Differential ozone sensitivity of rice cultivars as indicated by visible injury and grain yield

Surface ozone pollution may cause reductions in rice ( Oryza sativa L.) yield. Ozone sensitivity in rice cultivars is often evaluated based on visible leaf injury at an early growth stage. However, it is not clear whether reduction in grain yield is related to visible injury. Therefore, visible damage and grain yield reduction were examined in Japanese and Asian rice cultivars exposed to ozone. In experiment 1, 3-week-old rice seedlings were exposed to ozone (min.: 20 nl·l⁻¹, max.:120 nl·l⁻¹) for 12 h in open-top chambers (OTCs). Visible leaf injury was quantified according to a leaf bronzing score. In experiment 2, rice plants were exposed to ozone in OTCs throughout the cropping season until grain harvest. Daily mean ozone concentrations were maintained at 2, 23, 28, 42, and 57 nl·l⁻¹ with a regular diurnal pattern of exposure. After harvest, grain yield was determined. Based on visible injury to the uppermost fully expanded leaf, the indica cultivar 'Kasalath' was most tolerant, and the japonica cultivar 'Kirara 397' was most sensitive to ozone. However, grain yields for both 'Kasalath' and 'Kirara 397' were significantly decreased after ozone exposure. The indica cultivar 'Jothi' suffered severe injury after ozone exposure but had no reduction in grain yield. Therefore, ozone sensitivity of rice cultivars evaluated by visible injury did not coincide with that evaluated by the reductions in grain yield. These results suggest that mechanisms that induce acute leaf injury do not relate to chronic ozone toxicity that reduces yield.     

Comparative kinetic analysis of ammonium and nitrate acquisition by tropical lowland rice: implications for rice cultivation and yield potential

Nitrogen limitation compromises the realization of yield potential in cereals more than any other single factor. In rice, the world's most important crop species, the assumption has long been that only ammonium-N is efficiently utilized. Consequently, nitrate utilization has been largely ignored, although fragmentary data have suggested that growth could be substantial on nitrate. Using the short-lived radiotracer ¹³N, we here provide direct comparisons of root transmembrane fluxes and cytoplasmic pool sizes for nitrate- and ammonium-N in a major variety of Indica rice ( Oryza sativa ), and show that nitrate acquisition is not only of high capacity and efficiency but is superior to that of ammonium. We believe our results have implications for rice breeding and molecular genetics as well as the design of water-management and fertilization regimes. Potential strategies to harness this hitherto unexplored N-utilization potential are proposed.     

Creation of the whole human genome microarray

Several companies have recently announced the availability of products that enable a scientist to probe gene expression from the entire human genome on a single DNA microarray. This review will focus on the underlying technological trends that have made this achievement possible, the particular methodologies which are employed to create such microarrays and the implications of the whole human genome microarray for future biological studies. The single genome array represents an important milestone on the path to unraveling the complexity of the cellular networks that control living processes. The microarrays being designed today may, however, become distant ancestors to the whole human genome arrays of the future as our understanding of the functioning of the human genome increases.     

水稻SBP基因家族的生物信息学分析(英文)

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SBP)转录因子家族是植物特有的一类转录因子。本文确定了20水稻基因组上编码的SBP基因。通过分类,染色体定位,保守区确定,亲缘关系,以及水稻SBP家族中的重复基因及该家族成员形成蛋白二聚体的可能性进行分析,其次利用了Affymetrix水稻基因组芯片数据,对所有这些基因的表达谱进行了分析。结果表明,水稻SBP基因在花和种子的发育过程中可能发挥重要作用,而其对环境胁迫却不敏感。这对进一步研究SBP的功能提供了有价值的线索和思路。     

Duplication and DNA segmental loss in the rice genome: implications for diploidization

* Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. * Through analysing the 370 Mb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago. * Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30-65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization. * Together with other lines of evidence, we propose that polyploidization is still an ongoing process in grasses of polyploidy origins.     

Comparative analysis of panicle proteomes of two upland rice varieties upon hyper-osmotic stress

Drought is a major environmental factor that limits the yield of rice dramatically. Upland rice is now regarded as a promising rice cultivar in water saving agriculture. Two varieties of upland rice Zhonghan 3 and IR29 were used to compare the physiological and proteomic responses to hyper-osmotic stress induced by 15% polyethyleneglycol (PEG) at the reproductive stage. Osmotic stress affected the growth development and caused the loss of production especially the grain yield. IR29 was more tolerant to PEG than Zhonghan 3 as shown by less yield loss under osmotic stress conditions. Comparative proteomic analysis of the panicle suggested that the up-regulation of glycolysis related proteins and defense proteins may contribute to the better osmotic tolerance in IR29.     

缺铁水稻根转录本微点阵分析

水稻不仅是非常重要的粮食作物 ,也是用于研究的模式植物之一 .由于水稻基因组测序的完成 ,用功能基因组学的现代方法来研究缺铁相关基因的表达调控是最高效的方法之一。在前期工作的基础上 ,精心设计了缺铁和EDTA鳌合二价铁诱导5天的水稻根实验 ,并进行了转录水平的微点阵 (microarray)分析。但只获得了第 5天的结果。在 10 5 31个水稻cDNA芯片图谱中 ,缺铁和加铁比较发现了 4 5 1个差异点。对缺铁诱导的 4 5 1个差异cDNA逐一地进行NCBI (美国国家生物技术信息中心 )的BLAST(局部定位排列搜索工具 )数据库检索、分析和归类。发现其中缺铁与加铁 ( -Fe/Fe -EDTAratio)之间的相对表达水平(REL)在 2 - 9.175之间的缺铁诱导上调基因为 2 0 3个 ,缺铁诱导的下调基因为 2 4 8个。对每一类上调基因都逐一地进行了NCBI-PubMed的文献检索。利用国际网络数据库进行了功能鉴定。     

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.     

A test of the efficacy of whole‐genome amplification on DNA obtained from low‐yield samples

Conservation and population genetic studies are sometimes hampered by insufficient quantities of high quality DNA. One potential way to overcome this problem is through the use of whole genome amplification (WGA) kits. We performed rolling circle WGA on DNA obtained from matched hair and tissue samples of North American red squirrels (Tamiasciurus hudsonicus). Following polymerase chain reaction (PCR) at four microsatellite loci, we compared genotyping success for DNA from different source tissues, both pre‐ and post‐WGA. Genotypes obtained with tissue were robust, whether or not DNA had been subjected to WGA. DNA extracted from hair produced results that were largely concordant with matched tissue samples, although amplification success was reduced and some allelic dropout was observed. WGA of hair samples resulted in a low genotyping success rate and an unacceptably high rate of allelic dropout and genotyping error. The problem was not rectified by conducting PCR of WGA hair samples in triplicate. Therefore, we conclude that WGA is only an effective method of enhancing template DNA quantity when the initial sample is from high‐yield material.     

A comparison of nitrate transport in four different rice(Oryza sativa L.) cultivars

As rice can use both nitrate (NO3-) and ammonium (NH4+), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO3- as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO3- and NH4+ nitrogen sources. All four types of rice,Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH4+ as the only N source.However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO3-, YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO3--elicited changes in membrane potential (ΔEm) of these four rice cultivars were significantly different when exposed to low external NO3- (＜1 mmol/L); while they were very similar at high external NO3- (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO3- than those of NK and SY917. The ΔEm values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO3-;while for the NK and SY917 the values became larger as the external NO3- increased. For YD cultivar, ΔEm was measured over a range of NO3- concentrations and a Michaelis-Menten fit to the data gave a Km value of 0.17 mmol/L. Net NO3- uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar Km in all the cultivars (0.2 mmol/L); the other much higher affinity system (0.03 mmol/L) was only present in NK and SY917. The expression pattern of twelve different NO3- transporter genes was tested using specific primers, but only OsNRT1.1 and OsNRT2. 1 expression could be detected showing significant differences between the four rice cultivars. The results from both the physiological and molecular experiments do provide some support for the hypothesis that the more popular rice cultivars grown in Jiangsu Province may be better at using NO3- as an N source.     

A comparison of nitrate transport in four different rice(Oryza sativa L.) cultivars

As rice can use both nitrate (NO3-) and ammonium (NH4+), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO3- as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO3- and NH4+ nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH4+ as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO3- YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO3- elicited changes in membrane potential (△Em) of these four rice cultivars were significantly different when exposed to low external NO3- (<1 mmol/L); while they were very similar at high external NO3- (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO3- than those of NK and SY917. The△Em values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO3-; while for the NK and SY917 the values became larger as the external NO3- increased. For YD cultivar,△Em was measured over a range of NO3- concentrations and a Michaelis-Menten fit to the data gave a Km value of 0.17 mmol/L. Net NO3- uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar Km in all the cultivars (0.2 mmol/L); the other much higher affinity system (0.03 mmol/L) was only present in NK and SY917. The expression pattern of twelve different NO3- transporter genes was tested using specific primers, but only OsNRT1.1 and OsNRT2.1 expression could be detected showing significant differences between the four rice cultivars. The results from both the physiological and molecular experiments do provide some support for the hypothesis that the more popular rice cultivars grown in Jiangsu Province may be better at using NO3- as an N source.     

Comparative study on the chloroplast,mitochondrial and nuclear genome differentiation in two cultivated rice species,Oryza sativa and O. glaberrima,by RFLP analyses

Summary Restriction fragment length polymorphisms of chloroplast (ct), mitochondrial (mt) and nuclear DNA were investigated using eight cultivars of Oryza sativa and two cultivars of O. glaberrima. Relative variability in the nuclear and cytoplasmic genomes was estimated by a common measure, genetic distance. Based on the average genetic distances among ten cultivars for each genome, the evolutionary variabilities of the mitochondrial and nuclear genomes were found to be almost the same, whereas the variability of the chloroplast genome was less than half that of the other two genomes. Cluster analyses on ct and mt DNA variations revealed that chloroplast and mitochondrial genomes were conservative within a taxon and that their differentiations were well-paralleled with respect to each other. For nuclear DNA variation, an array of different degrees of differentiation was observed in O. sativa, in contrast with little variation in O. glaberrima. As a whole, differentiation between O. sativa and O. glaberrima was clearly observed in all three genomes. In O. sativa, no notable difference was found between the cultivars Japonica and Javanica, whereas a large differentiation was noticed between Japonica (including Javanica) and Indica. In all three genomes, the average genetic distances within Indica were much larger than those within Japonica (including Javanica), and almost similar between Japonica (including Javanica) and Indica. These facts indicate that differentiation in O. sativa was due mainly to Indica.     

Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (> 10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.     

A method for screening copper-tolerant rice (Oryza sativa L.) cultivars based on hydroponic experiments and cluster analysis

A method for screening copper (Cu)-tolerant rice cultivars was studied by combining hydroponic experiments and cluster analysis, and the classification of cultivars in Cu stress tolerance was done. In the first hydroponic experiment, seedlings of Jiahe991 and Xiushui114 were planted in nutrient solution with different Cu²⁺ concentrations from 10 to 1800 μg/L. Results indicated that the toxic threshold of Cu concentration in solution ranged from 900 to 1200 μg/L, since SPAD (Soil and Plant Analyzer Development, SPAD-502, a portable chlorophyll meter, Minolta Camera Co. Ltd., Japan) values of leaves and seedlings biomass of the treatments with ≥900 and/or 1200 µg/L were significantly lower than the control. The second experiment was conducted with 16 local rice cultivars under three Cu treatments (10, 1000, and 1500 μg/L). The 16 cultivars were well classified into tolerant, normal, and sensitive groups as a result of cluster analysis based on the relative SPAD (Soil and Plant Analyzer Development, SPAD-502, a portable chlorophyll meter, Minolta Camera Co. Ltd., Japan) value, shoot and root dry weights, root length and root dehydrogenase activity, and oxidizing capacity and shoot Cu concentration. Xiushui123, Xiushui134, Jiahe991, and Xianghu301 belonged to the tolerant group; Xiushui137 belonged to the sensitive group. The cluster analysis based on hydroponic experiments is an effective method for identifying rice cultivars that are tolerant to Cu stress. In addition, four cultivars (Xiushui123, Xiushui134, Jiahe991, and Xianghu301) are recommended in local practice.     

Accessing genes in the tertiary gene pool of rice by direct introduction of total DNA fromZizania palustris (wild rice)

Transfer of useful genes from wild relatives of crop plants has relied upon successful conventional crossing or the availability of the cloned gene. Co-bombardment of rice callus with total genomic DNA from wild rice (Zizania palustris) and a plasmid containing a gene confirming hygromycin resistance allowed recovery under selection of transgenic plants with grain characteristics from wild rice. Amplified Fragment Length Polymorphism (AFLP) analysis suggested that a significant amount of DNA fromZizania was introduced by this procedure. One plant had 16 of a possible 122Zizania specific AFLP markers detected with the primers used. This approach may have potential for introgression of genes from wild relatives in other cases where highly efficient transformation methods are available.     

Use of non-radioactive digoxigenin-labeled DNA probes for RFLP analysis in rice

A simple procedure for the detection of rice RFLPs with non-radioactive probes is described. Rice single-copy DNA was labeled with non-radioactive digoxigenin-d UTP. When digested total DNA was hybridized with the non-radioactive labeled DNA probes, RFLPs for rice single-copy DNA could be successfully detected.