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Two ABCI family transporters,OsABCI15 and OsABCI16,are involved in grain-filling in rice

Journal of genetics and genomics 2024年第5期51卷 492-506页

作者： Bin Ma Xiubiao Cao Xiaoyuan Li Zhong Bian Qi-Qi Zhang Zijun Fang Jiyun Liu Qun Li Qiaoquan Liu Lin Zhang Zuhua He Jiangsu Key Laboratory of Crop genomics and molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of plant Functional genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop genetics and Physiology Agricultural College of Yangzhou UniversityYangzhouJiangsu 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhouJiangsu 225009China National Key Laboratory of plant molecular genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China Institute of Biotechnology Hangzhou Academy of Agricultural SciencesHangzhouZhejiang 310024China Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education Yangzhou UniversityYangzhouJiangsu 225009China

Seed development is critical for plant reproduction and crop yield,with panicle seed-setting rate,grain-filling,and grain weight being key seed characteristics for yield ***,few genes are known to regulate grain ***,we identify two adenosine triphosphate(ATP)-binding cassette(ABC)I-type transporter genes,OsABCI15 and OsABCI16,involved in rice *** genes are highly expressed in developing seeds,and their proteins are localized to the plasma membrane and ***,knockout of OsABCI15 and OsABCI16 results in a significant reduction in seed-setting rate,caused predominantly by the severe empty pericarp phenotype,which differs from the previously reported low seed-setting phenotype resulting from failed *** analysis indicates that OsABCI15 and OsABCI16 participate in ion homeostasis and likely export ions between filial tissues and maternal tissues during grain ***,overexpression of OsABCI15 and OsABCI16 enhances the seed-setting rate and grain yield in transgenic plants and decreases ion accumulation in brown ***,the OsABCI15/16 orthologues in maize exhibit a similar role in kernel development,as demonstrated by their disruption in transgenic ***,ourﬁndings reveal the important roles of two ABC transporters in cereal grain filling,highlighting their value in crop yield improvement.

关键词： ABC transporters Rice Grain filling Ion homeostasis Grain yield

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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu Key Laboratory of Crop genetics and Physiology/Key Laboratory of plant Functional genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

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Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang Jiangsu Key Laboratory of Crop genomics and molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of plant Functional genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing Crop improvement molecular design breeding

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Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun Wang Shuangyi Yin Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Zefeng Yang Chenwu Xu Jiangsu Key Laboratory of Crop genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： Maize protein oil starch QTL mapping candidate genes

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OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in Rice

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Rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China Jiangsu Key Laboratory of Crop genetics and Physiology/Key Laboratory of plant Functional genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop genomics and molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

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Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses

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molecular plant 2024年第3期17卷 478-495页

作者： Yeling Zhou Yuzhu Wang Dong Zhang Jiansheng Liang institute of plant and Food Science Department of BiologySchool of Life SciencesSouthern University of Science and Technology(SUSTech)Shenzhen 518055China Key Laboratory of molecular Design for plant Cell Factory of Guangdong Higher Education Institutes Southern University of Science and Technology(SUSTech)Shenzhen 518055China jiangsu Key Laboratory of Crop genetics and Physiology/Co-lnnovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China

ATP-binding cassette(ABC)transporters are integral membrane proteins that have evolved diverse func-tions fulfilled via the transport of various *** Arabidopsis,the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress *** this study,we revealed that two Arabidopsis ABCG transporters,ABCG16 and ABCG25,engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester(ABA-GE),*** first revealed that ABCG16 contributes to osmotic stress tolerance via ABA *** specifically,ABCG16 induces cellular ABA efflux in both yeast and plant *** FRET analysis,we showed that ABCG16 forms oblig-atory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA,undergoing notable conformational ***,we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum(ER)membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco *** specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhib-itory role of these twoABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER *** endomembrane-specific analysis of the FRET signals derived from the homo-or heterodimerized ABcG complexes allowed us to link endomembrane-biased dimerization to the transloca-tion of distinct substrates by ABcG transporters,providing a prototypic framework for understanding the omnipotence of ABcG transporters in plant development and stress responses.

关键词： abscisic acid ABCG transporter dimerization endomembrane substrate selectivity

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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 *** soybean is a photoperiod-sensitive crop,its cultivation and yield are limited by the photoperiodic conditions in the *** contrast to other major crops,soybean has a special plant architecture and a special symbiotic nitrogen fixation system,representing two unique breeding ***,flowering time,plant architecture,and symbiotic nitrogen fixation are three critical or unique yielddetermining *** review summarizes the progress made in our understanding of these three critical yield-determining factors in ***,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

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Modern phenomics to empower holistic crop science, agronomy, and breeding research

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Journal of genetics and genomics 2024年第8期51卷 790-800页

作者： Ni Jiang Xin-Guang Zhu Institute of genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Center of Excellence for molecular plant Sciences Chinese Academy of SciencesShanghai 200032China

Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional *** modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal *** multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop *** challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.

关键词： Crop phenomics High-throughput phenotyping Traits Crop designer breeding Agronomy

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

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

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

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Genetic and lipidomic analyses reveal the key role of lipid metabolism for cold tolerance in maize

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Journal of genetics and genomics 2024年第3期51卷 326-337页

作者： Lei Gao Haifang Jiang Minze Li Danfeng Wang Hongtao Xiang Rong Zeng Limei Chen Xiaoyan Zhang Jianru Zuo Shuhua Yang Yiting Shi State Key Laboratory of plant Environmental Resilience College of Biological SciencesFrontiers Science Center for Molecular Design BreedingCenter for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory of Wheat&Maize Crop Science College of Life SciencesHenan Agricultural UniversityZhengzhouHenan 450002China State Key Laboratory of plant genomics Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Suihua Branch of Heilongjiang Academy of Agricultural Machinery Sciences SuihuaHeilongjiang 152052China

Lipid remodeling is crucial for cold tolerance in ***,the precise alternations of lipidomics during cold responses remain elusive,especially in maize(Zea mays L.).In addition,the key genes responsible for cold tolerance in maize lipid metabolism have not been ***,we integrate lipidomic,transcriptomic,and genetic analysis to determine the profile of lipid remodeling caused by cold *** find that the homeostasis of cellular lipid metabolism is essential for maintaining cold tolerance of ***,we detect 210 lipid species belonging to 13 major classes,covering phospholipids,glycerides,glycolipids,and free fatty *** lipid metabolites undergo specific and selective alterations in response to cold stress,especially mono-/di-unsaturated lysophosphatidic acid,lysophosphatidylcholine,phosphatidylcholine,and phosphatidylinositol,as well as polyunsaturated phosphatidic acid,monogalactosyldiacylglycerol,diacylglycerol,and *** addition,we identify a subset of key enzymes,including ketoacyl-acyl-carrier protein synthase II(KAS II),acyl-carrier protein 2(ACP2),male sterility33(Ms33),and stearoyl-acyl-carrier protein desaturase 2(SAD2)involved in glycerolipid biosynthetic pathways are positive regulators of maize cold *** results reveal a comprehensive lipidomic profile during the cold response of maize and provide genetic resources for enhancing cold tolerance in crops.

关键词： Maize Cold stress Lipid metabolism Transcriptome Lipidomic

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