Global and Comparative Proteome Analysis of Nitrogen-Stress Responsive Proteins in the Root, Stem and Leaf of Brassica napus

Nitrogen(N)is one of the basic nutrients and signals for plant development and deficiency of it would always limit the productions of crops in the field.Quantitative research on expression of N-stress responsive proteins on a proteome level remains elusive.In order to gain a deep insight into the proteins responding to nitrogen stress in rapeseed(Brassica napus L.),comparative proteomic analysis was performed to investigate changes of protein expression profiles from the root,stem and leaf under different N concentrations,respectively.More than 200 differential abundance proteins(DAPs)were detected and categorized into groups according to annotations,including“binding and catalytic activity”,“involved in primary metabolism and cellular processes”,“stress-response”and so on.Variation in chlorophyll(Chl)content and antioxidant activities further revealed that oxidative stress raised with the increase of N concentration.Bioinformatics analysis based on the expression level of total proteins suggested these DAPs might play important roles in adaptation to N-stress conditions.Generally,these results provides a new aspect into N-stress responding proteins in Brassica plants.

Genome-Wide Association Study for Milled Grain Appearance Traits Using Multi-Parent Advanced Generation Intercross Population in Rice

The identification of loci and markers associated with milled grain appearance traits is essential for breeding high-yielding and good-quality rice variety.To detect stable loci for these characteristics,grain length(GL),grain width(GW),grain length/width(GLW),chalkiness degree(CD),chalky-grain rate(CR)and translucency degree(TD)of 378 rice lines were evaluated in three seasons.These lines were derived from a multi-parent advanced generation intercross(MAGIC)population.

Effect of temperature on the development of sclerotia in Villosiclava virens

The sclerotia of Villosiclava virens were found commonly in high altitude and the temperate regions, where the temperatures are relatively low in rice filling stage. To make sure if low temperature induce the sclerotial formation in V. virens, the inoculated rice panicles in laboratory and the diseased rice panicles cut from paddy fields were treated under different temperatures. The results showed that 3 days of night temperature at 15°C were enough to induce the sclerotial formation. The low temperature was much more effective for young balls with intact membranes. After appearance of chlamydospores on the ball surfaces, the sclerotium could not differentiate anymore. The sclerotia began to differentiate below the chlamydospore layer and gradually grew onto the ball surfaces. This suggests that low temperature in the early development stage of false smut balls is an important factor to induce the sclerotial differentiation, and rice cultivars with long growth periods are able to produce more sclerotium-bearing balls, which will produce mass of spores in paddy field in the coming year.

Fine mapping and marker-assisted selection (MAS) of a low glutelin content gene in rice

Rice with low glutelin content is suitable as functional food for patients affected with diabetes and kidney failure. The fine mapping of the gene(s) responsible for low glutelin content will provide information regarding the distribution of glutelin related genes in rice genome and will generate markers for the selection of low glutelin rice varieties. Following an SDS-PAGE screen of rice germplasm from Taihu Valley of China, Japonica selection W3660 is identified to be a novel mutant characterized with low glutelin content. For fine mapping the mutant gene for low glutelin content, F2 and F3 populations were derived from a cross between W3660 and Jingrennuo. SDS-PAGE analysis of the total endosperm protein showed that the low glutelin content trait was controlled by a single dominant nuclear gene. Genetic mapping, using SSRs, located this gene to chromosome 2, in the region between SSR2-001/SSR2-004 and RM1358. The dis- tances of the two markers to the target gene were 1.1 cM and 3.8 cM respectively. By semi-quantitative RT-PCR analysis, the transcripts of GluB4/GluB5 genes located within the region do not change. However, GluB5 gene located proximal to SSR2-001/SSR2-004 was specifically reduced. SSR profiles of seven Japonica varieties were compared with that of W3660 for loci in the relevant genetic region. The markers SSR2-004 and RM1358 were used for marker- assisted selection. The selection efficiencies of SSR2-004 and RM1358 were 96.8% and 92.7% respectively. This provides a standard starting point for the breeding of low glutelin content rice varieties in China.

Metal Contamination in Nullah Dek Water and Accumulation in Rice

A research study was carried out to determine the electrical conductivity (EC), residual sodium carbonate (RSC), sodium adsorption ratio (SAR), pH and metals in metal-polluted irrigation water from a nullah and those in soils over a period of time, and the effect of metals on rice yield and metal concentrations in rice grain and straw. Two sites (I and II) were selected on the bank of Nullah Dek at Thatta Wasiran in Sheikhupura District (Pakistan), with two rice varieties, Super Basmati and Basmati 385, at both sites. Water samples were collected during rice crop growth at 15-day intervals from August 3 to November 1, 2002. The results showed that Nullah Dek water had an EC >1.0 dS m-1 and RSC of 2.78-4.11 mmolc L-1, which was hazardous for crops, but the SAR was within the safe limit. Cu, Mn Cd and Sr were also within safe limits. The soil analysis showed that Site II was free from salinity/sodicity, whereas Site I was saline sodic. Among metals, Zn was sometimes deficient, Cu, Mn and Fe were adequate, and Sr, Ni and Cd were within safe limits in the soil at both the sites. After the rice crop harvest, concentrations of all metals tested were usually slightly increased, being higher in the upper soil layer than the lower. In addition, Basmati 385 produced higher rice grain and straw yield than Super Basmati. Chemical analysis of rice grain indicated the presence of Zn, Cu, Fe, Mn, Pb and Sr, whereas rice straw contained Zn, Cu, Fe, Mn and Sr, with Cd and Ni both being found in minute quantities.

A Genetic Linkage Map of Kenaf (Hibiscus cannabinus L.) Based on SRAP, ISSR and RAPD Markers

Kenaf （Hibiscus cannabinus L.） is one of the most economically important crops for non-wood fiber production. The objective of this study was to establish a genetic linkage map of kenaf with higher density of molecular markers. A semi- wild variety Ga42 and a cultivar Alain kenaf were used as parents to construct an F2 population consisting of 155 plants. The genetic linkage map comprising 134 marker loci was constructed, including 65 sequence-related amplified polymorphism （SRAP）, 56 inter-simple sequence repeat （ISSR）, and 13 randomly amplified polymorphic DNA （RAPD） markers. This map spans 2 108.9 cM and contains 20 linkage groups with an average marker density of 15.7 cM between the adjacent markers.

Optimization of Agrobacterium tumefaciens-Mediated Immature Embryo Transformation System and Transformation of Glyphosate-Resistant Gene 2mG2-EPSPS in Maize(Zea mays L.)

Since maize is one of the most important cereal crops in the world,establishment of an efficient genetic transformation system is critical for its improvement.In the current study,several elite corn lines were tested for suitability of Agrobacterium tumefaciens-mediated transformation by using immature embryos as explants.Infection ability and efficiency of transformation of A.tumefaciens sp.strains EHA105 and LBA4404,different heat treatment times of immature embryos before infection,influence of L-cysteine addition in co-cultivation medium after transformation,and how different ways of selection and cultivation influence the efficiency of transformation were compared.Glyphosate-resistant gene 2mG2-EPSPS was transformed into several typical maize genotypes including 78599,Zong 31 and BA,under the optimum conditions.Results showed that the hypervirulent Agrobacterium tumefaciens sp.strain EHA105 was more infectious than LBA4404.Inclusion of L-cysteine（100 mg L-1） in co-cultivation medium,and heating of the immature embryos for 3 min prior to infection led to a significant increase in the transformation efficiency.Growth in resting medium for 4-10 d and delaying selection was beneficial to the survival of resistant calli.During induction of germination,adding a high concentration of 6-BA（5 mg L-1） and a low concentration of 2,4-D（0.2 mg L-1） to regeneration medium significantly enhanced germination percentage.Using the optimized transformation procedure,more than 800 transgenic plants were obtained from 78599,Zong 31 and BA.By spraying herbicide glyphosate on leaves of transgenic lines,we identified 66 primary glyphosate-resistant plants.The transformation efficiency was 8.2%.PCR and Southern-blot analyses confirmed the integration of the transgenes in the maize genome.

Identification of Wheat Canopy Structure Using Hyperspectral Data

Some winter wheat varieties were selected in this experiment. The results were as follows： 1） Leaf orientation value （LOV） and leaf area index （LAI） of wheat had different contributions to canopy spectral reflectance （CSR）. For example, LOV affected greatly canopy spectra more than LAI did in jointing stage, but LAI had a greater effect on CSR than LOV did after the ground was near to be covered completely. 2） Twenty treatments including different varieties and densities were arranged in this experiment, and the result of cluster analysis showed that all these treatments can be parted into four clusters according to LAI and LOV： varieties with erect leaves and low LAI （denoted as A）, varieties with erect leaves and high LAI （denoted as B）, varieties with horizontal leaves and low LAI （denoted as C）, varieties with horizontal leaves and high LAI （denoted as D）. Their CSR had difference in 400-700 nm and 700-1 150 nm at jointing stage, especially in different plant types. 3） There was obvious distribution difference among different clusters in scatter plot （X=△R890, Y=R890）, △R890 was the reflectance increment from jointing to booting stage. It was seen from the Y-axis direction that R890 of horizontal varieties were higher than the erect ones, and seen from the X-axis direction that the greater △R890 was, the lower LAI one within the same plant type varieties, which indicted that the combination of plant-type and the population magnitude can be initially identified by this method.

Toward Development of a Whole-genome, BAC/BIBAC-based Integrated Physical/Genetic Map of the Cotton Genome Using the Upland Genetic Standard TM-1: BAG and BIBAC Library Construction, SSR Marker Development, and Physical/Genetic Map Integration

Integrative physical mapping is the centerpieceof and essential for advanced genomics research.Upland cotton(Gossypium hirsutum L.)geneticstandard line TM-1 is used as the referencegenotype to develop a whole-genome,BAC/BIBAC-based integrated physical/genetic map ofthe cotton genome.From the TM-1 line we haveconstructed two BAC libraries with HindIII

Small-Scale Duplications Play a Significant Role in Rice Genome Evolution

Genes are continually being created by the processes of genome duplication （ohnolog） and gene duplication （paralog）. Whole-genome duplications have been found to be widespread in plant species and play an important role in plant evolution. Clearly un-overlapping duplicated blocks of whole-genome duplications can be detected in the genome of sequenced rice （Oryza sativa）. Syntenic ohnolog pairs （ohnologues） of the whole-genome duplications in rice were identified based on their syntenic duplicate lines. The paralogs of ohnologues were further scanned using multi-round reciprocal BLAST best-hit searching （E〈e^-14）. The results indicated that an average of 0.55 sister paralogs could be found for every ohnologue in rice. These results suggest that small-scale duplications, as well as whole-genome duplications, play a significant role in the two duplicated rice genomes.

Cytogenetics and the Utilization of Gossypium Germplasm

Interspecific introgression contributessignificantly to genetic improvement of cotton(Gossypium hirsutum L.).Cytogenetics hasfigured prominently in the creation ofinterspecific hybrids,synthetic polyploids,backcrosses,and other stocks essential to early-and mid-stage manipulation of germplasm

Toward Development of a Whole-genome, BAC/BIBAC-based IntegratedPhysical/Genetic Map of the Cotton Genome Using the Upland Cotton Genetic Standard TM-1: BAC Fingerprinting and Physical Map Contig Construction

We are developing a whole-genome,BAC/BIBAC-based integrated physical/genetic map ofthe cotton(Gossypium hirsutum L.)genomeusing its genetic standard line TM-1 as thereference genotype.Whole-genome physicalmaps integrated with genetic maps will providerevolutionized tools and platforms for all kindsof genomics researeh,including large-scale

Adaptability and Stability Analysis of Soybean Genotypes Using Toler and Centroid Methods

Soybean (Glycine max L. Merr.) adaptation to new environments has been hard to predict based on maturity group. The aim of this study was to evaluate the performance of 14 soybean genotypes, from the Soybean Breeding Program of the Federal University of Uberlandia, in their adaptive capacity and seed yield stability at 3 locations and 2 growing seasons. For the adaptability and stability analysis the Toler and Centroid methods were used;5 genotypic groups were identified in the first whereas 4 groups were identified in the latter. By the Toler method group A was composed by 4 genotypes, UFU-001, UFU-003, UFU-0010, and UFU-001. They showed a convex pattern of adaptability and stability. In contrast, the genotypes UFU-008 and UFU-0013 were classified in Group E with a concave pattern of adaptability and stability. Regarding results from the Centroid method, the Genotype UFU-002, with higher seed yield than average, was the only genotype in Ideotype VI with moderate adaptability to favorable environments. In contrast, 10 genotypes were included in the Ideotype V, of medium general adaptability. The genotypes UFU-001, UFU-002, UFU-006, UFU-0010, and UFU-0011 were recommended for use in the Brazilian Cerrado growing region. These genotypes had high seed yield potential in high quality environments.

Termites Improve the Horizontal Movement of Carbonized Particles:A Step towards Sustainable Utilization of Biochar

Soil amendments containing carbonized materials increase the soil carbon reservoir,influence plant productivity,and,ultimately,help to clean the environment.There is data on the effect of such additions on soil physicochemical properties or plant growth,but few studies have focused on how these carbonized materials are distributed by termite species in the soil ecosystem.It is the first comprehensive study of the transportation of biochar(BC)by termite species under tropical environmental conditions in Pakistan.The present study was carried out to test the hypothesis that if termite species I)were involved in the distribution of biochar particles II)if yes,then how far these particles were transported during the study period(10 days)and III)check their preference between the enriched BC(EBC)and non-enriched BC.BC was enriched with the cattle slurry after its pyrolysis in the study.The results showed that EBC particles were significantly more widely distributed than non-enriched BC particles,but both types of BC were transported more than 4 cm(ring 4)within 10 days(at the end of the experiment).The current study also revealed that EBC was easily attached to the setae,cuticle,and legs of termites,implying that it could potentially be transported over a greater distance.Furthermore,transportation of EBC over larger distances indicated a potential preference of termite species between the EBC and BC particles.During the study,however,the preference among the termite species was also observed.Under the prevailing study conditions,the Coptotermes heimi and Heteroterme indicola species transported the EBC further than Microtermes obesi and Odontotermes obesus.These findings revealed that transportation preferences were observed among the four termite species.In conclusion,the current study found that termites were involved in the distribution of BC particles,with a preference for EBC and that these have the potential to transport BC particles more than 4 cm within 10 days.Furthermore,two species Coptotermes heimi and Heteroterme indicola may be more suitable candidates for EBC transpiration in Pakistani soils.It was necessary to conduct additional research into the effect of temperature on the transportation process.

Effects of Hydrogels on Tree Seedling Performance in Temperate Soils before and after Water Stress

Super Absorbent Polyacrylate (SAP) hydrogels absorb and store water thereby aiding plant establishment when incurporated in the soil. The effect of cross-linked SAP hydrogel amendment on the performance of tree seedlings of Picea abies, Pinus sylivestris and Fagus sylvatica grown in temperate soils under water stress and non-water stress periods was investigated in a green house. The objective was to compare the root and shoot biomass of seedlings of the three species grown in sand, loam and clay soils amended with 0.4% w/w hydrogel in non water stress conditions as well as survival, root and shoot biomass after subjection to water stress. The seedlings were grown for 16 weeks, harvested and shoot as well as root biomass determined before water stress. The seedlings were also subjected to water stress and their biomass assessed at death following the water stress. The results showed that root and shoot biomass were generally higher in hydrogel amended soils compared to the controls. Root and shoot biomass of Fagus sylvatica was lower compared to Picea abies and Pinus sylivestris before water stress. The 0.4% hydrogel amendment significantly increased species’ survival in the different soils studied. Although root biomass was higher in hydrogel amended sandy soil compared to other soils, P. sylivestris and F. sylvatica shoot biomass were higher in hydrogel amended clay and loam soils compared to the sandy soil after water stress. Biomass was higher in sand compared to loam and clay soils under non-water and water stressed conditions. Since SAP hydrogel amendment improved the survival and biomass production of tree seedlings before and after water stress, use of SAPs could be promoted to enhance seedling production in water stress and non-water stress environments.

Weed genomics:yielding insights into the genetics of weedy traits for crop improvement

Weeds cause tremendous economic and ecological damage worldwide.The number of genomes established for weed species has sharply increased during the recent decade,with some 26 weed species having been sequenced and de novo genomes assembled.These genomes range from 270 Mb(Barbarea vulgaris)to almost 4.4 Gb(Aegilops tauschii).Importantly,chromosome-level assemblies are now available for 17 of these 26 species,and genomic investigations on weed populations have been conducted in at least 12 species.The resulting genomic data have greatly facilitated studies of weed management and biology,especially origin and evolution.Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement.In this review,we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.

Reimagining safe lithium applications in the living environment and its impacts on human,animal,and plant system

Lithium's(Li)ubiquitous distribution in the environment is a rising concern due to its rapid proliferation in the modern electronic industry.Li enigmatic entry into the terrestrial food chain raises many questions and uncertainties that may pose a grave threat to living biota.We examined the leverage existing published articles regarding advances in global Li resources,interplay with plants,and possible involvement with living organisms,especially humans and animals.Globally,Li concentration(<10 e300 mg kg
1)is detected in agricultural soil,and their pollutant levels vary with space and time.High mobility of Li results in higher accumulation in plants,but the clear mechanisms and specific functions remain unknown.Our assessment reveals the causal relationship between Li level and biota health.For example,lower Li intake(<0.6 mM in serum)leads to mental disorders,while higher intake(>1.5 mM in serum)induces thyroid,stomach,kidney,and reproductive system dysfunctions in humans and animals.However,there is a serious knowledge gap regarding Li regulatory standards in environmental compartments,and mechanistic approaches to unveil its consequences are needed.Furthermore,aggressive efforts are required to define optimum levels of Li for the normal functioning of animals,plants,and humans.This review is designed to revitalize the current status of Li research and identify the key knowledge gaps to fight back against the mountainous challenges of Li during the recent digital revolution.Additionally,we propose pathways to overcome Li problems and develop a strategy for effective,safe,and acceptable applications.

Bi-directional Selection in Upland Rice Leads to Its Adaptive Differentiation from Lowland Rice in Drought Resistance and Productivity

Drought resistance is required in rice breeding to address the challenge of frequent droughts . However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water-soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are comm on and greatly shape the evolutio n of drought resista nee in upland rice . In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland agro-ecosystems.Using genome-wide association analysis, we ide ntified several valuable quantitative trait loci associated with drought resista nee, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and droughtresistance rice.

Soil microbes alleviate allelopathy of invasive plants

土壤微生物是这块地里的 allelopathic 效果的最重要的决定因素之一。然而，在生物侵略测试 allelopathy 的角色的大多数研究没考虑土壤微生物的角色。这里，我们测试了假设能降级的土壤微生物 allelochemicals 可以由改编随着时间的过去在土壤积累因此增加 allelochemicals 的降级并且在生物侵略减轻 allelopathic 效果。是期望，土壤微生物显著地减少了在九侵略植物种的八的叶 leachates 的 allelopathic 效果学习了。另外， Ageratina adenophora 在土壤显示出更低的 allelopathic 效果与长或在中间侵略历史比那些在有短侵略历史的土壤。侵略者的二主要 allelochemicals 与在土壤增加侵略历史更快被降级。相应地，土壤微生物的生物资源和活动与短侵略历史比在那在有长侵略历史的土壤是更高的。我们的结果显示土壤微生物可以逐渐地适应 Ageratina 的 allelochemicals 并且减轻它的 allelopathic 效果并且因此支持上述假设。当在生物侵略测试 allelopathy 或新奇武器假设的角色时，考虑土壤微生物的效果是必要的。