): 811-816
DOI: 10.1111/j.1744-7909.2007.00506.x

Red rice is an interfertile, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the crop in the southern US, reducing yields and contaminating harvests. No wild Oryza species occur in North America and the weed has been proposed to have evolved through multiple mechanisms, including “de-domestication?of US crop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from “crop mimics? which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have indicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, which have never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show genetic similarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomics of this aggressive weed.

Abstract (Browse 2464)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Micro RNAs and Short-interfering RNAs in Plants  
Author: Ramanjulu Sunkar and Jian-Kang Zhu
Journal of Integrative Plant Biology 2007 49(6): 817-826
DOI: 10.1111/j.1744-7909.2007.00499.x

Gene silencing can occur either at the transcriptional level or post-transcriptional level or both. Many instances of sequence-specific silencing requires small RNAs that can be divided into two major classes: microRNAs (miRNAs) and short-interfering RNAs (siRNAs). miRNAs function in post-transcriptional gene silencing by guiding mRNA degradation or translational repression. Endogenous siRNAs are more diverse in plants than in animals and can direct post-transcriptional gene silencing through mRNA degradation or transcriptional gene silencing by triggering DNA methylation and histone modifications. This review discusses recent advances in the field of small RNA-guided gene silencing in plants including rice.

Abstract (Browse 2031)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
The WRKY Gene Family in Rice (Oryza sativa)  
Author: Christian A. Ross, Yue Liu and Qingxi J. Shen
Journal of Integrative Plant Biology 2007 49(6): 827-842
DOI: 10.1111/j.1744-7909.2007.00504.x

WRKY genes encode transcription factors that are involved in the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded in plants. To facilitate the study of the evolutionary history and functions of this supergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted in a comprehensive list of WRKY gene models in Oryza sativa L. ssp. indica and L. ssp. japonica. Mapping of these genes to individual chromosomes facilitated elimination of the redundant, leading to the identification of 98 WRKY genes in japonica and 102 in indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetic tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and japonica chromosomes, we identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes in disease resistance and responses to salicylic acid and jasmonic acid, seed development and germination mediated by gibberellins, other developmental processes including senescence, and responses to abiotic stresses and abscisic acid in rice and other plants. The signaling pathways mediating WRKY gene expression are also discussed.

Abstract (Browse 4090)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Stress & Phytochemistry
BWMK1 Responds to Multiple Environmental Stresses and Plant Hormones  
Author: Wai-Foong Hong, Chaozu He, Lijun Wang, Dong-Jiang Wang, Leina M. Joseph, Chatchawan Jantasuriyarat, Liangying Dai, Guo-Liang Wang
Journal of Integrative Plant Biology 2007 49(6): 843-851
DOI: 10.1111/j.1744-7909.2007.00505.x

Many plant mitogen-activated protein kinases (MAPKs) play an important role in regulating responses to both abiotic and biotic stresses. The first reported rice MAPK gene BWMK1 is induced by both rice blast (Magnaporthe grisea) infection and mechanical wounding. For further analysis of its response to other environmental cues and plant hormones, such as jasmonic acid (JA), salicylic acid (SA), and benzothiadiazole (BTH), the promoter of BWMK1 was fused with the coding region of the ?glucuronidase (GUS) reporter gene. Two promoter-GUS constructs with a 1.0- and 2.5-kb promoter fragment, respectively, were generated and transformed into the japonica rice cultivars TP309 and Zhonghua 11. Expression of GUS was induced in the transgenic lines by cold, drought, dark, and JA. However, light, SA, and BTH treatments suppressed GUS expression. These results demonstrate that BWMK1 is responsive to multiple abiotic stresses and plant hormones and may play a role in cross-talk between different signaling pathways.

Abstract (Browse 2781)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Omics & Epigenetics
Expressional and Biochemical Characterization of Rice Disease Resistance Gene Xa3/Xa26 Family  
Author: Songjie Xu, Yinglong Cao, Xianghua Li and Shiping Wang
Journal of Integrative Plant Biology 2007 49(6): 852-862
DOI: 10.1111/j.1744-7909.2007.00494.x

The rice (Oryza sativa L.) Xa3/Xa26 gene, conferring race-specific resistance to bacterial blight disease and encoding a leucine-rich repeat (LRR) receptor kinase-like protein, belongs to a multigene family consisting of tandem clustered homologous genes, colocalizing with several uncharacterized genes for resistance to bacterial blight or fungal blast. To provide more information on the expressional and biochemical characteristics of the Xa3/Xa26 family, we analyzed the family members. Four Xa3/Xa26 family members in the indica rice variety Teqing, which carries a bacterial blight resistance gene with a chromosomal location tightly linked to Xa3/Xa26, and five Xa3/Xa26 family members in the japonica rice variety Nipponbare, which carries at least one uncharacterized blast resistance gene, were constitutively expressed in leaf tissue. The result suggests that some of the family members may be candidates of these uncharacterized resistance genes. At least five putative N-glycosylation sites in the LRR domain of XA3/XA26 protein are not glycosylated. The XA3/XA26 and its family members MRKa and MRKc all possess the consensus sequences of paired cysteines, which putatively function in dimerization of the receptor proteins for signal transduction, immediately before the first LRR and immediately after the last LRR. However, no homo-dimer between the XA3/XA26 molecules or hetero-dimer between XA3/XA26 and MRKa or MRKc were formed, indicating that XA3/XA26 protein might function either as a monomer or a hetero-dimer formed with other protein outside of the XA3/XA26 family. These results provide valuable information for further extensive investigation into this multiple protein family.

Abstract (Browse 2092)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Proteomic Analysis of Rice Plasma Membrane-associated Proteins in Response to Chitooligosaccharide Elicitors  
Author: Fang Chen, Qun Li and Zuhua He
Journal of Integrative Plant Biology 2007 49(6): 863-870
DOI: 10.1111/j.1744-7909.2007.00496.x

Chitooligomers or chitooligosaccharides (COS) are elicitors that bind to the plasma membrane (PM) and elicit various defense responses. However, the PM-bound proteins involved in elicitor-mediated plant defense responses still remain widely unknown. In order to get more information about PM proteins involved in rice defense responses, we conducted PM proteomic analysis of the rice suspension cells elicited by COS. A total of 14 up- or down-regulated protein spots were observed on 2-D gels of PM fractions at 12 h and 24 h after COS incubation. Of them, eight protein spots were successfully identified by MS (mass spectrography) and predicted to be associated to the PM and function in plant defense, including a putative PKN/PRK1 protein kinase, a putative pyruvate kinase isozyme G, a putative zinc finger protein, a putative MAR-binding protein MFP1, and a putative calcium-dependent protein kinase. Interestingly, a COS-induced pM5-like protein was identified for the first time in plants, which is a transmembrane nodal modulator in transforming growth factor-b (TGFb) signaling in vertebrates. We also identified two members of a rice polyprotein family, which were up-regulated by COS. Our study would provide a starting point for functionality of PM proteins in the rice basal defense.

Abstract (Browse 2202)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci  
Author: Lubin Tan, Fengxia Liu, Wei Xue, Guijuan Wang, Sheng Ye, Zuofeng Zhu, Yongcai Fu, Xiangkun Wang and Chuanqing Sun
Journal of Integrative Plant Biology 2007 49(6): 871-884
DOI: 10.1111/j.1744-7909.2007.00497.x

Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67?.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%?0% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teqing background. These O. rufipogon -O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

Abstract (Browse 2706)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa  
Author: Xuan Yao, Hong Ma, Jian Wang and Dabing Zhang
Journal of Integrative Plant Biology 2007 49(6): 885-897
DOI: 10.1111/j.1744-7909.2007.00509.x

Several TCP genes have been reported to play important roles in plant development; the TCP homologs encode a plant-specific family of putative transcription factors. To understand the evolutionary relationship of TCP genes of Arabidopsis thaliana and Oryza sativa L. (hereafter called rice), we have identified 23 and 22 TCP genes in the Arabidopsis and rice genomes, respectively. Using phylogenetic analysis, we grouped these TCP genes into three classes. In addition, the motifs outside the TCP domain further support the evolutionary relationships among these genes. The genome distribution of the TCP genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the TCP gene family. The expression pattern of the TCP genes was analyzed further, providing useful clues about the function of these genes.

Abstract (Browse 3208)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Signal Transduction
Identification, Expression and Functional Analysis of a Receptor-like Cytoplasmic Kinase, OsRLCK1, in Rice  
Author: Zhaosheng Kong, Wenying Xu, Qun Li and Yongbiao Xue
Journal of Integrative Plant Biology 2007 49(6): 898-907
DOI: 10.1111/j.1744-7909.2007.00512.x

Pollination involves a series of complex cellular interactions and signal transduction events. Numerous reports have suggested a central role for protein kinases in pollen germination and pollen tube growth and a large number of receptor-like kinases have been detected exclusively in pollen in higher plants. However, few are well characterized, especially for the receptor-like cytoplasmic kinases. Here we report a receptor-like kinase gene, OsRLCK1, which belongs to the receptor-like cytoplasmic kinase VIII subfamily. Real-time quantitative polymerase chain reaction analysis and whole mount RNA in situ hybridization showed that OsRLCK1 is a pollen-specific gene and expressed only in the mature pollen. When expressed in the onion epidermal cells, the OsRLCK1-GFP fusion protein was diffused throughout the cell, indicating its cytoplasmic and nuclear localization. The Maltose Binding Protein-OsRLCK1 recombinant protein was found to be capable of autophosphorylation on threonine residue, showing that it encodes a functional kinase. These results suggest that OsRLCK1 is likely to play a role in a signaling pathway associated with pollen performance during pollination in rice.

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Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice  
Author: Zhen-Lan Liu, Hong Xu Jing-Xin Guo and Yao-Guang Liu
Journal of Integrative Plant Biology 2007 49(6): 908-914
DOI: 10.1111/j.1744-7909.2007.00493.x

The so-called “wild abortive?(WA) type of cytoplasmic male sterility (CMS) derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene(s) remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondrial genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondrial expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nad5 and orf153 genes and the other having the ribosomal protein gene rpl5, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.

Abstract (Browse 3024)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza  
Author: Chuanzhu Fan, Maria D. Vibranovski, Ying Chen and Manyuan Long
Journal of Integrative Plant Biology 2007 49(6): 915-926
DOI: 10.1111/j.1744-7909.2007.00503.x

To systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments.

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Duplication and Divergence of Floral MADS-Box Genes in Grasses: Evidence for the Generation and Modification of Novel Regulators  
Author: Guixia Xu and Hongzhi Kong
Journal of Integrative Plant Biology 2007 49(6): 927-939
DOI: 10.1111/j.1744-7909.2007.00502.x

The process of flowering is controlled by a hierarchy of floral genes that act as flowering time genes, inflorescence/floral meristem identity genes, and/or floral organ-identity genes. The most important and well-characterized floral genes are those that belong to the MADS-box family of transcription factors. Compelling evidence suggests that floral MADS-box genes have experienced a few large-scale duplication events. In particular, the pre-core eudicot duplication events have been considered to correlate with the emergence and diversification of core eudicots. Duplication of floral MADS-box genes has also been documented in monocots, particularly in grasses, although a systematic study is lacking. In the present study, by conducting extensive phylogenetic analyses, we identified pre-Poaceae gene duplication events in each of the AP1, PI, AG, AGL11, AGL2/3/4, and AGL9 gene lineages. Comparative genomic studies further indicated that some of these duplications actually resulted from the genome doubling event that occurred 66-70 million years ago (MYA). In addition, we found that after gene duplication, exonization (of intron sequences) and pseudoexonization (of exon sequences) have contributed to the divergence of duplicate genes in sequence structure and, possibly, gene function.

Abstract (Browse 2329)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide Analysis of Kelch Repeat-containing F-box Family  
Author: Yujin Sun, Xiaofan Zhou and Hong Ma
Journal of Integrative Plant Biology 2007 49(6): 940-952
DOI: 10.1111/j.1744-7909.2007.00498.x

The ubiquitin-dependent protein degradation pathway plays diverse roles in eukaryotes. Previous studies indicate that both F-box and Kelch motifs are common in a variety of organisms. F-box proteins are subunits of E3 ubiquitin ligase complexes called SCFs (SKP1, Cullin1, F-box protein, and Rbx1); they have an N-terminal F-box motif that binds to SKP1 (S-phase kinase associated protein), and often have C-terminal protein-protein interaction domains, which specify the protein substrates for degradation via the ubiquitin pathway. One of the most frequently found protein interaction domains in F-box proteins is the Kelch repeat domain. Although both the F-box and Kelch repeats are ancient motifs, Kelch repeats-containing F-box proteins (KFB) have only been reported for human and Arabidopsis previously. The recent sequencing of the rice genome and other plant genomes provides an opportunity to examine the possible evolution history of KFB. We carried out extensive BLAST searches to identify putative KFBs in selected organisms, and analyzed their relationships phylogenetically. We also carried out the analysis of both gene duplication and gene expression of the KFBs in rice and Arabidopsis. Our study indicates that the origin of KFBs occurs before the divergence of animals and plants, and plant KFBs underwent rapid gene duplications.

Abstract (Browse 2749)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          New Technology
Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System  
Author: Xiaomin Tang, Weidong Bao, Wenli Zhang and Zhukuan Cheng
Journal of Integrative Plant Biology 2007 49(6): 953-960
DOI: 10.1111/j.1744-7909.2007.00508.x

To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAC) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza sativa L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

Abstract (Browse 2059)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       


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