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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

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

Oil crops: From the classical traits to genetic improvement

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Journal of Integrative Plant Biology 2021年第6期63卷 979-980页

作者： Zhicheng Dong Zhixi Tian baohui Liu Guangzhou Key Laboratory of Crop Gene Editing Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510405China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignThe Chinese Academy of SciencesBeijing 100101China

Soybean, oilseed rape, peanut, and so on, are importantresources of vegetable oil for human beings. Cultivation and production of these oil crops are expected to increase due to continuous population growth, which pos... 详细信息

关键词： crops Cultivation resources

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

The soybean-specific maturity gene E1 family of floral repressors controls night-break responses through down-regulation of FLOWERING LOCUS T orthologs

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The soybean-specific maturity gene E1 family of floral repre...

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

2016年全国植物生物学大会

作者： baohui Liu Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of Sciences

Photoperiodism is a rhythmic change of sensitivity to light,which helps plants to adjust flowering time accor to seasonal changes in day length and to adapt to growing conditions at various latitudes. To reveal the molecular basis of photoperiod is min soybean(Glycine max),a facultative short-day plant,we analyzed the transcriptional profiles of the maturity gene E1 family and two FLOWERING LOCUS T(FT) orthologs(FT2a and FT5a). E1,a repressor for FT2 a and FT5 a,and its two homologs,E1-like-a(E1La) and E1 Lb,exhibited two peaks of expression in long days. Using two different approaches(experiments with transition between light and dark phases and night-break experiments),we revealed that the E1 family genes were expressed only during light periods and that their induction after dawn in long days required a period of light before dusk the previous day. In the cultivar Toyomusume,which lacks the E1 gene,virus-induced silencing of E1 La and E1 Lb up-regulated the expression of FT2 a and FT5 a and led to early flowering. Therefore,E1,E1 La,and E1 Lb function similarly in flowering. Regulation of E1 and E1 L expression by light was under the control of E3 and E4,which encode phytochrome A proteins. Our data suggest that phytochrome A-mediated transcriptional induction of E1 and its homologs by light plays a critical role in photoperiodic induction of flowering in soybean.

关键词： photoperiodism soybean flowering E1 gene

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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

Antifertility effects of levonorgestrel,quinestrol,and their mixture(EP-1)on plateau zokor in the Qinghai–Tibetan Plateau

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Integrative Zoology 2022年第6期17卷 1002-1016页

作者： Yukun KANG Yuchen TAN Chan WANG baohui YAO Kang AN Ming liu Junhu SU College of Grassland Science Key Laboratory of Grassland Ecosystem(Ministry of Education)Gansu Agricultural UniversityLanzhouChina Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity Gansu Agricultural UniversityLanzhouChina International Society of Zoological Sciences BeijingChina

The plateau zokor(Eospalax baileyi)is a key species in the Qinghai-Tibetan Plateau ecosystem,and fertility control could be an ideal approach to manage populations of this subterranean species.In this laboratory study,we explored the effects of the mixture of levonorgestrel and quinestrol(EP-1,1:2),quinestrol(E),and levonorgestrel(P)on the reproductive status of plateau zokors.Groups of 5 animals of each sex were treated with different concentrations of EP-1(1,5,and 10 mg/kg),E(0.33,3.3,and 6.6 mg/kg),and P(0.67,3.35,and 6.7 mg/kg)by oral gavage over 7 successive days and killed on day 15.Body mass reduction was observed in the EP-1 and E groups.EP-1 and E signiﬁcantly reduced the weight of testis and epididymis at 10 and 3.3 mg/kg,respectively.Sperm count and motility were signiﬁcantly reduced by 5 mg/kg EP-1 and 0.33 mg/kg E.The levels of serum testosterone,estradiol,luteinizing hormone,and follicle stimulating hormone were signiﬁcantly reduced by 5 mg/kg EP-1 and 3.3 mg/kg E.EP-1 and E signiﬁcantly increased the uterine and ovarian weights at 10 and 3.3 mg/kg,respectively.In the plateau zokors,treatment with P had no inﬂuence on the reproductive status.These data demonstrate that EP-1 and E have an inhibitory effect on a range of reproductive parameters in the plateau zokors.Further assessment is required to determine the effects on breeding and recruitment in enclosure orﬁeld experiments.

关键词： EP-1 fertility inhibition levonorgestrel quinestrol subterranean rodent