Application of Transgenic Technology in Identification for Gene Function on Grasses

Perennial grasses have developed intricate mechanisms to adapt to diverse environments,enabling their resistance to various biotic and abiotic stressors.These mechanisms arise from strong natural selection that contributes to enhancing the adaptation of forage plants to various stress conditions.Methods such as antisense RNA technology,CRISPR/Cas9 screening,virus-induced gene silencing,and transgenic technology,are commonly utilized for investigating the stress response functionalities of grass genes in both warm-season and cool-season varieties.This review focuses on the functional identification of stress-resistance genes and regulatory elements in grasses.It synthesizes recent studies on mining functional genes,regulatory genes,and protein kinase-like signaling factors involved in stress responses in grasses.Additionally,the review outlines future research directions,providing theoretical support and references for further exploration of(i)molecular mechanisms underlying grass stress responses,(ii)cultivation and domestication of herbage,(iii)development of high-yield varieties resistant to stress,and(iv)mechanisms and breeding strategies for stress resistance in grasses.

Predicting Arabidopsis thaliana Gene Function by Transitiving Co-expression in Shortest-path

The present paper predicted the function of unknow genes by analyzing the co-expression data of Arabidopsis thaliana from biological pathway based on the shortest-path algorithm. This paper proposed that transitive co-expression among genes can be used as an important attribute to link genes of the same biological pathway. The genes from the same biological pathway with similar functions are strongly correlated in expression. Moreover,the function of unknown genes can be predicted by the known genes where they are strongly correlated in expression lying on the same shortest-path from the biological pathway. Analyzing the Arabidopsis thaliana from the biological pathway,this study showed that this method can reliably reveal function of the unknown Arabidopsis thaliana genes and the approach of predicting gene function by transitiving co-expression in shortest-path is feasible and effective.

Integrating Gene Ontology and Blast to predict gene functions

A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology (GO) annotations together. The operation system was based on Debian Linux 3.1, with Apache as the web server and Mysql database as the data storage system. FASTA files with GO annotations were taken as the sequence source for blast alignment, which were formatted by wu-formatdb program. The GoBlast system includes three Bioperl modules in Perl:a data input module, a data process module and a data output module. A GoBlast query starts with an amino acid or nucleotide sequence. It ends with an output in an html page, presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts. A simple click on a GO term leads to the detailed explanation of the specific gene function. This avails gene function prediction by Blast. GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.

A callus transformation system for gene functional studies in soybean

Obtaining transgenic plants is a common method for analyzing gene function. Unfortunately, stable genetic transformation is difficult to achieve, especially for plants（e.g., soybean）, which are recalcitrant to genetic transformation. Transient expression systems, such as Arabidopsis protoplast, Nicotiana leaves, and onion bulb leaves are widely used for gene functional studies. A simple method for obtaining transgenic soybean callus tissues was reported recently. We extend this system with simplified culture conditions to gene functional studies, including promoter analysis, expression and subcellular localization of the target protein, and protein-protein interaction. We also evaluate the plasticity of this system with soybean varieties, different vector constructs, and various Agrobacterium strains. The results indicated that the callus transformation system is efficient and adaptable for gene functional investigation in soybean genotype-, vector-, and Agrobacterium strain-independent modes. We demonstrated an easy set-up and practical homologous strategy for soybean gene functional studies.

Regulatory potential of soil available carbon,nitrogen,and functional genes on N_(2)O emissions in two upland plantation systems

Dynamic nitrification and denitrification processes are affected by changes in soil redox conditions,and they play a vital role in regulating soil N_(2)O emissions in rice-based cultivation.It is imperative to understand the influences of different upland crop planting systems on soil N_(2)O emissions.In this study,we focused on two representative rotation systems in Central China:rapeseed–rice(RR)and wheat–rice(WR).We examined the biotic and abiotic processes underlying the impacts of these upland plantings on soil N_(2)O emissions.The results revealed that during the rapeseed-cultivated seasons in the RR rotation system,the average N_(2)O emissions were 1.24±0.20 and 0.81±0.11 kg N ha^(–1)for the first and second seasons,respectively.These values were comparable to the N_(2)O emissions observed during the first and second wheat-cultivated seasons in the WR rotation system(0.98±0.25 and 0.70±0.04 kg N ha^(–1),respectively).This suggests that upland cultivation has minimal impacts on soil N_(2)O emissions in the two rotation systems.Strong positive correlations were found between N_(2)O fluxes and soil ammonium(NH_(4)^(+)),nitrate(NO_(3)^(–)),microbial biomass nitrogen(MBN),and the ratio of soil dissolved organic carbon(DOC)to NO_(3)^(–)in both RR and WR rotation systems.Moreover,the presence of the AOA-amoA and nirK genes were positively associated with soil N_(2)O fluxes in the RR and WR systems,respectively.This implies that these genes may have different potential roles in facilitating microbial N_(2)O production in various upland plantation models.By using a structural equation model,we found that soil moisture,mineral N,MBN,and the AOA-amoA gene accounted for over 50%of the effects on N_(2)O emissions in the RR rotation system.In the WR rotation system,soil moisture,mineral N,MBN,and the AOA-amoA and nirK genes had a combined impact of over 70%on N_(2)O emissions.These findings demonstrate the interactive effects of functional genes and soil factors,including soil physical characteristics,available carbon and nitrogen,and their ratio,on soil N_(2)O emissions during upland cultivation seasons under rice-upland rotations.

Genome-wide analysis of nuclear factor Y genes and functional investigation of watermelon ClNF-YB9 during seed development

The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.

A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants

Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding.The gene of interest is transferred to the vector by molecular cloning technology.Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity,efficiency,and standardization.In this study,we developed a"pNC"vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants.These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning.We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes,including the study of gene ectopic expression,protein subcellular localization,protein-protein interaction,gene silencing(RNAi),virus-induced gene silencing,promoter activity,and CRISPR-Cas9-mediated genome editing.The"pNC"vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.

Development of a rapid and efficient system for CR genes identification based on hairy root transformation in Brassicaceae

Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by Plasmodiophora brassicae infection.Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease.The traditional way of R gene functional validation requires stable transformation that is both time-and labor-consuming.In this study,a rapid and efficient hairy-root transgenic protocol mediated by Agrobacterium rhizogenes was developed.The transformation positive rate was over 80%in Brassica napus showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation.The system was applicable to different B.napus varieties and other cruciferous crops including Brassica rapa and Brassica oleracea.In particular,two known CR genes,CRA3.7.1 and CRA8.2.4 were used respectively,as example to show that the system works well for CR gene study combined with subsequent P.brassicae infection in B.napus.Most importantly,it works both in over-expression that led to disease resistance,as well as in RNAi which led to disease susceptible phenotype.Therefore,this system can be used in batch-wise identification of CR genes,and also offered the possibility of manipulating key genes within the P.brassicae genome that could improve our knowledge on host-pathogen interaction.

Research Progress on Functional Analysis of Rice WRKY Genes

Rice is a model plant for genomic study of grass species. Functional identification and definition of rice genes becomes the object of its functional genomics research. WRKY gene superfamily, one of the transcription factor gene families, was recently suggested to play important roles in plant development and stress response. In rice, the results of analyses of expression pattern and ectopic overexpressor lines also support this viewpoint, and the evidences implicate rice WRKY proteins in transcriptional reprogramming during biotic or abiotic stresses, senescence, sugar metabolites, and morphological architecture. In this paper, we review the advance in study of rice WRKY gene family and also propose unified nomenclature for rice WRKY factors to eliminate confusion.

A Method of Gene-Function Annotation Based on Variable Precision Rough Sets

It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.

Alloy gene Gibbs energy partition function and equilibrium holographic network phase diagrams of AuCu_3-type sublattice system

Taking AuCu3-type sublattice system as an example, three discoveries have been presented: First, the third barrier hindering the progress in metal materials science is that researchers have got used to recognizing experimental phenomena of alloy phase transitions during extremely slow variation in temperature by equilibrium thinking mode and then taking erroneous knowledge of experimental phenomena as selected information for establishing Gibbs energy function and so-called equilibrium phase diagram. Second, the equilibrium holographic network phase diagrams of AuCu3-type sublattice system may be used to describe systematic correlativity of the composition?temperature-dependent alloy gene arranging structures and complete thermodynamic properties, and to be a standard for studying experimental subequilibrium order-disorder transition. Third, the equilibrium transition of each alloy is a homogeneous single-phase rather than a heterogeneous two-phase, and there exists a single-phase boundary curve without two-phase region of the ordered and disordered phases; the composition and temperature of the top point on the phase-boundary curve are far away from the ones of the critical point of the AuCu3 compound.

Alloy gene Gibbs energy partition function and equilibrium holographic network phase diagrams of Au_3Cu-type sublattice system

Taking Au3Cu-type sublattice system as an example, three discoveries have been presented. First, the fourth barrier to hinder the progress of metal materials science is that today’s researchers do not understand that the Gibbs energy function of an alloy phase should be derived from Gibbs energy partition function constructed of alloy gene sequence and their Gibbs energy sequence. Second, the six rules for establishing alloy gene Gibbs energy partition function have been discovered, and it has been specially proved that the probabilities of structure units occupied at the Gibbs energy levels in the degeneracy factor for calculating configuration entropy should be degenerated as ones of component atoms occupied at the lattice points. Third, the main characteristics unexpected by today’s researchers are as follows. There exists a single-phase boundary curve without two-phase region coexisting by the ordered and disordered phases. The composition and temperature of the top point on the phase-boundary curve are far away from those of the critical point of the Au3Cu compound; At 0 K, the composition of the lowest point on the composition-dependent Gibbs energy curve is notably deviated from that of the Au3Cu compounds. The theoretical limit composition range of long range ordered Au3Cu-type alloys is determined by the first jumping order degree.

Application of Functional Markers to Identify Genes for Bacterial Blight Resistance in Oryza rufipogon

Field resistances of nine accessions of common wild rice （Oryza rufipogon Griff.） and one rice variety （IR24） were evaluated by using nine strains of bacterial blight pathogen （Xanthomonas oryzae pv. oryzae） from the Philippines. IR24 was highly susceptible to all the strains, and six common wild rice accessions resisted all the nine strains, with a resistance frequency of 67%. The accessions Yulin and Wanning were only susceptible to PXO280 and PXO71, respectively. The accession Gaozhou was susceptible to the three strains PXO79, PXO99 and PXO339, whereas resistant to the other six strains. It could be concluded that there is at least one resistance gene in each common wild rice accession. The functional markers of the genes xa5, xa13, Xa21 and Xa27 were used to detect the presence of these resistance genes in the nine tested wild rice accessions, and it was found that four wild rice accessions contained heterozygous xa13. Among the nine common wild rice accessions, five were homozygous for Xa27 and three homozygous for xa27, and the accession Laibin contained neither xa27 nor Xa27. In addition, there were no xa5 and Xa21 in all of these accessions.

Expression pattern and function analyses of the MADS thranscription factor genes in wheat(Triticum aestivum L.) under phosphorusstarvation condition

supported by the National Natural Science Foundation of China （31201674 and 31371618）;the National Transgenic Major Program, China （2011ZX08008）

TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction

Gene Ontology(GO)has been widely used to annotate functions of genes and gene products.Here,we proposed a new method,Triplet GO,to deduce GO terms of protein-coding and noncoding genes,through the integration of four complementary pipelines built on transcript expression profile,genetic sequence alignment,protein sequence alignment,and naīve probability.Triplet GO was tested on a large set of 5754 genes from 8 species(human,mouse,Arabidopsis,rat,fly,budding yeast,fission yeast,and nematoda)and 2433 proteins with available expression data from the third Critical Assessment of Protein Function Annotation challenge(CAFA3).Experimental results show that Triplet GO achieves function annotation accuracy significantly beyond the current state-of-the-art approaches.Detailed analyses show that the major advantage of Triplet GO lies in the coupling of a new triplet network-based profiling method with the feature space mapping technique,which can accurately recognize function patterns from transcript expression profiles.Meanwhile,the combination of multiple complementary models,especially those from transcript expression and protein-level alignments,improves the coverage and accuracy of the final GO annotation results.The standalone package and an online server of Triplet GO are freely available at https://zhanggroup.org/Triplet GO/.

A Network Partition Algorithm for Mining Gene Functional Modules of Colon Cancer from DNA Microarray Data

Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data and have applied it tocolon cancer. First, a colon cancer gene network and a normal colon tissue genenetwork were constructed using correlations between the genes. Then the modulesthat tended to have a homogeneous functional composition were identified by split-ting up the network. Analysis of both networks revealed that they are scale-free.Comparison of the gene functional modules for colon cancer and normal tissuesshowed that the modules’ functions changed with their structures.

Applications of virus-induced gene silencing for identification of gene function in fruit

With the development of bioinformatics,it is easy to obtain information and data about thousands of genes,but the determi nation of the functions of these genes depends on methods for rapid and effective functi on al identification.Virus-induced gene sile ncing(VIGS)is a mature method of gene functional identification developed over the last 20 years,which has been widely used in many research fields involving many species.Fruit quality formation is a complex biological process,which is closely related to ripening.Here,we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.

Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (Oryza sativa)

Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.

Association of polymorphisms of Nramp1 gene with immune function and production performance of large white pig

The present research was designed to study the association of polymorphism of natural resistance-associated macrophage proteinl （Nrampl） with some immune function and the production performance in Large White pig. The PCR-RFLP technique was applied to analyze the correlation between the polymorphisms of Nrampl gene and immune function [value of Polymorphonuclear Leukocytes （PMN） obtained by Nitroblue Tetrazolium （NBT） Reduction and effect of Cytotoxin in Monocyte] and production performance in 165 Large White pigs. The results showed that there was one Nde I restriction locus in Large White pig, and both values of PMN by NBT Reduction and effect of Cytotoxin in Monocyte in genotype BB were higher than those in genotype AB （P〈0.05）. Simultaneously, the weight of 180-day-old pigs with genotype BB was higher than that with genotype AB （P〈0.05）. The results indicated that there was a significant correlation between different genotypes of Nrampl gene and Immune function and production performance, and it can be regarded as a candidate gene of disease resistance. All these results provide valuable reference to further studies of pig disease resistance.

Cloning and Functional Analysis of Lycopene ε-Cyclase (IbLCYe) Gene from Sweetpotato, Ipomoea batatas (L.) Lam.

This paper reported firstly successful cloning of lycopene ε-cyclase （lbLCYe） gene from sweetpotato, lpomoea batatas （L.） Lam. Using rapid amplification of cDNA ends （RACE）, lbLCYe gene was cloned from sweetpotato cv. Nongdafu 14 with high carotenoid content. The 1 805 bp cDNA sequence oflbLCYe gene contained a 1236 bp open reading frame （ORF） encoding a 411 amino acids polypeptide with a molecular weight of 47 kDa and an isoelectric point （pI） of 6.95. IbLCYe protein contained one potential lycopene ε-cyclase domain and one potential FAD （flavinadenine dinucleotide）/NAD（P） （nicotinamide adenine dinucleotide phosphate）-binding domain, indicating that this protein shares the typical characteristics of LCYe proteins. The gDNA oflbLCYe gene was 4 029 bp and deduced to contain 5 introns and 6 exons. Real-time quantitative PCR analysis revealed that the expression level of IbLCYe gene was significantly higher in the storage roots of Nongdafu 14 than those in the leaves and stems. Transgenic tobacco （cv. Wisconsin 38） expressing [bLCYe gene accumulated significantly more ^-carotene compared to the untransformed control plants. These results showed that lbLCYe gene has an important function for the accumulation of carotenoids of sweetpotato.