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Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

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Science China(Life Sciences) 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang Xianrui Guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han State key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China key laboratory for plant Genetics and Breeding Sichuan Agricultural UniversityChengdu 611130China Division of Biological Science University of MissouriColumbia 65211-7400USA

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle *** their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across *** functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains *** this study,we comprehensively characterized the sequence composition and organization of rye *** findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed *** systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 *** minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in ***,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in ***,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere *** work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye *** knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

Wide hybridizations reveal the robustness of functional centromeres in Triticum-Aegilops species complex lines

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Journal of Genetics and Genomics 2024年第5期51卷 570-573页

作者： Yuhong Huang Qinghua Shi Chen Zhou Chunhui Wang Yang Liu Congyang Yi Handong Su Fangpu Han State key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Bejing 100049China national key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China

The Triticum-Aegilops complex groups demonstrated high cross-affinity with each other to overcome the barriers of distant hybridization(Loureiro et al.,2023).Distant hybridization involves two distinct yet closely related events:hybridization and genome *** studies have indicated that bursts of transposable elements(TEs)can occur as a consequence or concomitant to hybridization or genome duplication(Parisod et al.,2010).This raises an important scientific question regarding how the TEs-rich centromere region copes with genomic shock(McClintock,1984).The Triticum-Aegilops species complexes,particularly in the F1,So,and subsequent early generations resulting from successive selfcrossing,offer an opportunity to investigate whether the centromere environment undergoes reconstruction and the associated mechanisms that maintain genomic stability.

关键词： centromere Triticum complex

Distinct roles of H3K27me3 and H3K36me3 in vernalization response,maintenance,and resetting in winter wheat

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Science China(Life Sciences) 2024年第10期67卷 2251-2266页

作者： Xuemei Liu Min Deng Bingxin Shi Kehui Zhu Jinchao Chen Shujuan Xu Xiaomin Bie Xiansheng Zhang Xuelei Lin Jun Xiao key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Institute of Science and Technology Austria(ISTA) Klosterneuburg 3400Austria national key laboratory of Wheat Improvement College of Life SciencesShandong Agricultural UniversityTai’an 271018China Centre of Excellence for plant and Microbial Science(CEPAMS) JIC-CASBeijing 100101China

Winter plants rely on vernalization,a crucial process for adapting to cold conditions and ensuring successful ***,understanding the role of histone modifications in guiding the vernalization process in winter wheat remains *** this study,we investigated the transcriptome and chromatin dynamics in the shoot apex throughout the life cycle of winter wheat in the *** core histone modifications,H3K27me3 and H3K36me3,exhibited opposite patterns on the key vernalization gene VERNALIZATION1(VRN1),correlating with its induction during cold ***,the H3K36me3 level remained high at VRN1 after cold exposure,which may maintain its active *** in FERTILIZATION-INDEPENDENT ENDOSPERM(TaFIE)and SET DOMAIN GROUP 8/EARLY FLOWERING IN SHORT DAYS(TaSDG8/TaEFS),components of the writer complex for H3K27me3 and H3K36me3,respectively,affected flowering ***,VRN1 lost its high expression after the cold exposure memory in the absence of *** embryo development,VRN1 was silenced with the removal of active histone modifications in both winter and spring wheat,with selective restoration of H3K27me3 in winter *** mutant of Tafie-cr-87,a component of H3K27me3“writer”complex,did not influence the silence of VRN1during embryo development,but rather attenuated the cold exposure requirement of winter *** gene expression with H3K27me3 and H3K36me3 patterns identified potential regulators of *** study unveils distinct roles of H3K27me3 and H3K36me3 in controlling vernalization response,maintenance,and resetting in winter wheat.

关键词： vernalization H3K27me3 H3K36me3 winter wheat resetting maintenance

Integrative regulatory mechanisms of stomatal movements under changing climate

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Journal of Integrative plant Biology 2024年第3期66卷 368-393页

作者： Jingbo Zhang Xuexue Chen Yajing Song Zhizhong Gong State key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesNational Academy of Agriculture Green DevelopmentChina Agricultural UniversityBeijing 100193China State key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State key laboratory of plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100094China Institute of Life Science and Green Development School of Life SciencesHebei UniversityBaoding 071001China

Global climate change-caused drought stress,high temperatures and other extreme weather profoundly impact plant growth and development,restricting sustainable crop *** cope with various environmental stimuli,plants can optimize the opening and closing of stomata to balance CO_(2)uptake for photosynthesis and water loss from *** cells perceive and integrate various signals to adjust stomatal pores through turgor pressure *** mechanisms and signaling networks underlying the stomatal movements in response to environmental stresses have been extensively studied and *** review focuses on the molecular mechanisms of stomatal movements mediated by abscisic acid,light,CO_(2),reactive oxygen species,pathogens,temperature,and other *** discussed the significance of elucidating the integrative mechanisms that regulate stomatal movements in helping design smart crops with enhanced water use efficiency and resilience in a climate-changing world.

关键词： environmental stress guard cell plant regulatory mechanisms stomatal movements

Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

Establishment of a transformation system in close relatives of wheat under the assistance of TaWOX5

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Journal of Integrative Agriculture 2024年第6期23卷 1839-1849页

作者： Yanan Chang Junxian Liu Chang Liu Huiyun Liu Huali Tang Yuliang Qiu Zhishan Lin Ke Wang Yueming Yan Xingguo Ye Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Beijing key laboratory of plant Gene Resources and Biotechnology for Carbon Reduction and Environment Improvement/College of Life Science Capital Normal UniversityBeijing 100048China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China State key laboratory of plant cell and chromosome engineering/Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China

Species closely related to wheat are important genetic resources for agricultural production,functional genomics studies and wheat *** this study,a wheat gene related to regeneration,TaWOX5,was applied to establish the Agrobacterium-mediated transformation systems of Triticum monococcum,hexaploid triticale,and rye(Secale cereale L.)using their immature *** plants were efficiently *** the transformation process,the Agrobacterium infection efficiency was assessed by histochemical staining forβ-glucuronidase(GUS).Finally,the transgenic nature of regenerated plants was verified by polymerase chain reaction(PCR)-based genotyping for the presence of the GUS and bialaphos resistance(bar)genes,histochemical staining for GUS protein,and the QuickStix strip assay for bar *** transformation efficiency of *** genotype PI428182 was 94.4%;the efficiencies of four hexaploid triticale genotypes Lin456,ZS3297,ZS1257,and ZS3224 were 52.1,41.2,19.4,and 16.0%,respectively;and the transformation efficiency of rye cultivar Lanzhou Heimai was 7.8%.Fluorescence in situ hybridization(FISH)and genomic in situ hybridization(GISH)analyses indicated that the GUS transgenes were integrated into the distal or near centromere(proximal)regions of the chromosomes in transgenic *** and hexaploid triticale *** the transgenic hexaploid triticale plants,the foreign DNA fragment was randomly integrated into the AABB and RR ***,the transgene was almost stably inherited in the next generation by Mendel’s *** findings in this study will promote the genetic improvement of the three plant species for grain or forage production and the improvement of cereal species including wheat for functional genomics studies.

关键词： Triticum monococcum hexaploid triticale rye TaWOX5 Agrobacterium transformation efficiency

Genetic insights into adaptation of alfalfa

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Molecular plant 2024年第8期17卷 1170-1171页

作者： Yafei Guo Lipeng Kang Fei Lu State key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChineseAcademyof SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina CAS-JIC Centre of Excellence for plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Climate change is increasingly affecting agricultural outputs,as evidenced by the changing global temperature and extreme weather events that significantly impact crop yields(Lesk et al.,2016).To address this challenge,there is a growing interest in developing crops that can endure these adverse conditions to ensure food *** examples in nature show how crops have adapted to diverse environments(Gutaker and Purugganan,2023),leaving behind a rich genomic *** genomics has started to provide insights into these adaptive processes from evolutionary and genetic perspectives(Savolainen et al.,2013;Aguirre-Liguori et al.,2021;Sang et al.,2022).Recently,Zhang et al.(Zhang et al.,2024)investigated alfalfa(Medicago sativa ***),known as the"queen of forages,"for its broad *** analyzing whole-genome sequencing data of 702 accessions from 24 Medicago species,this study enriches our understanding of how to develop crops and meet the challenges of climate change.

关键词： sativa crops environments

TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat

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Journal of Integrative plant Biology 2024年第7期66卷 1295-1312页

作者： Dongzhi Wang Xiuxiu Zhang Yuan Cao Aamana Batool Yongxin Xu Yunzhou Qiao Yongpeng Li Hao Wang Xuelei Lin Xiaomin Bie Xiansheng Zhang Ruilian Jing Baodi Dong Yiping Tong Wan Teng Xigang Liu Jun Xiao key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022China key laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTai'an 271018China State key laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Education key laboratory of Molecular and cellular Biology Hebei Research Center of the Basic Discipline of Cell BiologyHebei Collaboration Innovation Center for Cell Signaling and Environmental AdaptationHebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityShijiazhuang 050024China Centre of Excellence for plant and Microbial Science(CEPAMS) JIC‐CASBeijing 100101China

Cultivating high-yield wheat under limited water resources is crucial for sustainable agriculture in semiarid *** water scarcity,plants activate drought response signaling,yet the delicate balance between drought tolerance and development remains *** genome-wide association studies and transcriptome profiling,we identified a wheat atypical basic helix-loop-helix(b HLH)transcription factor(TF),Tab HLH27-A1,as a promising quantitative trait locus candidate for both relative root dry weight and spikelet number per spike in *** HLH27-A1/B1/D1 knockout reduced wheat drought tolerance,yield,and water use efficiency(WUE).Tab HLH27-A1 exhibited rapid induction with polyethylene glycol(PEG)treatment,gradually declining over *** activated stress response genes such as Ta CBL8-B1 and Ta CPI2-A1 while inhibiting root growth genes like Ta SH15-B1 and Ta WRKY70-B1 under short-term PEG *** distinct transcriptional regulation of Tab HLH27-A1 involved diverse interacting factors such as Ta ABI3-D1 and Tab *** variations of Tab HLH27-A1influence its transcriptional responses to drought stress,with Tab HLH27-A1^(Hap-II)associated with stronger drought tolerance,larger root system,more spikelets,and higher WUE in ***,the excellent Tab HLH27-A1^(Hap-II)was selected during the breeding process in China,and introgression of Tab HLH27-A1^(Hap-II)allele improved drought tolerance and grain yield,especially under water-limited *** study highlights Tab HLH27-A1's role in balancing root growth and drought tolerance,providing a genetic manipulation locus for enhancing WUE in wheat.

关键词： drought tolerance GWAS root growth wheat WUE

plant cuticles repress organ initiation and development during skotomorphogenesis in Arabidopsis

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plant Communications 2024年第6期5卷 100-116页

作者： Yuru Ma Wenwen Chang Yongpeng Li Jiahui Xu Yongli Song Xinmiao Yao Lei Wang Yu Sun Lin Guo Hao Zhang Xigang Liu Ministry of Education key laboratory of Molecular and cellular Biology College of Life SciencesHebei Normal UniversityShijiazhuangHebei 050024China Hebei Research Center of the Basic Discipline of cell Biology College of Life SciencesHebei Normal UniversityShijiazhuangHebei 050024China Hebei Collaboration Innovation Center for cell Signaling and Environmental Adaptation College of Life SciencesHebei Normal UniversityShijiazhuangHebei 050024China Hebei key laboratory of Molecular and cellular Biology College of Life SciencesHebei Normal UniversityShijiazhuangHebei 050024China State key laboratory of plant cell and chromosome engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangHebei 050021China

After germination in the dark,plants produce a shoot apical hook and closed cotyledons to protect the quiescent shoot apical meristem(SAM),which is critical for seedling survival during *** factors that coordinate these processes,particularly SAM repression,remain *** cuticles,multilayered structures of lipid components on the outermost surface of the aerial epidermis of all land plants,provide protection against desiccation and external environmental *** and how cuticles regulate plant development are still ***,we demonstrate that mutants of BODYGUARD1(BDG1)and long-chain acyl-CoA synthetase2(LACS2),key genes involved in cutin biosynthesis,produce a short hypocotyl with an opened apical hook and cotyledons in which the SAM is activated during *** signaling represses expression of BDG1 and LACS2,as well as cutin *** analysis revealed that cuticles are critical for skotomorphogenesis,particularly for the development and function of *** and molecular analyses showed that decreased HOOKLESS1 expression results in apical hook opening in the *** hypoxia-induced expression of LITTLE ZIPPER2 at the SAM promotes organ initiation in the mutants,the de-repressed expression of cell-cycle genes and the cytokinin response induce the growth of true *** results reveal previously unrecognized developmental functions of the plant cuticle during skotomorphogenesis and demonstrate a mechanism by which light initiates photomorphogenesis through dynamic regulation of cuticle synthesis to induce coordinated and systemic changes in organ development and growth during the skotomorphogenesis-to-photomorphogenesis transition.

关键词： plant cuticles SAM quiescence organ initiation skotomorphogenesis photomorphogenesis