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From genes to networks: The genetic control of leaf development

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Journal of Integrative Plant Biology 2021年第7期63卷 1181-1196页

作者： Hongfeng Wang Fanjiang Kong Chuanen Zhou The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266101China Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510006China

Substantial diversity exists for both the size andshape of the leaf,the main photosynthetic organofflowering plants.The two major forms of leaf aresimple leaves,in which the leaf blade is undivided,and compound leaves,which comprise severalleaflets.Leaves form at the shoot apical meristemfrom a group of undifferentiated cells,whichfirstestablish polarity,then grow and differentiate.Each of these processes is controlled by a com-bination of transcriptional regulators,microRNAsand phytohormones.The present review docu-ments recent advances in our understanding ofhow these various factors modulate the develop-ment of both simple leaves(focusing mainly on themodel plantArabidopsis thaliana)and compoundleaves(focusing mainly on the model legumespeciesMedicago truncatula).

关键词： compound leaves genetic network leaf develop-ment leaf polarity simple leaves

Mechanisms underlying key agronomic traits and implications for molecular breeding in soybean

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Journal of Genetics and Genomics 2024年第4期51卷 379-393页

作者： Chao Fang Haiping Du Lingshuang Wang Baohui Liu Fanjiang Kong Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouGuangdong 510006China

Soybean(Glycine max[L.]Merr.)is an important crop that provides protein and vegetable oil for human consumption.As soybean is a photoperiod-sensitive crop,its cultivation and yield are limited by the photoperiodic conditions in the field.In contrast to other major crops,soybean has a special plant architecture and a special symbiotic nitrogen fixation system,representing two unique breeding directions.Thus,flowering time,plant architecture,and symbiotic nitrogen fixation are three critical or unique yielddetermining factors.This review summarizes the progress made in our understanding of these three critical yield-determining factors in soybean.Meanwhile,we propose potential research directions to increase soybean production,discuss the application of genomics and genomic-assisted breeding,and explore research directions to address future challenges,particularly those posed by global climate changes.

关键词： Soybean Grain yield Flowering time Plant architecture Nodulation Symbiotic nitrogen fixation Genome study

Understandings and future challenges in soybean functional genomics and molecular breeding

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Journal of Integrative Plant Biology 2023年第2期65卷 468-495页

作者： Haiping Du Chao Fang Yaru Li Fanjiang Kong Baohui Liu Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China

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.

关键词： flowering time functional genomics grain yield nodulation plant architecture response to nutrition deficiency seed quality soybean stress resistance

Molecular mechanisms for the photoperiodic regulation of flowering in soybean

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Journal of Integrative Plant Biology 2021年第6期63卷 981-994页

作者： Xiaoya Lin Baohui Liu James LWeller Jun Abe Fanjiang Kong Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510642China Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbin 150081China School of Natural Sciences University of TasmaniaHobartTasmania 7001Australia Research Faculty of Agriculture Hokkaido UniversitySapporo 060-8589Japan

Photoperiodic flowering is one of the most important factors affecting regional adaptation and yield in soybean(Glycine max). Plant adaptation to long-day conditions at higher latitudes requires early flowering and a reduction or loss of photoperiod sensitivity;adaptation to short-day conditions at lower latitudes involves delayed flowering, which prolongs vegetative growth for maximum yield potential. Due to the influence of numerous major loci and quantitative trait loci(QTLs), soybean has broad adaptability across latitudes. Forward genetic approaches have uncovered the molecular basis for several of these major maturity genes and QTLs. Moreover, the molecular characterization of orthologs of Arabidopsis thaliana flowering genes has enriched our understanding of the photoperiodic flowering pathway in soybean. Building on early insights into the importance of the photoreceptor phytochrome A, several circadian clock components have been integrated into the genetic network controlling flowering in soybean: E1, a repressor of FLOWERING LOCUS T orthologs, plays a central role in this network. Here, we provide an overview of recent progress in elucidating photoperiodic flowering in soybean, how it contributes to our fundamental understanding of flowering time control, and how this information could be used for molecular design and breeding of high-yielding soybean cultivars.

关键词： molecular-designed breeding photoperiodic flowering soybean

Natural variation and artificial selection of photoperiodic flowering genes and their applications in crop adaptation

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aBIOTECH 2021年第2期2卷 156-169页

作者： Xiaoya Lin Chao Fang Baohui Liu Fanjiang Kong Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhouChina

Flowering links vegetative growth and reproductive growth and involves the coordination of local environmental cues and plant genetic information.Appropriate timing of floral initiation and maturation in both wild and cultivated plants is important to their fitness and productivity in a given growth environment.The domestication of plants into crops,and later crop expansion and improvement,has often involved selection for early flowering.In this review,we analyze the basic rules for photoperiodic adaptation in several economically important and/or well-researched crop species.The ancestors of rice(Oryza sativa),maize(Zea mays),soybean(Glycine max),and tomato(Solanum lycopersicum)are short-day plants whose photosensitivity was reduced or lost during domestication and expansion to high-latitude areas.Wheat(Triticum aestivum)and barley(Hordeum vulgare)are long-day crops whose photosensitivity is influenced by both latitude and vernalization type.Here,we summarize recent studies about where these crops were domesticated,how they adapted to photoperiodic conditions as their growing area expanded from domestication locations to modern cultivating regions,and how allelic variants of photoperiodic flowering genes were selected during this process.A deeper understanding of photoperiodic flowering in each crop will enable better molecular design and breeding of high-yielding cultivars suited to particular local environments.

关键词： Adaptation Photoperiodic flowering Crops Artificial selection

GIGANTEA orthologs,E2 members,redundantly determine photoperiodic flowering and yield in soybean

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Journal of Integrative Plant Biology 2023年第1期65卷 188-202页

作者： Lingshuang Wang Haiyang Li Milan He Lidong Dong Zerong Huang Liyu Chen Haiyang Nan Fanjiang Kong Baohui Liu Xiaohui Zhao Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life Sciences Guangzhou UniversityGuangzhou 510006 China National Key Laboratory of Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementJiangsu Collaborative Innovation Center for Modern Crop Production Nanjing Agricultural UniversityNanjing 210095 China

Soybean(Glycine max L.)is a typical photoperiodsensitive crop,such that photoperiod determines its flowering time,maturity,grain yield,and phenological adaptability.During evolution,the soybean genome has undergone two duplication events,resulting in about 75%of all genes being represented by multiple copies,which is associated with rampant gene redundancy.Among duplicated genes,the important soybean maturity gene E2 has two homologs,E2-Like a(E2La)and E2-Like b(E2Lb),which encode orthologs of Arabidopsis GIGANTEA(GI).Although E2 was cloned a decade ago,we still know very little about its contribution to flowering time and even less about the function of its homologs.Here,we generated single and double mutants in E2,E2La,and E2Lb by genome editing and determined that E2 plays major roles in the regulation of flowering time and yield,with the two E2 homologs depending on E2 function.At high latitude regions,e2 single mutants showed earlier flowering and high grain yield.Remarkably,in terms of genetic relationship,genes from the legume-specific transcription factor family E1 were epistatic to E2.We established that E2 and E2-like proteins form homodimers or heterodimers to regulate the transcription of E1 family genes,with the homodimer exerting a greater function than the heterodimers.In addition,we established that the H3 haplotype of E2 is the ancestral allele and is mainly restricted to low latitude regions,from which the loss-of-function alleles of the H1 and H2haplotypes were derived.Furthermore,we demonstrated that the function of the H3 allele is stronger than that of the H1 haplotype in the regulation of flowering time,which has not been shown before.Our findings provide excellent allelic combinations for classical breeding and targeted gene disruption or editing.

关键词： E2 E2-Like flowering time GIGANTEA natural variation redundancy yield

Agronomical selection on loss-of-function of GIGANTEA simultaneously facilitates soybean salt tolerance and early maturity

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Journal of Integrative Plant Biology 2022年第10期64卷 1866-1882页

作者： Lidong Dong Zhihong Hou Haiyang Li Zhaobo Li Chao Fang Lingping kong Yongli Li Hao Du Tai Li Lingshuang Wang Milan He Xiaohui Zhao Qun Cheng Fanjiang Kong Baohui Liu Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou Higher Education Mega Center230 Waihuanxi RoadGuangzhou 510006China The Innovative Academy of Seed Design Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesHarbin 150081China College of Agriculture Heilongjiang Bayi Agricultural UniversityDaqingChina National Key Laboratory of Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjing 210095China College of Agriculture Jilin Agricultural Science and Technology UniversityJilin 132101China

Salt stress and flowering time are major factors limiting geographic adaptation and yield productivity in soybean(Glycine max).Although improving crop salt tolerance and latitude adaptation are essential for efficient agricultural production,whether and how these two traits are integrated remains largely unknown.Here,we used a genome-wide association study to identify a major salt-tolerance locus controlled by E2,an ortholog of Arabidopsis thaliana GIGANTEA(GI).Loss of E2 function not only shortened flowering time and maturity,but also enhanced salt-tolerance in soybean.E2 delayed soybean flowering by enhancing the transcription of the core flowering suppressor gene E1,thereby repressing Flowering Locus T(FT)expression.An E2 knockout mutant e2^(CR) displayed reduced accumulation of reactive oxygen species(ROS)during the response to salt stress by releasing peroxidase,which functions in ROS scavenging to avoid cytotoxicity.Evolutionary and population genetic analyses also suggested that loss-of-function e2 alleles have been artificially selected during breeding for soybean adaptation to high-latitude regions with greater salt stress.Our findings provide insights into the coupled selection for adaptation to both latitude and salt stress in soybean;and offer an ideal target for molecular breeding of early-maturing and salt-tolerant cultivars.

关键词： floweringtime GIGANTEA ROS saltstress soybean

Perspectives on the Application of Genome-Editing Technologies in Crop Breeding

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Molecular Plant 2019年第8期12卷 1047-1059页

作者： Kai Hua Jinshan Zhang Jose Ramon Botella Changle Ma Fanjiang Kong Baohui Liu Jian-Kang Zhu Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China School of Agriculture and Food Sciences University of QueenslandBrisbaneQLD 4072Australia Shandong Provincial Key Lab of Plant Stress School of Life SciencesShandong Normal UniversityJinanChina School of Life Sciences Guangzhou UniversityGuangzhouChina Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIN 47907USA

Most conventional and modern crop-improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of the progenies of multiple generations derived from time-consuming genetic crosses.Genome-editing systems,in contrast,provide the means to rapidly modify genomes in a precise and predictable way,making it possible to introduce improvements directly into elite varieties.Here,we describe the range of applications available to agricultural researchers using existing genome-editing tools.In addition to providing examples of genome-editing applications in crop breeding,we discuss the technical and social challenges faced by breeders using genome-editing tools for crop improvement.

关键词： genome editing crop breeding mutations base editing plants

Soybean AP1 homologs control flowering time and plant height

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Journal of Integrative Plant Biology 2020年第12期62卷 1868-1879页

作者： Liyu Chen Haiyang Nan Lingping kong Lin Yue Hui Yang Qingsong Zhao Chao Fang Haiyang Li Qun Cheng Sijia Lu Fanjiang Kong Baohui Liu Lidong Dong Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510006China The Key Laboratory of Crop Genetics and Breeding of Hebei Institute of Cereal and Oil CropsHebei Academy of Agricultural and ForestrySciencesShijiazhuang 050000China National Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Collaborative Innovation Center for Modern CropProductionNanjing Agricultural UniversityNanjing 210000China The Innovative Academy of Seed Design Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography andAgroecologythe Chinese Academy of SciencesHarbin 150000China

Flowering time and plant height are key agronomic traits that directly affect soybean(Glycine max)yield.APETALA1(AP1)functions as a class A gene in the ABCE model for floral organ development,helping to specify carpel,stamen,petal,and sepal identities.There are four AP1 homologs in soybean,all of which are mainly expressed in the shoot apex.Here,we used clustered regularly interspaced short palindromic repeats(CRISPR)–CRISPR-associated protein 9 technology to generate a homozygous quadruple mutant,gmap1,with loss-of-function mutations in all four GmAP1 genes.Under short-day(SD)conditions,the gmap1 quadruple mutant exhibited delayed flowering,changes in flower morphology,and increased node number and internode length,resulting in plants that were taller than the wild type.Conversely,overexpression of GmAP1a resulted in early flowering and reduced plant height compared to the wild type under SD conditions.The gmap1 mutant and the overexpression lines also exhibited altered expression of several genes related to flowering and gibberellic acid metabolism,thereby providing insight into the role of GmAP1 in the regulatory networks controlling flowering time and plant height in soybean.Increased node number is the trait with the most promise for enhancing soybean pod number and grain yield.Therefore,the mutant alleles of the four AP1 homologs described here will be invaluable for molecular breeding of improved soybean yield.

关键词： soybean breeding height