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Methane Emission from Rice Fields:Necessity for Molecular Approach for Mitigation

Rice science 2024年第2期31卷 159-178页

作者： Sujeevan RAJENDRAN Hyeonseo PARK Jiyoung KIM Soon Ju PARK Dongjin SHIN Jong-Hee LEE Young Hun SONG Nam-Chon PAEK Chul Min KIM department of Horticulture Industry Wonkwang UniversityIksan 54538Korea plant Molecular Biology and biotechnology Research Center Gyeongsang National UniversityJinju 52828Korea department of Southern Area Crop Science National Institute of Crop ScienceMiryang 50424Korea department of Agricultural biotechnology Seoul National UniversitySeoul 08826Korea department of plant Science Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Korea

Anthropogenic methane emissions are a leading cause of the increase in global averagetemperatures,often referred to as global warming.Flooded soils play a significant role in methaneproduction,where the anaerobic conditions promote the production of methane by methanogenicmicroorganisms.Rice fields contribute a considerable portion of agricultural methane emissions,as riceplants provide both factors that enhance and limit methane production.Rice plants harbor both methaneproducingand methane-oxidizing microorganisms.Exudates from rice roots provide source for methaneproduction,while oxygen delivered from the root aerenchyma enhances methane oxidation.Studies haveshown that the diversity of these microorganisms depends on rice cultivars with some genes characterizedas harboring specific groups of microorganisms related to methane emissions.However,there is still aneed for research to determine the balance between methane production and oxidation,as rice plantspossess the ability to regulate net methane production.Various agronomical practices,such as fertilizerand water management,have been employed to mitigate methane emissions.Nevertheless,studiescorrelating agronomic and chemical management of methane with productivity are limited.Moreover,evidences for breeding low-methane-emitting rice varieties are scattered largely due to the absence ofcoordinated breeding programs.Research has indicated that phenotypic characteristics,such as rootbiomass,shoot architecture,and aerenchyma,are highly correlated with methane emissions.This reviewdiscusses available studies that involve the correlation between plant characteristics and methaneemissions.It emphasizes the necessity and importance of breeding low-methane-emitting rice varieties inaddition to existing agronomic,biological,and chemical practices.The review also delves into the idealphenotypic and physiological characteristics of low-methane-emitting rice and potential breeding techniques,drawing from studies conducted with diverse varieties,mutants,and transgenic p

关键词： methane emission rice breeding aerenchyma greenhouse gas radial oxygen loss

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Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

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Oil Crop Science 2024年第2期9卷 69-80页

作者： Farjana Afroz Susmi Tasmina Islam Simi Md Nahid Hasan Md Abdur Rahim department of Genetics and plant breeding Sher-e-Bangla Agricultural UniversityDhaka1207Bangladesh

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health benefits.SHI RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical processes.They also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress responses.Nevertheless,the SRS gene family was not reported in sesame yet.In this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in S.indicum.We identified total six SiSRS genes on seven different linkage groups in the S.indicum genome by comparing with the other species,including the model plant Arabidopsis thaliana.The SiSRS genes showed variation in their structure like2–5 exons and 1–4 introns.Like other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'domains.Then,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of S.indicum,A.thaliana,and some other plant species.The cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1011561)showed the highest 13 and 16 elements for light-and phytohormone-responses whereas,SiSRS1(SIN_1015187)showed the highest 15 elements for stress-response.The ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1009100).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions in.S.indicum.Two SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variable expression patterns between control vs PEG-tre

关键词： SiSRS gene family SHI Transcription factor Characterization Sesamum indicum

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Mucosal immune responses to Ichthyophthirius multifiliis in the ocular mucosa of rainbow trout(Oncorhynchus mykiss,Walbaum),an ancient teleost fish

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Marine Life Science & Technology 2024年第2期6卷 266-279页

作者： Weiguang Kong Guangyi Ding Gaofeng Cheng Peng Yang Zhen Xu Key Laboratory of breeding biotechnology and Sustainable Aquaculture Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China department of Aquatic Animal Medicine College of FisheriesHuazhong Agricultural UniversityWuhan 430070China

The eye,as a specialized visual organ,is directly exposed to the external environment,and,therefore,it faces constant chal-lenges from external pathogenic organisms and toxins.In the ocular mucosa(OM)of mammals,mucosal-associated lymphoid tissues(MALTs)constitute the primary line of defense.However,the immune defense role of the OM remains unknown in aquatic vertebrates.To gain insights into the immune processes within the OM of teleost fish,we developed an infection model of rainbow trout(Oncorhynchus mykiss)OM using a parasite,Ichthyophthirius multifiliis(Ich).Immunofluorescence,qPCR,and H&E staining revealed that Ich successfully infiltrates the OM of rainbow trout,leading to pathological struc-tural changes,as evidenced by A&B staining.Importantly,the qPCR results indicate an up-regulation of immune-related genes following Ich infection in the OM.Moreover,transcriptome analyses were conducted to detect immune responses and impairments in eye function within the OM of rainbow trout with Ich infection.The results of the transcriptome analysis that Ich infection can cause an extensive immune response in the OM,ultimately affecting ocular function.To the best of our knowledge,our findings represent for the first time that the teleost OM could act as an invasion site for parasites and trigger a strong mucosal immune response to parasitic infection.

关键词： Ocular mucosa Mucosal immunity Transcriptome analysis Oncorhynchus mykiss Ichthyophthirius multifiliis

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OsWRKY65 enhances immunity against fungal and bacterial pathogens in rice

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The Crop Journal 2024年第2期12卷 470-481页

作者： Seungmin Son Giha Song Suhyeon Nam Jinjeong Lee Duk-Ju Hwang Eun-Jung Suh Sang Ryeol Park National Institute of Agricultural Sciences Rural Development AdministrationJeonju 54874Republic of Korea department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea department of Crop Science and biotechnology Jeonbuk National UniversityJeonju 54896Republic of Korea

Diverse bacterial and fungal pathogens attack plants,causing biotic stress and severe yield losses globally.These losses are expected to become more serious as climate change improves conditions for many pathogens.Therefore,identifying genes conferring broad-spectrum disease resistance and elucidating their underlying mechanisms provides important resources for plant breeding.WRKY transcription factors affect plant growth and stress responses.However,the functions of many WRKY proteins remain to be elucidated.Here,we demonstrated the role of rice(Oryza sativa)WRKY groupⅢtranscription factor OsWRKY65 in immunity.OsWRKY65 localized to the nucleus and acted as transcriptional repressor.Genetic and molecular functional analyses showed that OsWRKY65 increases resistance to the fungal pathogen Fusarium fujikuroi through downregulation of GA signaling and upregulation of JA signaling.Moreover,OsWRKY65 modulated the expression of the key genes that confer susceptibility or resistance to Xanthomonas oryzae pv.oryzae to enhance immunity against the pathogen.In particular,OsWRKY65directly bound to the promoter region of OsSWEET13 and repressed its expression.Taken together,our findings demonstrate that the OsWRKY65 enhances resistance to fungal and bacterial pathogens in rice.

关键词： Bacterial blight Bakanae disease Broad-spectrum disease resistance Oriza sativa OsWRKY65 Rice

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Differences in leaf cuticular wax induced by whole-genome duplication in autotetraploid sour jujube

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Horticultural plant Journal 2024年第1期10卷 66-76页

作者： Meng Li Chenxing Zhang Lu Hou Xinru Liu Hanqing Zhao Xiaoming Pang Wenhao Bo Yingyue Li National Engineering Research Center of Tree breeding and Ecological Restoration College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China Key Laboratory of Genetics and breeding in Forest Trees and Ornamental plants Ministry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China The Tree and Ornamental plant breeding and biotechnology Laboratory of National Forestry and Grassland Administration Beijing Forestry UniversityBeijing 100083China

Drought-resistant plants exhibit strong water retention capability.In this regard,the autotetraploid sour jujube leaves exhibit better water retention than diploid leaves.Morphological comparisons and physiological comparisons of diploid and autotetraploid leaves showed that the autotetraploid leaves had thicker leaf cuticles and more leaf wax accumulation than the diploid leaves,which could reduce cuticle permeability and improve the drought tolerance of leaves.In this study,the cuticular wax crystalloids on the adaxial and abaxial sides of young and mature jujube leaves were observed in the two ploidy types,and unique cuticular wax crystalloids covering a large area of the cuticle on autotetraploid sour jujube leaves may provide an advantage in reducing leaf non-stomata transpiration and improving plant drought tolerance.Based on the transcriptome,115 differentially expressed genes between diploids and autotetraploids were further analyzed and found to be involved in the accumulation of cuticular wax components,including terpenoids,fatty acids,and lipids,as well as ABC transporter and wax biosynthetic process.Finally,14 genes differentially expressed between glossy autotetraploid leaves and nonglossy diploid leaves,such as LOC107414787,LOC107411574 and LOC107413721,were screened as candidate genes by qRT-PCR analysis.This findings provided insights into how polyploidization improved drought tolerance.

关键词： Autotetraploid Jujube Drought tolerance Cuticular wax RNA-seq

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Callus proliferation-induced hypoxic microenvironment decreases shoot regeneration competence in Arabidopsis

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Molecular plant 2024年第3期17卷 395-408页

作者： Dohee Koo Hong Gil Lee Soon Hyung Bae Kyounghee Lee Pil Joon Seo department of Chemistry Seoul National UniversitySeoul 08826Korea plant Genomics and breeding Institute Seoul National UniversitySeoul 08826Korea Research Institute of Basic Sciences Seoul National UniversitySeoul 08826Korea

plants are aerobic organisms that rely on molecular oxygen for respiratory energy production.Hypoxic conditions,with oxygen levels ranging between 1%and 5%,usually limit aerobic respiration and affect plant growth and development.Here,we demonstrate that the hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regener-ation competence of the callus in Arabidopsis thaliana.We showed that hypoxia-repressed plant regener-ation is mediated by the RELATED TO APETALA2.12(RAP2.12)protein,a memberof the Ethylene Response Factor VIl(ERF-Vll)family.We found that the hypoxia-activated RAP2.12 protein promotes salicylic acid(SA)biosynthesis and defense responses,thereby inhibiting pluripotency acquisition and de novo shoot regeneration in calli.Molecular and genetic analyses revealed that RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2(SID2)gene promoter and activate SA biosynthesis,repressing plant regeneration possibly via a PLETHORA(PLT)-dependent pathway.Consistently,the rap2.12 mutant calli exhibits enhanced shoot regeneration,which is impaired by SA treatment.Taken together,these find-ings uncover that the cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12-SID2 module.

关键词： callus cell proliferation-induced hypoxia SID2 plant regeneration salicylic acid RAP2.12

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Low temperature-mediated repression and far-red light-mediated induction determine morning FLOWERING LOCUS T expression levels

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Journal of Integrative plant Biology 2024年第1期66卷 103-120页

作者： Hayeon Kim Hye Won Kang Dae Yeon Hwang Nayoung Lee Akane Kubota Takato Imaizumi Young Hun Song department of Agricultural biotechnology Seoul National UniversitySeoul 08826Korea department of Biology Ajou UniversitySuwon 16499Korea plant Genomics and breeding Institute Seoul National UniversitySeoul 08826Korea Graduate School of Science and Technology Nara Institute of Science and TechnologyIkomaNara 630‐0192Japan department of Biology University of WashingtonSeattleWA 98195USA Institute of Agricultural Life Sciences Seoul National UniversitySeoul 08826Korea

In order to flower in the appropriate season,plants monitor light and temperature changes and alter downstream pathways that regulate florigen genes such as Arabidopsis(Arabidopsis thaliana)FLOWERING LOCUS T(FT).In Arabidopsis,FT messenger RNA levels peak in the morning and evening under natural long-day conditions(LDs).However,the regulatory mechanisms governing morning FT induction remain poorly understood.The morning FT peak is absent in typical laboratory LDs characterized by high red:far-red light(R:FR)ratios and constant temperatures.Here,we demonstrate that ZEITLUPE(ZTL)interacts with the FT repressors TARGET OF EATs(TOEs),thereby repressing morning FT expression in natural environments.Under LDs with simulated sunlight(R:FR=1.0)and daily temperature cycles,which are natural LD-mimicking environmental conditions,FT transcript levels in the ztl mutant were high specifically in the morning,a pattern that was mirrored in the toe1 toe2 double mutant.Low night-to-morning temperatures increased the inhibitory effect of ZTL on morning FT expression by increasing ZTL protein levels early in the morning.Far-red light counteracted ZTL activity by decreasing its abundance(possibly via phytochrome A(phyA))while increasing GIGANTEA(GI)levels and negatively affecting the formation of the ZTL-GI complex in the morning.Therefore,the phyA-mediated high-irradiance response and GI play pivotal roles in morning FT induction.Our findings suggest that the delicate balance between low temperature-mediated ZTL activity and the far-red light-mediated functions of phyA and GI offers plants flexibility in fine-tuning their flowering time by controlling FT expression in the morning.

关键词： far-red light FLOWERING LOCUS T flowering time GIGANTEA low night-to-morning temperature natural long days phytochrome A red to far-red ratio ZEITLUPE

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Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

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Journal of Integrative plant Biology 2024年第4期66卷 645-659页

作者： Lei Liang Yuancong Wang Yanbin Han Yicong Chen Mengfei Li Yibo Wu Zeyang Ma Han Zhao Rentao Song State Key Laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100091China Institute of Crop Germplasm and biotechnology Jiangsu Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing 210014China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China

ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time.Using MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 families.We also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation population.Using the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter line.The Mu-starter genome also improved the assignment of 117,689(54.5%)germinal insertions.The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions.These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two genomes.As a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

关键词： ChinaMu Mutator MuT-seq PPR gene Zea mays

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Phytochemical analysis, antioxidant, acetylcholinesterase, and α-amylase inhibitors from Hippeastrum hybridum extract

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Journal of Traditional Chinese Medicine 2024年第3期44卷 496-504页

作者： Naila Sher Mushtaq Ahmed Nadia Mushtaq department of biotechnology University of Science and Technology department of Botany University of Science and Technology

OBJECTIVE:To investigate the effects of Hippeastrum hybridum（HH） as a free radical scavenger,and an inhibitor of the two enzymes i-e Alpha-amylase（α-amylase） and acetylcholinesterase（AChE）.METHODS:In this study,HH plant was preliminary analyzed for phytochemical screening and then tested for its antioxidant,anti-α-amylase,and anti-AChE efficiency via standard procedures.RESULTS:Phytochemical analysis shows the existence of different compounds;while Coumarins and quinones were absent.The total phenolic,flavonoid,and tannins content were found to be（78.52±0.69） mg GAE/g,（2.01±0.04） mg RUE/g,and（58.12±0.23） mg TAE/g of plant extract respectively.28.02%±0.02% alkaloid and 2.02%±0.05% saponins were present in the HH extract.The HH extract showed the anti-oxidant property with IC50（50%inhibition） of（151.01±0.13）(HH),（79.01±0.04）(Ascorbic acid) for ferric reducing,（91.48±0.13）(HH),（48.02±0.11）(Ascorbic acid) against Ammonium molybdenum,（156.02±0.31）(HH),（52.38±0.21）(Ascorbic acid) against DPPH,136.01±0.21（HH）,52.02±0.31（Ascorbic acid） against H2O2,and 154.12±0.03（HH）,（40.05±0.15）(Ascorbic acid)μg/mL against ABTS respectively.Statistical analysis indicated that HH caused a competitive type of inhibition of α-amylase(Vmaxremained constant and Km increases from 10.65 to84.37%) while Glucophage caused the un-competitive type of inhibition i-e both Km and Vmaxdecreased from40.49 to 69.15%and 38.86 to 69.61%respectively.The Ki,（inhibition constant）;KI,（dissociation constant）,Km,（Michaelis-Menten constant）,and IC50 were found to be62,364,68.1,and 38.08±0.22 for HH and 12,101.05,195,34.01±0.21 for Glucophage.Similarly,HH causes an anon-competitive type of inhibition of AChE i-e Km remains constant while Vmaxdecreases from 60.5%to74.1%.The calculated Ki,KI,Km,and IC50 were found to be 32,36.2,0.05,and 18.117±0.018.CONCLUSION:From the current results,it is concluded that HH extract contains bioactive compounds,and could be a good alternative to controlling oxidants,Alzheimer‘s and Type-Ⅱ diabetic diseases.

关键词： Hippeastrum hybridum acetylcholinesterase alpha-amylase antioxidant phytochemicals

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Woody plant cell walls:Fundamentals and utilization

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Molecular plant 2024年第1期17卷 112-140页

作者： Wei Li Ying-Chung Jimmy Lin Ying-Lan Chen Chenguang Zhou Shuang Li Nette De Ridder Dyoni M.Oliveira Lanjun Zhange Baocai Zhang Jack P.Wang Changzheng Xu Xiaokang Fu Keming Luo Ai-Min Wu Taku Demura Meng-Zhu Lu Yihua Zhou Laigeng Li Toshiaki Umezawa Wout Boerjan Vincent L.Chiang State Key Laboratory of Tree Genetics and breeding Northeast Forestry UniversityHarbin 150040China department of Life Science National Taiwan UniversityTaipeiTaiwanChina department of biotechnology and Bioindustry Sciences College of Bioscience and BiotechnologyNational Cheng Kung UniversityTainanTaiwanChina department of plant biotechnology and Bioinformatics Ghent UniversityTechnologiepark 719052 GhentBelgium VIB Center for plant Systems Biology Technologiepark 719052 GhentBelgium State Key Laboratory of plant Genomics Insttute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Forest biotechnology Group Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC 27695USA Chongqing Key Laboratory of plant Resource Conservation and Germplasm Innovation Integrative Science Center of Germplasm CreationSchool of Life SciencesSouthwest UniversityChongqing 400715China Guangdong Key Laboratory for Innovative Developmentand Utilization of Forest plant Germplasm College of Forestry and Landscape ArchitecturesSouth China Agricultural UniversityGuangzhou510642China Center for Digital Green-innovation Nara Institute of Science and TechnologykomaNara 630-0192Japan State Key Laboratory of Subtropical Siviculture College of Forestry and BiotechnologyZhejang A&F UniversityHangzhou 311300China CAS Center for Excellence in Molecular plant Sciences Chinese Academy of Sciences300 Fenglin RoadShanghai 200032China Laboratoryof MetabolicScienceofForest plants and Microorganisms Rsearch Institute for Sustainable HumanosphereKyoto UniversityUjiKyoto 611-0011 Japan

Cell walls in plants,particularly forest trees,are the major carbon sink of the terrestrial ecosystem.Chemical and biosynthetic features of plant cell walls were revealed early on,focusing mostly on herbaceous model species.Recent developments in genomics,transcriptomics,epigenomics,transgenesis,and associated analytical techniques are enabling novel insights into formation of woody cell walls.Here,we review multilevel regulation of cell wall biosynthesis in forest tree species.We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees.We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.

关键词： regulation of cell wall formation biosynthesis of cell wall components lignin cellulose hemicellulose cell wall utilization

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