Second-order lower radial tangent derivatives and applications to set-valued optimization.

We introduce the concepts of second-order radial composed tangent derivative, second-order radial tangent derivative, second-order lower radial composed tangent derivative, and second-order lower radial tangent derivative for set-valued maps by means of a radial tangent cone, second-order radial tangent set, lower radial tangent cone, and second-order lower radial tangent set, respectively. Some properties of second-order tangent derivatives are discussed, using which second-order necessary optimality conditions are established for a point pair to be a Henig efficient element of a set-valued optimization problem, and in the expressions the second-order tangent derivatives of the objective function and the constraint function are separated.

Molecular characterization and primary functional analysis of PeMPEC, a magnesium-protoporphyrin IX monomethyl ester cyclase gene of bamboo (Phyllostachys edulis).

KEY MESSAGE: A homologous gene of MPEC from Phyllostachys edulis was isolated and characterized. Its overexpression in Arabidopsis thaliana increased chlorophyll concentration and photosynthesis efficiency, indicating it is involved in chlorophyll biosynthesis. Magnesium-protoporphyrin IX monomethyl ester cyclase (MPEC) is an essential enzyme in the biosynthesis of chlorophyll, which plays an important role in photosynthesis. However, limited information is available on the roles of MPEC gene in bamboo. A homologous gene, PeMPEC was identified from Phyllostachys edulis, which comprised 1474 bp and contained an open reading frame encoding 415 amino acids. PeMPEC was transcribed abundantly in leaf blade where photosynthesis predominantly occurs, which agreed with the protein accumulation pattern confirmed by Western blotting. The PeMPEC transcription was promoted by continuous darkness for 24 h, and was suppressed by increasing light intensity (100-1500 µmo1 m(-2) s(-1)) and high temperature (42 °C). However, transcription was induced within 0.5 h and thereafter declined with prolonged treatment (up to 12 h) under low temperature (4 °C). Although PeMPEC expressed weakly in etiolated leaves, transcript levels increased gradually with subsequent light treatment (200 µmol m(-2) s(-1)). Overexpression of PeMPEC in Arabidopsis thaliana resulted in increased chlorophyll concentration and photosynthesis efficiency in sense transgenic plants compared with a reduction in antisense transgenic plants. These changes were consistent with the transcript levels of PeMPEC. These results indicated that PeMPEC might be involved in chlorophyll biosynthesis and play important roles in maintaining the stability of photosystems, and provide a basis for the study of chlorophyll biosynthesis and dissection of photosynthesis in bamboo.

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species.

Characterization of the floral transcriptome of Moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-seq analysis.

BACKGROUND: As an arborescent and perennial plant, Moso bamboo (Phyllostachys edulis (Carrière) J. Houzeau, synonym Phyllostachys heterocycla Carrière) is characterized by its infrequent sexual reproduction with flowering intervals ranging from several to more than a hundred years. However, little bamboo genomic research has been conducted on this due to a variety of reasons. Here, for the first time, we investigated the transcriptome of developing flowers in Moso bamboo by using high-throughput Illumina GAII sequencing and mapping short reads to the Moso bamboo genome and reference genes. We performed RNA-seq analysis on four important stages of flower development, and obtained extensive gene and transcript abundance data for the floral transcriptome of this key bamboo species. RESULTS: We constructed a cDNA library using equal amounts of RNA from Moso bamboo leaf samples from non-flowering plants (CK) and mixed flower samples (F) of four flower development stages. We generated more than 67 million reads from each of the CK and F samples. About 70% of the reads could be uniquely mapped to the Moso bamboo genome and the reference genes. Genes detected at each stage were categorized to putative functional categories based on their expression patterns. The analysis of RNA-seq data of bamboo flowering tissues at different developmental stages reveals key gene expression properties during the flower development of bamboo. CONCLUSION: We showed that a combination of transcriptome sequencing and RNA-seq analysis was a powerful approach to identifying candidate genes related to floral transition and flower development in bamboo species. The results give a better insight into the mechanisms of Moso bamboo flowering and ageing. This transcriptomic data also provides an important gene resource for improving breeding for Moso bamboo.

Arbuscular mycorrhizal fungal mediation of plant-plant interactions in a marshland plant community.

Obligate aerobic AMF taxa have high species richness under waterlogged conditions, but their ecological role remains unclear. Here we focused on AM fungal mediation of plant interactions in a marshland plant community. Five cooccurring plant species were chosen for a neighbor removal experiment in which benomyl was used to suppress AMF colonization. A Phragmites australis removal experiment was also performed to study its role in promoting AMF colonization by increasing rhizosphere oxygen concentration. Mycorrhizal fungal effects on plant interactions were different for dominant and subdominant plant species. AMF colonization has driven positive neighbor effects for three subdominant plant species including Kummerowia striata, Leonurus artemisia, and Ixeris polycephala. In contrast, AMF colonization enhanced the negative effects of neighbors on the dominant Conyza canadensis and had no significant impact on the neighbor interaction to the dominant Polygonum pubescens. AM colonization was positively related to oxygen concentration. P. australis increased oxygen concentration, enhanced AMF colonization, and was thus indirectly capable of influencing plant interactions. Aerobic AM fungi appear to be ecologically relevant in this wetland ecosystem. They drive positive neighbor interactions for subdominant plant species, effectively increasing plant diversity. We suggest, therefore, that AM fungi may be ecologically important even under waterlogged conditions.

BambooGDB: a bamboo genome database with functional annotation and an analysis platform.

Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein-protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org.

Transcriptome sequencing and analysis of the fast growing shoots of moso bamboo (Phyllostachys edulis).

BACKGROUND: The moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo. RESULTS: The fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < -2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots. CONCLUSION: Firstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.

Identification and characterization of microRNAs in the leaf of ma bamboo (Dendrocalamus latiflorus) by deep sequencing.

MicroRNAs (miRNAs), a class of non-coding small endogenous RNAs of approximately 22 nucleotides, regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Thousands of miRNAs have been identified in many species. However, there is no information available concerning miRNAs in ma bamboo (Dendrocalamus latiflorus), one of the most important non-timber forest products, which has essential ecological roles in forests. To identify miRNAs in D. latiflorus, a small RNA library was constructed from leaf tissues. Using next generation high-throughput sequencing technology and bioinformatics analysis, we obtained 11,513,607 raw sequence reads and identified 84 conserved miRNAs (54 mature miRNAs and 30 star miRNAs) belonging to 17 families, and 81 novel miRNAs (76 mature miRNAs and five star miRNAs) in D. latiflorus. One hundred and sixty-two potential targets were identified for the 81 novel bamboo miRNAs. Several targets for the novel miRNAs are transcription factors that play important roles in plant development. Among the novel miRNAs, 30 were selected and their expression profiles in response to different light conditions were validated by qRT-PCR. This study provides the first large-scale cloning and characterization of miRNAs in D. latiflorus. Eighty-four conserved and 81 novel miRNAs were identified in D. latiflorus. Our results present a broad survey of bamboo miRNAs based on experimental and bioinformatics analysis. Although it will be necessary to validate the functions of miRNAs by further experimental research, these results represent a starting point for future research on D. latiflorus and related species.

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).

Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between drought-responsive and flowering genes.

[Photosynthetic parameters and chlorophyll fluorescence characteristics of Pleioblastus kongosanensis f. aureostriaus under drought stress].

A pot experiment was conducted to study the variations of Pleioblastus kongosanensis f. aureostriaus plant morphology, leaf water content (LWC) , leaf water potential (LWP) , photosynthetic parameters, chlorophyll fluorescence parameters, and soil water content (SWC) under natural drought stress, as well as the relationships between these variations and environmental factors. On the 17th day under the stress, the P. kongosanensis presented damaged symptom. Its leaves dehydrated, drooped, and wrap-formed. On the 43rd day, the aboveground part of the plant died from dehydration. When the plant was re-watered for 10 days, the chlorophyll fluorescence parameters had no significant differences with those on the 43rd day under the stress. The SWC decreased significantly in 0-21 d of the stress, and the LWP and LWC dropped rapidly and significantly after 17 d and 29 d, respectively. With the increase of drought stress, the leaf transpiration rate (Tr) and stomatal conductance (g(s)) had a persistent decline, photosynthetic rate (Pn) had a greater fluctuation, and instantaneous water use efficiency (PWUE) decreased after an initial increase. After 17 d drought stress, the limiting factor of Pn was from stomatal to non-stomatal, and the actual photosynthetic efficiency (phiPS II) declined significantly; after 25 d, the photosynthetic organ was damaged, and the maximum photochemical efficiency of PS II (Fv/Fm) and non-photochemical quenching (qN) changed significantly from 0.64 to -0.11 and from 0.79 to 0.33, respectively. The Tr, g(s), and PWUE had close correlations with LWP; the Pn, Tr, and g(s) were sensitive to air relative humidity (RH); and the gs was the main factor causing the diurnal variations of photosynthetic parameters. It was suggested that P. kongosanensis could grow well on the soil with relative moisture content > or = 12% and drought duration less than 25 d.

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences.

BACKGROUND: With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies. RESULTS: Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, Phyllostachys heterocycla cv. pubescens, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study. CONCLUSION: Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.

[Soil microelements under different vegetation restoration patterns in yellow soil slope region of mid-subtropics].

With the Nüerzhai watershed in Wuling Mountain as a case, this paper studied the contents and availabilities of soil microelements and their relationships with soil organic matter and pH value in yellow soil slope region of mid-subtropics under seven typical vegetation restoration patterns, i. e., Pinus massoniana natural forest (I), Cunninghamia lanceolata plantation (II), Eucommia ulmoides plantation (III), Vernicia fordii plantation (IV), Machilus pingii secondary forest (V), Phyllostachys edulis - C. lanceolata mixed forest (VI), and wasteland-shrub community (VII). It was found that in 0-20 cm soil layer, the contents of B and Mn, Mo and Cu, Zn, and Fe reached the peaks under VII, IV, III and VI; while in 20-40 cm soil layer, III, IV, Vand VII had the highest contents of Cu, Zn, B, and Fe and Mn, Mo, respectively. In both two soil layers under VI, the contents of B, Mo, Cu and Mn were the lowest. Mn had the biggest single element available index, while Cu had the smallest one. The biggest and smallest total available index of soil microelements was 12.28 for VII and 2.95 for VI, respectively. There existed the regularities of Mn > Zn > Fe > Mo > B > Cu for single microelement available index and VII > V > III > IV > I > II > VI for comprehensive microelement available index under different vegetation patterns. A good linear relationship was observed between soil organic matter and B and Zn availabilities, and the relationship of soil organic matter with available Mn could be described by a quadratic equation. Soil pH was highly positively correlated with soil Cu and Zn contents, correlated with soil Mo and Mn contents, slightly correlated with soil B content, and slightly negatively correlated with soil Fe content.

A molecular phylogenetic and fruit evolutionary analysis of the major groups of the paleotropical woody bamboos (Gramineae: Bambusoideae) based on nuclear ITS, GBSSI gene and plastid trnL-F DNA sequences.

This study presented the first molecular phylogenetic analysis of the major clades of woody bamboos of the Old World tropics based on nuclear and chloroplast sequences (ITS, GBSSI and trnL-F). Sequence data from 53 species, representing 17 paleotropical woody bamboo genera, were analyzed using the maximum parsimony and Bayesian inference methods. All examined ingroup taxa were clustered into two clades, i.e., the Bambusinae+Dinochloa clade and the Melocanninae clade. The former clade included Bambusa, Bonia, Dendrocalamus, Dendrocalamopsis, Dinochloa, Gigantochloa, Molecalamus, Neomicrocalamus, Neosinocalamus, Oxytenanthera s. str. (sensu stricto), Racemobambos and Thyrsostachys. The Melocanninae clade consisted of Cephalostachyum, Leptocanna (better treated as part of Cephalostachyum), Melocanna, Pseudostachyum and Schizostachyum s. str. The subtribe Racemobambosinae and tribes Dendrocalameae and Oxytenanthereae were not supported and may be better placed in subtribe Bambusinae. The ovary characters seemed to be good criteria to distinguish these two clades. The reconstruction of ancestral fruit characters indicated that the bacoid caryopsis, namely, fleshy or berry-like fruits, was found to be scattered in three lineages of the examined paleotropical woody bamboos. Fruit characters are thus not reliable indicators of phylogeny and bacoid caryopsis likely represents a specialization for particular ecological conditions.

[Research advances on BVOCs emission from forest].

BVOCs play an important role in atmospheric environmental quality, global tropospheric chemistry, and global carbon balance, while forest is the main sources of them. This paper summarized the seasonal and diurnal variations of BVOCs emission from forest and its affecting factors including habitat variation, environmental change, forest development phase and its physiological status, and exotic interference. The ecological significance of forest BVOCs emission was further discussed, and some suggestions were proposed on ecological healthcare forest resources exploitation and urban forest construction.

[Application value of organic ground surface mulch in urban forestry construction].

This paper summarized the development process of organic ground surface mulch, and analyzed its important application value (such as the functions of improving soil physical and chemical properties, promoting plant growth, beautifying urban landscape, and preventing soil dust, etc.), and its values in protecting environment and benefiting economy. The problems in the application process of organic ground surface mulch were discussed, and the actual impendence and broad development space of its production and application in our urban forestry construction were pointed out.

[Research advances in ecosystem flux].

To develop the long-term localized observation and investigation on ecosystem flux is of great importance. On the basis of generalizing the concepts and connotations of ecosystem flux, this paper introduced the construction and development histories of Global Flux Networks, Regional Flux Networks (Ameri-Flux, Euro-Flux and Asia-Flux) and China-Flux, as well as the main methodologies, including micrometeorological methods (such as eddy correlation method, mass balance method, energy balance method and air dynamic method)and chamber methods (static and dynamic chamber methods), and their basic operation principles. The research achievements, approaches and advances of CO2, N2O, CH4, and heat fluxes in forest ecosystem, farmland ecosystem, grassland ecosystem and water ecosystem were also summarized. In accordance with the realities and necessities of ecosystem flux research in China, some suggestions and prospects were put forward.

[Light environment characteristics of forest gap in deciduous broad-leaved forest and its effects on growth features of Gynostemma pentaphyllum in Jianghuai watershed].

The daily total light intensity, various wave band light intensities, spectrum composition, and the growth characteristics and total saponia content of Gynostemma pentaphyllum in forest gap and under forest were studied in deciduous forest (Liquidambar formosana) in Jianghuai watershed. The results showed that the intensities of full wavelength daily total light, blue light(400-510 nm), yellow-green light(510-610 nm), red-orange light (610-720 nm) and near-infrared light(720-1100 nm) in forest gap were higher than those under forest. The intensities and spectra compositions of blue light and red-orange light in forest gaps were significantly higher than those under forest. Additionally, the differences between those in forest gap and under forest varied seasonally. The relative intensity of blue light in April, July and October in forest gap was 8.32%-28.83%, 30.00%-579.17% and 6.70%-88.74% more than those under forest, respectively, and that of red-orange light in April, July and October in forest gap was 8.72%-28.83%, 30.19%-502.69%, 6.76%-91.57% more than those under forest, respectively. The spectrum composition of blue light in forest gap in these 3 months was 5.76%, 33.14% and 17.29% higher than those under forest, respectively, and that of red-orange light in forest gap in these 3 months was 5.04%, 53.34% and 10.23% higher than those under forest, respectively. The net photosynthetic rate, total dry-matter weight, and total saponia content of Gynostemma pentaphyllum growing in forest gap were higher than those under forest. Gynostemma pentaphyllum growing in forest gap had more dry-matter distributed in stem. The results could be available to utilize the light environment of deciduous broad-leaved forest and further building comprehensive management model of Gynostemma pentaphyllum in Jianghuai watershed zone.

[Land-use strategy in riverine area].

The land near river is one kind of land zone that is inseparably related to the ecological process of river and lake, and directly affected or endangered by flood. Combined with ecological principles and the theory of forest eco-network system in China, the landscape security, the principles and directional thoughts, the theoretical basis and strategy were comprehensively studied in this paper. The landscape security should include three aspects of ecological benefit security, economical benefit security, and social benefit security. The land-use principles should be to find the best uniting section and ensure integration of the three principles together. The directional thoughts should be to combine management and development together, strengthen the landscape security by various measures, and carry out the near natural land-use and managing strategy by increasing the proportion of forest. Different development models should be selected in different rivers and regions. According to the risk grades of flood disturbance and spatial differentiation of lands near river, the different managing strategy with different disturbance degree should be carried out in different reach in upstream, midstream, and downstream based on the spatial differentiation of river and lands nearby in longitudinal direction, while based on the spatial differentiation and security during flood in cross direction, the utilization strategy should be classified and aimed at fragile use zone, stable use zone, and elastic use zone, respectively.