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Genomic and genic sequence variation in synthetic hexaploid wheat (AABBDD) as compared to their parental species

Progress in Natural Science:Materials International 2008年第5期18卷 533-538页

作者： Lihong Nie, Zongfu Han, Lahu Lu, Yingyin Yao, Qixin Sun, Zhongfu Ni key laboratory of Crop Heterosis and Utilization (MOE) and state key laboratory for Agrobiotechnology, key laboratory of Crop Genomics and genetic Improvement (MOA), Beijing key laboratory of Crop genetic Improvement, Department of Plant genetics & Breeding, China Agricultural University, Beijing 100094, China key laboratory of Crop Heterosis and Utilization (MOE) and state key laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement (MOA) Beijing Key Laboratory of Crop Genetic Improvement Department of Plant Genetics & Breeding China Agricultural University Beijing 100094 China

In order to understand the genomic changes during the evolution of hexaploid wheat, two sets of synthetic hexaploid wheat from hybridization between maternal tetraploid wheat (AABB) and paternal diploid goat grass (DD) were used for DNA-AFLP and single strand conformation polymorphism (SSCP) analysis to determine the genomic and genic variation in the synthetic hexaploid wheat. Results indicated that more DNA sequences from paternal diploid species were eliminated in the synthetic hexaploid wheat than from maternal tetraploid wheat, suggesting that genome from parental species of lower ploidity tends to be eliminated preferentially. However, sequence variation detected by SSCP procedure was much lower than those detected by DNA-AFLP, which indicated that much less variation in the genic regions occurred in the synthetic hexaploid wheat, and sequence variations detected by DNA-AFLP could be derived mostly from non-coding regions and repetitive sequences. Our results also indicated that sequence variation in 4 genes can be detected in hybrid F1, which suggested that this type of sequence variation could be resulted from distant hybridization. It was interesting to note that 3 out of the 4 genes were mapped and clustered on the long arm of chromosome 2D, which indicated that variation in genic sequences in synthetic hexaploid wheat might not be a randomized process.

关键词： Synthetic hexaploid wheat Polyploidy Genome Sequence variation

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Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)

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Progress in Natural Science:Materials International 2007年第10期17卷 1177-1184页

作者： Li Zhenxing, Ni Zhongfu, Peng Huiru, Liu Zhiyong, Nie Xiuling, Xu Shengbao, Liu Gang and Sun Qixin(key laboratory of Crop Heterosis and Utilization and state key laboratory for Agrobiotechnology, key laboratory of Crop Genomics and genetic Improvement, Beijing key laboratory of Crop genetic Improvement, Department of Plant genetics & Breeding, China Agricultural University, Beijing 100094, China) key laboratory of Crop Heterosis and Utilization Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China key laboratory of Crop Genomics and genetic Improvement Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China Beijing key laboratory of Crop genetic Improvement Department of Plant Genetics and Breeding China Agricultural University Beijing 100094 China

Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together.

关键词： QTLs roots wheat seedling RIL P-deficiency.

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Cloning and expression profiles of 15 genes encoding WRKY transcription factor in wheat (Triticum aestivem L.)

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Progress in Natural Science:Materials International 2008年第6期18卷 697-705页

作者： Hualing Wu,Zhongfu Ni,Yingyin Yao,Ganggang Guo,Qixin Sun* Department of Plant genetics&Breeding and state key laboratory for Agrobiotechnology,key laboratory of Crop Heterosis and Utilization,Ministry of Education,key laboratory of Crop Genomics and genetic Improvement,Ministry of Agriculture/Beijing key laboratory of Crop genetic Improvement,China Agricultural University,Beijing 100094,China Department of Plant genetics & Breeding and state key laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilization Ministry of Education Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

WRKY proteins are involved in various physiological processes,including biotic and abiotic stress responses,hormone responses and ***,no systematic identification,expression and function analysis of WRKY genes in wheat were *** this study,we isolated 15 wheat cDNAs with complete open reading frame(ORF)encoding putative WRKY proteins using in silico *** analysis indicated that the 15 wheat WRKY genes belonged to three major WRKY *** analysis revealed that most genes expressed drastically in leaf,except TaWRKY10 which expressed in crown *** genes were strongly up-reg-ulated with the senescence of *** genes were responsive to low temperature,high temperature,NaCl or PEG ***-over,dierential expression patterns were also observed between wheat hybrid and its parents,and some genes were more responsive to PEG treatment in the *** results demonstrated that wheat WRKY genes are involved in leaf senescing and abiotic *** the changed expression of these WRKY genes in hybrid might contribute to the heterosis by improving the stress tolerance in hybrids.

关键词： Wheat WRKY transcription factor Gene cloning Gene expression Heterosis

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Sequencing,annotation and comparative analysis of nine BACs of the giant panda(Ailuropoda melanoleuca)

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Science China(Life Sciences) 2010年第1期53卷 107-111页

作者： ZHENG Yang1,2,3,CAI Jing4,LI JianWen3,6,LI Bo3,LIN RunMao3,TIAN Feng3,WANG XiaoLing3 & WANG Jun3,5 1Beijing Institute of Genomics,Chinese Academy of Sciences(CAS),Beijing 100029,China 2College of Life Science,Graduate University of Chinese Academy of Sciences,Beijing 100049,China 3Beijing Genomics Institute at Shenzhen,Shenzhen 518083,China 4CAS-Max Planck Junior Research Group on Evolutionary Genomics,state key laboratory of genetic resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences(CAS),Kunming 650223,China 5Department of Biology,University of Copenhagen,Copenhagen DK-2200,Denmark 6School of Biological Science and Engineering,South China University of Technology,Guangzhou 510006,China Beijing Institute of Genomics Chinese Academy of Sciences (CAS) Beijing China College of Life Science Graduate University of Chinese Academy of Sciences Beijing China Beijing Genomics Institute at Shenzhen Shenzhen China CAS-Max Planck Junior Research Group on Evolutionary Genomics State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences (CAS) Kunming China School of Biological Science and Engineering South China University of Technology Guangzhou China Department of Biology University of Copenhagen Copenhagen Denmark

A 10-fold BAC library for the giant panda was constructed and nine BACs were selected to generate finish *** BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of the giant panda newly generated by Illumina GA sequencing *** Sanger sequencing,assembly,annotation and comparative analysis were carried out on the selected BACs of a joint length 878 *** search and de novo prediction methods were used to annotate genes and *** protein coding genes were predicted,seven of which could be functionally *** seven genes have an average gene size of about 41 kb,an average coding size of about 1.2 kb and an average exon number of 6 per ***,seven tRNA genes were *** 27 percent of the BAC sequence is composed of repeats.A phylogenetic tree was constructed using a neighbor-join algorithm across five species,including the giant panda,human,dog,cat and mouse,which reconfirms dog as the most closely related species to the giant *** results provide detailed sequence and structure information for new genes and repeats of the giant panda,which will be helpful for further studies about the giant panda.

关键词： giant panda BAC sequencing assembly annotation evolution

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Effect of leachate inoculum on biopretreatment of municipal solid waste by a combined hydrolytic-aerobic process

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Journal of Environmental Sciences 2009年第8期21卷 1162-1168页

作者： ZHANG Dongqing, HE Pinjing, SHAO Liming state key laboratory of Pollution Control and resources Reuse, key laboratory of Yangtze River Water Environment, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China. state key laboratory of Pollution Control and resources Reuse Key Laboratory of Yangtze River Water Environment College of Environmental Science and Engineering Tongji University Shanghai 200092 China

The biopretreatment of municipal solid waste by a combined hydrolytic-aerobic process has become of great interest for biostabilization or biodrying. The study aimed at investigating the effect of leachate inoculurn on the biopretreatment. During the hydrolytic stage, the inoculum addition at the ratio of leachate to waste （LWR） of 5% and 7% stimulated the start-up of hydrolysis and enhanced the hydrolysis rate by 27.4% and 24.2%, respectively; whereas the inoculation at LWR of 1% had almost no effect on the hydrolysis rate and the inoculation at LWR of 10% reduced the hydrolysis rate by 12.7%. During the subsequent aerobic stage, the inoculations at LWRs greater than 5% decreased organics degradation rate. As a whole, compared with none inoculation, the total degradation rates of organics for inoculating trials at LWRs of 5%, 7% and 10% decreased by 14.5%, 14.3% and 32.7%, respectively. Correspondingly, their net water removal rates were reduced by 4.4%, 5.8% and 19.0%. The inoculation at LWR of 1% could not significantly affect the biopretreatment. The inoculum addition at LWR of 5% and 7% could shorten hydrolytic stage and thus accelerate the whole combined process. Moreover, the inoculations at LWRs greater than 5% were favorable for lignocelluloses degradation.

关键词： biopretreatment hydrolysis-aeration inoculation leachate municipal solid waste

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Effect of proteins,polysaccharides,and particle sizes on sludge dewaterability

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Journal of Environmental Sciences 2009年第1期21卷 83-88页

作者： SHAO Liming,HE Peipei,YU Guanghui,HE Pinjing state key laboratory of Pollution Control and resources Reuse,key laboratory of Yangtze River Water Environment,College of Environmental Science and Engineering,Tongji University,Shanghai 200092,China state key laboratory of Pollution Control and resources Reuse Key Laboratory of Yangtze River Water Environment College of Environmental Science and Engineering Tongji University Shanghai 200092 China. E-mail: solidwaste@***

Four batch experiments of hydrolysis and acidification were carried out to investigate the distributions of proteins （PN） and polysaccharides （PS） in the sludge, the PN/PS ratio, the particle sizes, and their relationship with sludge dewaterability （as determined by capillary suction time, CST）. The sludge flocs were stratified through centrifugation- and ultrasound-based method into four fractions：（1） slime, （2） loosely bound extracellular polymeric substances （LB-EPS）, （3） tightly bound EPS （TB-EPS）, and （4） pellet. The results showed that PN was mainly partitioned in the pellet （80.7%） and TB-EPS （9.6%） fractions, while PS distributed evenly in the four fractions. During hydrolysis and acidification, PN was transferred from the pellet and TB-EPS fractions to the slime fraction, but PS had no significant transfer trends. The mean particle sizes of the sludge flocs decreased with hydrolysis and acidification. The pH had a more significant influence on the dewaterability of sludge flocs than temperature. Sludge dewaterability during hydrolysis and acidification processes greatly deteriorated from 9.7 s at raw sludge to 340-450 s under alkaline conditions. However, it was just slightly increased under acidic conditions. Further investigation suggested that CST was affected by soluble PN, soluble PN/PS, and particle sizes of sludge flocs, but was affected slightly by total PN, PS, or PN/PS in the whole sludge flocs and other fractions （except slime）.

关键词： dewaterability extracellular polymeric substances particle size polysaccharides proteins sewage sludge

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PII,the key regulator of nitrogen metabolism in the cyanobacteria

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Science China(Life Sciences) 2008年第12期51卷 1056-1065页

作者： ZHANG Ying & ZHAO JinDong state key laboratory of Protein and Plant genetic Engineering, College of Life Science, Peking University, Beijing 100871, China state key laboratory of Protein and Plant genetic Engineering College of Life Science Peking University Beijing China

PII proteins are a protein family important to signal transduction in bacteria and plants. PII plays a critical role in regulation of carbon and nitrogen metabolism in cyanobacteria. Through conformation change and covalent modification, which are regulated by 2-oxoglutarate, PII interacts with different target proteins in response to changes of cellular energy status and carbon and nitrogen sources in cyanobacteria and regulates cellular metabolism. This article reports recent progress in PII research in cyanobacteria and discusses the mechanism of PII regulation of cellular metabolism .

关键词： carbon metabolism cyanobacteria nitrogen metabolism PII protein

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Thermal stabilization of chromium slag by sewage sludge: Effects of sludge quantity and temperature

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Journal of Environmental Sciences 2010年第7期22卷 1110-1115页

作者： Changlin Wu,Hua Zhang,Pinjing He,Liming Shao state key laboratory of Pollution Control and resources Reuse,key laboratory of Yangtze River Water Environment,College of Environmental Science & Engineering,Tongji University,Shanghai 200092,China. state key laboratory of Pollution Control and resources Reuse Key Laboratory of Yangtze River Water Environment College of Environmental Science & Engineering Tongji University Shanghai 200092 China. E-mail: solidwaste@***

To investigate the feasibility of detoxifying chromium slag by sewage sludge, synthetic chromium slag containing 3% of Cr（Ⅵ） was mixed with sewage sludge followed by thermal treatment in nitrogen gas for stabilizing chromium. The effects of slag to sludge ratio （0.5, 1 and 2） and temperature （200, 300, 500, 700 and 900℃） on treatment efficiency were investigated. During the mixing process before thermal treatment, 59.8%-99.7% of Cr（Ⅵ） was reduced, but Cr could be easily leached from the reduction product. Increasing heating temperature and decreasing slag to sludge ratio strengthened the reduction and stabilization of Cr（Ⅵ）. When the slag to sludge ratio was 0.5 and thermal treatment temperature was 300℃, the total leached Cr and Cr（Ⅵ） declined to 0.55 mg/L and 0.17 mg/L respectively, and 45.5% of Cr in the thermally treated residue existed as residual fraction. A two-stage mechanism was proposed for the reduction and stabilization of Cr.

关键词： chromium slag sewage sludge reduction detoxification thermal treatment leached concentration

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Multistage evolution of continental collision orogen:A case study for western Dabie orogen

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Chinese Science Bulletin 2009年第15期54卷 2568-2579页

作者： WU YuanBao state key laboratory of Geological Processes and Mineral resources, Faculty of Earth Sciences, China University of Geosciences, Wuhan 430074, China state key laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an 710069, China state key laboratory of Geological Processes and Mineral resources Faculty of Earth Sciences China University of Geosciences Wuhan China state key laboratory of Continental Dynamics Department of Geology Northwest University Xi’an China

The foramtion and evolution of collisional orogen is a prominent feature along convergent plate margins, and is generally a complex process. This article presents an integrated study of zircon genesis, U-Pb age and Lu-Hf isotope composition as well as geological characteristics for the western Dabie orogen to constrain its multi-stage evolution history. The results suggest that the formation of oceanic crust in the Huwan area was constrained at ca. 400―430 Ma, which was slightly later than the collision of the northern Qinling with the North China Block. It formed in a marginal basin in the northern margin of the Yangtze Block. The peak metamorphism of eclogite in the Huwan area occurred at ca. 310 Ma, and the timing of the initial exhumation of oceanic eclogite was about 270 Ma. The high to ultrahigh pressure (HP-UHP) metamorphic rocks in the Xinxian and the Hong'an metamorphic zones have the same ages and natures as those of the HP-UHP metamorphic rocks in the other Dabie-Sulu terrains, and also have experienced multi-stage exhumation, and thus can be taken as a coherent part of the Dabie-Sulu orogen. Therefore, the Qinling-Dabie-Sulu orogen is a typical multi-stage continental collision orogen, with an amalgamation process extending more than 200 Ma.

关键词：大别造山带大陆碰撞西部演变超高压变质岩碰撞造山带苏鲁造山带变质岩区

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A prototype auto-human support system for spatial analysis

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Progress in Natural Science:Materials International 2006年第9期16卷 954-966页

作者： LI Lianfa and WANG Jinfeng (state key laboratory of resources & Environmental Information System, Institute of Geographical Sciences & Natural resources Research, Chinese Academy of Sciences, Beijing 100101, China) state key laboratory of resources and Environmental Information System Institute of Geographical Sciences and Natural Resources Re-search Chinese Academy of Sciences Beijing 100101 China

Spatial analysis is a multidisciplinary field that involves multiple influential factors, variation and uncertainty, and modeling of geospatial data is a complex procedure affected by spatial context, mechanism and assumptions. In order to make spatial modeling easier, some scholars have suggested a lot of knowledge from exploratory data analysis (EDA), specification of the model, fitness and diagnosis of the model, to interpretation of the model. Also an amount of software has improved some functionalities of spatial analysis, e. g. EDA by the dynamic link (GeoDa) and robust statistical calculation (R). However, there are few programs for spatial analysis that can automatically deal with unstructured declarative issues and uncertainty in machine modeling using the domain knowledge. Under this context, this paper suggests a prototype support system for spatial analysis that can automatically use experience and knowledge from the experts to deal with complexity and uncertainty in modeling. The knowledge base component, as the major contribution of the system, in support of the expert system shell, codes and stores declarative modeling knowledge, e.g. spatial context, mechanisms and prior knowledge to deal with declarative issues during the modeling procedure. With the open architecture, the system integrates functionalities of other components, e.g. GIS’ visualization, DBMS, and robust calculation in an interactive environment. An application case of spatial sampling, design and implementation of spatial modeling with such a system is demonstrated.

关键词： spatial analysis automatic support system modeling of spatial data artificial inference for modeling.

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