The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to ...The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.展开更多
A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae i...A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.展开更多
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 functiona...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.展开更多
Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold...Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.展开更多
Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions inclu...Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).展开更多
The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy ...The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy and IL4-signaling targeting strategies as a promising new approach for the treatment of advanced OvCa.Ovarian Cancer(OvCa)is the third most common gynecological malignant disease affecting women.2 It is often diagnosed at late stages and is characterized by heterogenous features with limited treatment options.Initial response to standard of care platinumbased chemotherapy combined with surgery is often followed by disease relapse and subsequent death of patients.Despite the recent success of immune checkpoint inhibition in different cancer entities,most OvCa patients do not benefit from immunotherapy-based treatment approaches.The responsiveness of ovarian tumors to immune checkpoint blockade(ICB)is thereby hindered by weak immunogenicity due to low mutational burden and an immune suppressive tumor microenvironment(TME)characterized by heterogenous immune cell infiltration.3 Still,functional evidence for key factors that govern cancer cellimmune cell interaction and drive immunotherapy resistance in OvCa remains limited.展开更多
Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model p...Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development,as well as symbiosis with rhizobia.Over the past decade,advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various traits.In this review,we comprehensively summarize research progress on Medicago genomics,growth and development(including compound leaf development,shoot branching,flowering time regulation,inflorescence development,floral organ development,and seed dormancy),resistance to abiotic and biotic stresses,and symbiotic nitrogen fixation with rhizobia,as well as molecular breeding.We propose avenues for molecular biology research on Medicago in the coming decade,highlighting those areas that have yet to be investigated or that remain ambiguous.展开更多
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 ge...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.展开更多
Rapeseed(Brassica napus L.)is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes.Improvements in genome sequencing and molec...Rapeseed(Brassica napus L.)is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes.Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield,quality,flowering time,and stress resistance.Moreover,introgression and pyra-miding of key functional genes have greatly accelerated the genetic improvement of important traits.Here we summarize recent progress in rapeseed genomics and genetics,and we discuss effective molecular breeding strategies by exploring thesefindings in rapeseed.These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture throughout the world.展开更多
As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
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...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.展开更多
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 Gree...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.展开更多
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 us...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.展开更多
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 ...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.展开更多
Since the completion of the rice genome sequencing project in 2005,we have entered the era of rice genomics,which is still in its ascendancy.Rice genomics studies can be classified into three stages:structural genomic...Since the completion of the rice genome sequencing project in 2005,we have entered the era of rice genomics,which is still in its ascendancy.Rice genomics studies can be classified into three stages:structural genomics,functional genomics,and quantitative genomics.Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence.This is fundamental for rice genetics and molecular biology research.Functional genomics aims to decode the functions of rice genes.Quantitative genomics is large-scale sequence-and statistics-based research to define the quantitative traits and genetic features of rice populations.Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding,making rice a good model plant for studying crop sciences.展开更多
Common wheat(Triticum aestivum L.)is one of the three major food crops in the world;thus,wheat breeding programs are important for world food security.Characterizing the genes that control important agronomic traits a...Common wheat(Triticum aestivum L.)is one of the three major food crops in the world;thus,wheat breeding programs are important for world food security.Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding.Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools,especially CRISPR/Cas9 genome editing technology,which allows multiplex genome engineering.Here,we describe the development of CRISPR/Cas9,which has revo-lutionized the field of genome editing.In addition,we emphasize technological breakthroughs(e.g.base editing and prime editing)based on CRISPR/Cas9.We also summarize recent applications and advances in the functional annotation and breeding of wheat,and we introduce the production of CRISPR-edited DNA-free wheat.Combined with other achievements,CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.展开更多
With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and...With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.展开更多
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrict...Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes（TILLING）, which combines traditional chemical mutagenesis with high‐throughput genome‐wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or evenallohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small‐scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2（or M3） plants.展开更多
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...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.展开更多
Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces cerevisiae.Here,we explore how two of these strategies,pathway re-...Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces cerevisiae.Here,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing strains.We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase enzyme.We then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains.Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes.Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway flux.Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase enzyme.We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron levels.The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.展开更多
文摘The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.
基金a grant from Biogreen 21 Project (No. 20080401034044)the Rural Development Administration of Korea, the Crop Functional Genomics Center (No. CG1141) of the 21st Century Frontier Research Program funded by the Ministry of Science and Technology of Koreathe Korean Research Foundation Grant (No. KRF-2006-005-J04701)
文摘A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.
基金supported by the Natural Science Foundation of China(Nos.21602162 and 31690090)the National Science and Technology Major Project(No.2016ZX08005003-001)the Fundamental Research Funds for the Central Universities(No.104862016)
文摘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.
基金supported by the National Natural Science Foundation of China(grant nos.32388201 and 32372126)Fundamental Research Funds for the Central Universities(YDZX2024041).
文摘Soybean,the fourth most important crop in the world,uniquely serves as a source of both plant oil and plant protein for the world’s food and animal feed.Although soybean production has increased approximately 13-fold over the past 60 years,the continually growing global population necessitates further increases in soybean production.In the past,especially in the last decade,significant progress has been made in both functional genomics and molecular breeding.However,many more challenges should be overcome to meet the anticipated future demand.Here,we summarize past achievements in the areas of soybean omics,functional genomics,and molecular breeding.Furthermore,we analyze trends in these areas,including shortages and challenges,and propose new directions,potential approaches,and possible outputs toward 2035.Our views and perspectives provide insight into accelerating the development of elite soybean varieties to meet the increasing demands of soybean production.
基金supported by the Provincial Technology Innovation Program of Shandong,Ningbo Science and Technology Innovation Project 2021Z132Weifang Seed Innovation Group.
文摘Dear Editor,Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber represents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).
基金funded by the Deutsche Forschungsgemeinschaft(DFG,German Research Foundation,LE 3613/3-1).
文摘The recent publication by Mollaoglu et al.1 in Cell reveals an unexpected role for tumor derived IL4 in driving immunotherapy resistance in ovarian cancer(OvCa).This finding nominates the combination of immunotherapy and IL4-signaling targeting strategies as a promising new approach for the treatment of advanced OvCa.Ovarian Cancer(OvCa)is the third most common gynecological malignant disease affecting women.2 It is often diagnosed at late stages and is characterized by heterogenous features with limited treatment options.Initial response to standard of care platinumbased chemotherapy combined with surgery is often followed by disease relapse and subsequent death of patients.Despite the recent success of immune checkpoint inhibition in different cancer entities,most OvCa patients do not benefit from immunotherapy-based treatment approaches.The responsiveness of ovarian tumors to immune checkpoint blockade(ICB)is thereby hindered by weak immunogenicity due to low mutational burden and an immune suppressive tumor microenvironment(TME)characterized by heterogenous immune cell infiltration.3 Still,functional evidence for key factors that govern cancer cellimmune cell interaction and drive immunotherapy resistance in OvCa remains limited.
基金supported by the National Key Research and Development Program of China(2023YFF1001400 to T.W.)the Young Elite Scientists Sponsorship Program by CAST(2023QNRC001 to Q.Y.)+1 种基金the National Natural Science Foundation of China(32370253 to J.D.,32325035 to H.L.)the US Department of Agriculture(USDA)US National Institute of Food and Agriculture(NIFA)grant(2022-38821-37353 to S.R.),and a US National Science Foundation Award(2217830 to S.R.).
文摘Medicago,a genus in the Leguminosae or Fabaceae family,includes the most globally significant forage crops,notably alfalfa(Medicago sativa).Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development,as well as symbiosis with rhizobia.Over the past decade,advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various traits.In this review,we comprehensively summarize research progress on Medicago genomics,growth and development(including compound leaf development,shoot branching,flowering time regulation,inflorescence development,floral organ development,and seed dormancy),resistance to abiotic and biotic stresses,and symbiotic nitrogen fixation with rhizobia,as well as molecular breeding.We propose avenues for molecular biology research on Medicago in the coming decade,highlighting those areas that have yet to be investigated or that remain ambiguous.
基金supported by grants from the National Science Fund for Distinguished Young Scholars(32225037)Hubei Hongshan Laboratory(2021HSZD004)+1 种基金HZAU-AGIS Cooperation Fund(SZYJY2022008)Higher Education Discipline Innovation Project(B20051)。
文摘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.
基金supported by the National Key Research and Development Program of China (2022YFD1200400)the National Natural Science Foundation of China (32201791)+3 种基金the China Postdoctoral Science Foundation (2020M682440)the Program for Modern Agricultural Industrial Technology System (CARS-12)the Postdoctoral Fellowship Program of CPSF (GZB20230825)the Top-notch Talent Postdoctor Introduction Program of Hubei Province in China.No conflict of interest is declared.
文摘Rapeseed(Brassica napus L.)is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial purposes.Improvements in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield,quality,flowering time,and stress resistance.Moreover,introgression and pyra-miding of key functional genes have greatly accelerated the genetic improvement of important traits.Here we summarize recent progress in rapeseed genomics and genetics,and we discuss effective molecular breeding strategies by exploring thesefindings in rapeseed.These insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture throughout the world.
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
文摘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.
基金the National High Technology Research and Development Program of China(2014AA10A604)the Bill&Melinda Gates Foundation(OPP1130530)+1 种基金the Earmarked Fund for the China Agricultural Research System of China(CARS-01-06)Hubei Special Major Projects for Technological Innovation(2019ABA104,2020ABA016).
文摘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.
基金supported by the National Natural Science Foundation of China (31501791, 31660579, and 31360492)Leading talents in science and technology (2016HA005)funded in part by Beijing Natural Science Foundation (6162017)
文摘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.
基金supported by the National Natural Science Foundation of China(32090064 and 31725021 to F.K.,31930083 to B.L.)the Major Program of Guangdong Basic and Applied Research(2019B030302006 to F.K.and B.L.)funded by the National Key Research and Development Program(2021YFF1001203 to B.L.)。
文摘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.
基金supported by grants from the National Natural Science Foundation of China(31788103)the Chinese Academy of Sciences(XDB27010301)to B.H.
文摘Since the completion of the rice genome sequencing project in 2005,we have entered the era of rice genomics,which is still in its ascendancy.Rice genomics studies can be classified into three stages:structural genomics,functional genomics,and quantitative genomics.Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence.This is fundamental for rice genetics and molecular biology research.Functional genomics aims to decode the functions of rice genes.Quantitative genomics is large-scale sequence-and statistics-based research to define the quantitative traits and genetic features of rice populations.Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding,making rice a good model plant for studying crop sciences.
基金the National Key R&D Program of China(2017YFD0101001)Beijing Munidpal Government Science Foundation(IDHT20170513)+1 种基金Provincial Natural Science Foundation of Hebei for Excellent Young Scholar(C2020204062)Starting Grant from Hebei Agricultural University(YJ201958).
文摘Common wheat(Triticum aestivum L.)is one of the three major food crops in the world;thus,wheat breeding programs are important for world food security.Characterizing the genes that control important agronomic traits and finding new ways to alter them are necessary to improve wheat breeding.Functional genomics and breeding in polyploid wheat has been greatly accelerated by the advent of several powerful tools,especially CRISPR/Cas9 genome editing technology,which allows multiplex genome engineering.Here,we describe the development of CRISPR/Cas9,which has revo-lutionized the field of genome editing.In addition,we emphasize technological breakthroughs(e.g.base editing and prime editing)based on CRISPR/Cas9.We also summarize recent applications and advances in the functional annotation and breeding of wheat,and we introduce the production of CRISPR-edited DNA-free wheat.Combined with other achievements,CRISPR and CRISPR-based genome editing will speed progress in wheat biology and promote sustainable agriculture.
基金supported by the National Natural Science Foundation of China(30970172)the 863 Project Grant2012AA10A304the Program for New Century Excellent Talents in University
文摘With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.
基金supported by the sub‐project of the 863 Program(2011AA100504,2013AA102902)of the Ministry of Science and Technologythe key project of Chinese Universities Scientific Fund+3 种基金Northwest A&F University(ZD2012002)the China 111 Project(B12007),P.R.Chinathe ACIAR Project(CIM/2005/111)of Australia.ALPsupported by the Biotechnology and Biological Sciences Research Council(BBSRC)of the UK under the 20:20 WheatInstitute Strategic Programme
文摘Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes（TILLING）, which combines traditional chemical mutagenesis with high‐throughput genome‐wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or evenallohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small‐scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2（or M3） plants.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010204)to J.X.,the Hebei Natural Science Foundation(C2021205013)"Full-time introduction of high-end talent research project"(2020HBQZYC004)to X.-g.L.+3 种基金the National Natural Science Foundation of China(U22A6009)to J.-m.L.the Research Program for Network Security and Information of the Chinese Academy of Sciences(CAS-WX2021SF-0109)to F.H.and J.X.the National Key Research and Developmental Program of China(2021YFD1201500)to J.X.a China Postdoctoral Science Foundation-funded project(2020M680742)to D.-z.W.
文摘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.
文摘Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces cerevisiae.Here,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing strains.We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase enzyme.We then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered strains.Pathway localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic enzymes.Cofactor-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway flux.Functional genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase enzyme.We then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron levels.The resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.
