Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 30 untranslated regions in translatomic variation in plants

The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.

Applications and roles of the CRISPR system in genome editing of plants

Genome editing is a valuable tool to target specific DNA sequences for mutagenesis in the genomes of microbes, plants, and animals. Although different genome editing technologies are available, the clustered regularly interspaced short palindromic repeats/Cas9 （CRISPR/ Cas9） system, which utilizes engineered endonucleases to generate a double-stranded DNA break （DSB） in the target DNA region and subsequently stimulates site-specific mutagenesis through DNA repair machineries, is emerging as a powerful genome editing tool for elucidating mecha- nisms of protection from plant viruses, plant disease resistance, and gene functions in basic and applied research. In this review, we provide an overview of recent advances in the CRISPR system associated genome editing in plants by focusing on application of this technology in model plants, crop plants, fruit plants, woody plants and grasses and discuss how genome editing associated with the CRISPR system can provide insights into genome modifications and functional genomics in plants.

Functional genomics of Brassica napus:Progresses,challenges,and perspectives

Brassica napus,commonly known as rapeseed or canola,is a major oil crop contributing over 13%to the stable supply of edible vegetable oil worldwide.Identification and understanding the gene functions in the B.napus genome is crucial for genomic breeding.A group of genes controlling agronomic traits have been successfully cloned through functional genomics studies in B.napus.In this review,we present an overview of the progress made in the functional genomics of B.napus,including the availability of germplasm resources,omics databases and cloned functional genes.Based on the current progress,we also highlight the main challenges and perspectives in this field.The advances in the functional genomics of B.napus contribute to a better understanding of the genetic basis underlying the complex agronomic traits in B.napus and will expedite the breeding of high quality,high resistance and high yield in B.napus varieties.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.

Chinese Glioma Genome Atlas(CGGA):A Comprehensive Resource with Functional Genomic Data from Chinese Glioma Patients

Gliomas are the most common and malignant intracranial tumors in adults.Recent studies have revealed the significance of functional genomics for glioma pathophysiological studies and treatments.However,access to comprehensive genomic data and analytical platforms is often limited.Here,we developed the Chinese Glioma Genome Atlas(CGGA),a user-friendly data portal for the storage and interactive exploration of cross-omics data,including nearly 2000 primary and recurrent glioma samples from Chinese cohort.Currently,open access is provided to whole-exome sequencing data(286 samples),mRNA sequencing(1018 samples)and microarray data(301 samples),DNA methylation microarray data(159 samples),and microRNA microarray data(198 samples),and to detailed clinical information(age,gender,chemoradiotherapy status,WHO grade,histological type,critical molecular pathological information,and survival data).In addition,we have developed several tools for users to analyze the mutation profiles,mRNA/microRNA expression,and DNA methylation profiles,and to perform survival and gene correlation analyses of specific glioma subtypes.This database removes the barriers for researchers,providing rapid and convenient access to high-quality functional genomic data resources for biological studies and clinical applications.CGGA is available at http://www.cgga.org.cn.

Mutant Resources for the Functional Analysis of the Rice Genome

Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.

RNA interference and its application in plants

RNA interference （RNAi）, a process that inhibits gene expression by the double-stranded RNA （dsRNA）, causes the degradation of target messenger RNA molecules. RNAi exists in almost all organisms. We review the recent history of RNAi studies, RNAi molecular mechanisms, characteristics and RNAi applications in higher plants. At the same time, the prospect of RNAi applications in functional genomics and genetic improvement of higher plants and possible future problems and possibilities are also discussed.

Current strategies and advances in wheat biology

The characterization of agronomically important genes has great potential for the improvement of wheat.However,progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous size of the wheat genome.Recent advances in genome sequencing and sequence assembly have produced a high-quality genome sequence for wheat.Here,we suggest that the strategies used to characterize biological mechanisms in model species,including mutant preparation and characterization,gene cloning methods,and improved transgenic technology,can be applied to wheat biology.These strategies will accelerate progress in wheat biology and promote wheat breeding program development.We also outline recent advances in wheat functional genomics.Finally,we discuss the future of wheat functional genomics and the rational design-based molecular breeding of new wheat varieties to contribute to world food security.

Cotton functional genomics reveals global insight into genome evolution and fiber development

Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution.Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDal were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.

Papaya Ring Spot Virus:An Understanding of a Severe Positive-Sense Single Stranded RNA Viral Disease and Its Management

Viral diseases have been studied in-depth for reducing quality,yield,health and longevity of the fruit,to highlight the economic losses.Positive-sense single-stranded RNA viruses are more devastating among all viruses that infect fruit trees.One of the best examples is papaya ringspot virus(PRSV).It belongs to the genus Potyvirus and it is limited to cause diseases on the family Chenopodiaceae,Cucurbitaceae and Caricaceae.This virus has a serious threat to the production of papaya,which is famous for its high nutritional and pharmaceutical values.The plant parts such as leaves,latex,seeds,fruits,bark,peel and roots may contain the biological compound that can be isolated and used in pharmaceutical industries as a disease control.Viral disease symptoms consist of vein clearing and yellowing of young leaves.Distinctive ring spot patterns with concentric rings and spots on fruit reduce its quality and taste.The virus has two major strains P and W.The former cause disease in papaya and cucurbits while the later one in papaya.Virion comprises 94.4%protein,including a 36 kDa coat protein which is a component responsible for a non-persistent transmission through aphids,and 5.5%nucleic acid.Cross protection,development of transgenic crops,exploring the resistant sources and induction of pathogen derived resistance have been recorded as effective management of PRSV.Along with these practices reduced aphid population through insecticides and plant extracts have been found ecofriendly approaches to minimize the disease incidence.Adoption of transgenic crops is a big challenge for the success of disease resistant papaya crops.The aim of this review is to understand the genomic nature of PRSV,detection methods and the different advanced control methods.This review article will be helpful in developing the best management strategies for controlling PRSV.

Understandings and future challenges in soybean functional genomics and molecular breeding

Soybean(Glycine max)is a major source of plant protein and oil.Soybean breeding has benefited from advances in functional genomics.In particular,the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies,the molecular mechanism of symbiotic nitrogen(N)fixation,biotic and abiotic stress tolerance,and the roles of flowering time in regional adaptation,plant architecture,and seed yield and quality.Nevertheless,many challenges remain for soybean functional genomics and molecular breeding,mainly related to improving grain yield through high-density planting,maize-soybean intercropping,taking advantage of wild resources,utilization of heterosis,genomic prediction and selection breeding,and precise breeding through genome editing.This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.

Boosting wheat functional genomics via an indexed EMS mutant library of KN9204

A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation.However,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding.In this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)mutagenesis.This library contains a vast developmental diversity of critical tissues and transition stages.Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type SNPs.We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and WFZP.We tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered sensitivity.Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic stress.Thus,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.

Altered leukocyte gene expression after traumatic spinal cord injury:clinical implications

In addition to changes in motor and sensory function, individuals with spinal cord injury （SCI） experience immunological changes. These changes are clinically significant, as infections are the leading cause of death for this population. Along with increased infections, inflammation is commonly observed in persons with SCI, where it may promote many common medical consequences. These include elevated risk of cardio- vascular disease, impaired wound healing, diabetes and neuropathic pain. It has also been proposed that chronic inflammation dampens neurological recovery. In order to identify therapeutic strategies to im- prove immune function, we need a greater understanding of the molecular changes that occur in immune cells after SCI. The purpose of this mini-review is to discuss two recent studies that used functional genom- ics to investigate gene expression in circulating leukocytes isolated from persons with SCI. In the future, the molecular pathways that are altered after SCI may be targeted to improve immunological function, as well as overall health and functional recovery, after SCI.

Genome-scale CRISPRi screening:A powerful tool in engineering microbiology

Deciphering gene function is fundamental to engineering of microbiology.The clustered regularly interspaced short palindromic repeats(CRISPR)system has been adapted for gene repression across a range of hosts,creating a versatile tool called CRISPR interference(CRISPRi)that enables genome-scale analysis of gene function.This approach has yielded significant advances in the design of genome-scale CRISPRi libraries,as well as in applica-tions of CRISPRi screening in medical and industrial microbiology.This review provides an overview of the recent progress made in pooled and arrayed CRISPRi screening in microorganisms and highlights representative studies that have employed this method.Additionally,the challenges associated with CRISPRi screening are discussed,and potential solutions for optimizing this strategy are proposed.

The function genomics study

Genomics is a biology term appeared ten years ago, used todescribe the researches of genomic mapping, sequencing,and structure analysis, etc. Genomics, the first journal forpublishing papers on genomics research was born in 1986.In the past decade, the concept of genomics has beenwidely accepted by scientists who are engaging in biologyresearch. Meanwhile, the research scope of genomics hasbeen extended continuously, from simple gene mappingand sequencing to function genomics study. To reflect thechange, genomics is divided into two parts now, thestructure genomics and the function genomics.Structure genomics retains the primary research con-tent of genomics, such as constructing high density genetic

Rice Functional Genomics Research： Past Decade and Future

Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Graft-accelerated virus-induced gene silencing facilitates functional genomics in rose flowers

Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors.Virus-induced gene silencing(VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose,called ‘graft-accelerated VIGS’, where axil ary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR, RhA G, and RhNUDXin rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.

From Green Super Rice to green agriculture:Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.

Using Genome-Referenced Expressed Sequence Tag Assembly to Analyze the Origin and Expression Patterns of Gossypium hirsutum Transcripts

We assembled a total of 297,239 Gossypium hirsutum （Gh, a tetraploid cotton, AADD） expressed sequence tag （EST） sequences that were available in the National Center for Biotechnology Information database, with reference to the recently published G. raimondii （Gr, a diploid cotton, DD） genome, and obtained 49,125 UniGenes. The average lengths of the U niGenes were increased from 804 and 791 bp in two previous EST assemblies to 1,019 bp in the current analysis. The number of putative cotton UniGenes with lengths of 3 kb or more increased from 25 or 34 to 1,223. As a result, thousands of originally independent G. hirsutum ESTs were aligned to produce large contigs encoding transcripts with very long open reading frames, indicating that the G. raimondii genome sequence provided remarkable advantages to assemble the tetraploid cotton transcriptome. Significant different distribution patterns within several GO terms, including transcription factor activity, were observed between D- and A-derived assemblies. Tran- scriptome analysis showed that, in a tetraploid cotton cell, 29,547 UniGenes were possibly derived from the D subgenome while another 19,578 may come from the A subgenome. Finally, some of the in silico data were confirmed by reverse transcription polymerase chain reaction experiments to show the changes in transcript levels for several gene families known to play key role in cotton fiber development. We believe that our work provides a useful platform for functional and evolutionary genomic studies in cotton.

The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement

After being domesticated from teosinte,cultivated maize(Zea mays ssp.mays)spread worldwide and now is one of the most important staple crops.Due to its tremendous phenotypic and genotypic diversity,maize also becomes to be one of the most widely used model plant species for fundamental research,with many important discoveries reported by maize researchers.Here,we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits,review the currently available resources for functional genomics studies in maize,and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement.Finally,we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.