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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk Jan van Dijk State Key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice

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Journal of Integrative Plant Biology 2024年第4期66卷 731-748页

作者： Peng Zeng Ting Xie Jiaxin Shen Taokai Liang Lu Yin Kexin Liu Ying He Mingming Chen Haijuan Tang Sunlu Chen Sergey Shabala Hongsheng Zhang Jinping Cheng National Key laboratory of Crop Genetics&Germplasm Enhancement and Utilization Jiangsu Collaborative Innovation Center for Modern Crop ProductionHainan Yazhou Bay Seed LabJiangsu Province Engineering Research Center of Seed Industry Science and TechnologyNanjing Agricultural UniversityNanjing 210095China International Research Center for Environmental Membrane Biology Foshan UniversityFoshan 528000China School of Biological Sciences University of Western AustraliaCrawley WA 6009Australia

Soil salinity has a major impact on rice seed germination,severely limiting rice ***,a rice germination defective mutant under salt stress(gdss)was identified by using chemical *** GDSS gene was detected via MutMap and shown to encode potassium transporter *** analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt ***9 is highly expressed in germinating seed *** contents and non-invasive micro-test technology results showed that OsHAK9 restricted K^(+)efflux in salt-exposed germinating seeds for the balance of K^(+)/Na^(+).Disruption of OsHAK9 significantly reduced gibberellin 4(GA4)levels,and the germination defective phenotype of oshak9a was partly rescued by exogenous GA_(3)treatment under salt *** sequencing(RNA-seq)and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress,and the expression of OsGA2ox7 was significantly inhibited by salt *** mutants of OsGA2ox7 created using clustered,regularly interspaced,short palindromic repeat(CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt ***,our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7,which provides a novel clue about the relationship between GA and OsHAKs in rice.

关键词： GDSS gibberellins potassium transporter rice salt tolerance seed germination

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Silencing transformer and transformer-2 in Zeugodacus cucurbitae causes defective sex determination with inviability of most pseudomales

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Journal of Integrative Agriculture 2024年第3期23卷 938-947页

作者： Qin Ma Zizhen Fan Ping Wang Siya Ma Jian Wen Fengqin Cao Xianwu Lin Rihui Yan Key laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests of Ministry of Education School of Plant ProtectionHainan UniversityHaikou 570228China School of Life Sciences HainanUniversityHaikou 570228China Hainan Yazhou Bay seed lab Sanya 572000China

transformer is a switch gene for sex determination in many insects, which cooperates with transformer-2 that is expressed in both sexes to regulate female differentiation, particularly in dipterans. Zeugodacus cucurbitae(Coquillett) is a very destructive pest worldwide, however, its sex determination pathway remains largely uncharacterized. Here, we show that the female sex ratio is sharply reduced with knockdown of either transformer or transformer-2 by RNA interference in early embryos of Z. cucurbitae. Most of the males grown from the embryos with transient transformer and transformer-2 suppression mated with wild-type females and produced mixed sex progeny, with one exception that produced only female progeny, and all of the few remaining males failed to mate with wild-type females and produced no progeny. The exceptional male and those males with mating failure were XX pseudomales as determined by the detection of Y chromosome-linked Maleness-on-the-Y, indicating that most XX pseudomales are not viable. The phenotypes of transformer and transformer-2 suggest that they play a key role in regulating sex determination and are required for female sexual development of Z. cucurbitae. Our results will be beneficial to the understanding of sex determination in Z. cucurbitae and can facilitate the development of genetic sexing strains for its biological control.

关键词： Zeugodacus cucurbitae transformer transformer-2 sex determination RNA interference biological control

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Engineering high amylose and resistant starch in maize by CRISPR/Cas9-mediated editing of starch branching enzymes

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The Crop Journal 2024年第4期12卷 1252-1258页

作者： Mingzheng Ma Shanqiu Sun Jinjie Zhu Xiantao Qi Gaoke Li Jianguang Hu Chuanxiao Xie Changlin Liu State Key laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Hainan Yazhou Bay seed lab Sanya 572024HainanChina Anhui Agricultural University Hefei 230036AnhuiChina Crops Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

To improve the amylose content(AC)and resistant starch content(RSC)of maize kernel starch,we employed the CRISPR/Cas9 system to create mutants of starch branching enzyme I(SBEI)and starch branching enzyme IIb(SBEIIb).A frameshift mutation in SBEI(E1,a nucleotide insertion in exon 6)led to plants with higher RSC(1.07%),lower hundred-kernel weight(HKW,24.71±0.14 g),and lower plant height(PH,218.50±9.42 cm)compared to the wild type(WT).Like the WT,E1 kernel starch had irregular,polygonal shapes with sharp edges.A frameshift mutation in SBEIIb(E2,a four-nucleotide deletion in exon 8)led to higher AC(53.48%)and higher RSC(26.93%)than that for the WT.E2 kernel starch was significantly different from the WT regarding granule morphology,chain length distribution pattern,X-ray diffraction pattern,and thermal characteristics;the starch granules were more irregular in shape and comprised typical B-type *** SBEI and SBEIIb(E12)had a synergistic effect on RSC,HKW,PH,starch properties,and starch biosynthesis-associated gene ***,SS1,SSIIa,SSIIIa,and SSIIIb were upregulated in E12 endosperm compared to WT *** study lays the foundation for rapidly improving the starch properties of elite maize lines.

关键词： Maize Gene editing Starch branching enzyme I Starch branching enzyme IIb

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Fusion of a rice endogenous N-methylpurine DNA glycosylase to a plant adenine base transition editor ABE8e enables A-toK base editing in rice plants

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aBIOTECH 2024年第2期5卷 127-139页

作者： Yucai Li Shaoya Li Chenfei Li Chen Zhang Lei Yan Jingying Li Yubing He Yan Guo Lanqin Xia Institute of Crop Sciences(ICS) Chinese Academy of Agricultural Sciences(CAAS)Beijing 100081China State Key laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China Hainan Yazhou Bay seed laboratory/National Nanfan Research Institute(Sanya) CAASSanya 572024China

Engineering of a new type of plant base editor for simultaneous adenine transition and transversion within the editing window will greatly expand the scope and potential of base editing in directed evolution and crop ***,we isolated a rice endogenous hypoxanthine excision protein,N-methylpurine DNA glycosylase(OsMPG),and engineered two plant A-to-K(K=G or T)base editors,rAKBE01 and rAKBE02,for simultaneous adenine transition and transversion base editing in rice by fusing OsMPG or its mutant mOsMPG to a plant adenine transition base editor,*** further coupled either OsMPG or mOsMPG with a transactivation factor VP64 to generate rAKBE03 and rAKBE04,*** these four rAKBEs,at five endogenous loci in rice protoplasts,indicated that rAKBE03 and rAKBE04 enabled higher levels of A-to-G base transitions when compared to ABE8e and ***,whereas rAKBE01 only enabled A-to-C/T editing at one endogenous locus,in comparison with rAKBE02 and rAKBE03,rAKBE04 could significantly improve the A-to-C/T base transversion efficiencies by up to 6.57-and 1.75-fold in the rice protoplasts,***,although no stable lines with A-to-C transversion were induced by rAKBE01 and rAKBE04,rAKBE04 could enable simultaneous A-to-G and A-to-T transition and transversion base editing,at all the five target loci,with the efficiencies of A-to-G transition and A-to-T transversion editing ranging from 70.97 to 92.31%and 1.67 to 4.84%in rice stable lines,***,these rAKBEs enable different portfolios of editing products and,thus,now expands the potential of base editing in diverse application scenario for crop improvement.

关键词： Rice(Oryza sativa L) Rice N-methylpurine DNA glycosylase(OsMPG) A-to-K base editor(AKBE) Transactivation module VP64

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Integrating phosphorus management and cropping technology for sustainable maize production

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Journal of Integrative Agriculture 2024年第4期23卷 1369-1380页

作者： Haiqing Gong Yue Xiang Jiechen Wu Laichao Luo Xiaohui Chen Xiaoqiang Jiao Chen Chen State Key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesCollege of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China Department of Sustainable Development Environmental Science and Engineering(SEED)KTH Royal Institute of TechnologyStockholm SE-10044Sweden Anhui Province Key lab of Farmland Ecological Conservation and Pollution Prevention School of Resources and EnvironmentAnhui Agricultural UniversityHefei 230036China Ministry of Education Key laboratory for Biodiversity Science and Ecological Engineering National Observations and Research Station for Wetland Ecosystems of the Yangtze EstuaryInstitute of Biodiversity Science and Institute of Eco-ChongmingCollege of Life SciencesFudan UniversityShanghai 200438China

Achieving high maize yields and efficient phosphorus(P)use with limited environmental impacts is one of the greatest challenges in sustainable maize *** plant density is considered an effective approach for achieving high maize ***,the low mobility of P in soils and the scarcity of natural P resources have hindered the development of methods that can simultaneously optimize P use and mitigate the P-related environmental footprint at high plant *** this study,meta-analysis and substance flow analysis were conducted to evaluate the effects of different types of mineral P fertilizer on maize yield at varying plant densities and assess the flow of P from rock phosphate mining to P fertilizer use for maize production in China.A significantly higher yield was obtained at higher plant densities than at lower plant *** application of single superphosphate,triple super-phosphate,and calcium magnesium phosphate at high plant densities resulted in higher yields and a smaller environmental footprint than the application of diammonium phosphate and monoammonium *** scenario analyses suggest that combining the optimal P type and application rate with a high plant density could increase maize yield by 22%.Further,the P resource use efficiency throughout the P supply chain increased by 39%,whereas the P-related environmental footprint decreased by 33%.Thus,simultaneously optimizing the P type and application rate at high plant densities achieved multiple objectives during maize production,indicating that combining P management with cropping techniques is a practical approach to sustainable maize *** findings offer strategic,synergistic options for achieving sustainable agricultural development.

关键词： maize plant density mineral phosphorus fertilizer meta-analysis substance flow analysis

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Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance

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Science China(Life Sciences) 2024年第1期67卷 149-160页

作者： Haofei Luo Xiaofei Wang Changqing You Xuedan Wu Duofeng Pan Zhiyao Lv Tong Li Dongmei Zhang Zhongbao Shen Xiaodong Zhang Guodao Liu Kaixuan He Qingtong Ye Yajun Jia Qinghua Zhao Xian Deng Xiaofeng Cao Xianwei Song Gai Huang State Key laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay seed lab Sanya 572025China University of Chinese Academy of Sciences Beijing 100049China Institute of Forage and Grassland Sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China Shandong Academy of Agricultural Sciences Jinan 250100China National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land Dongying 257345China Shandong Green Manure Ecological Technology Co. LtdDongying 257345China State Key laboratory of Tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal ***,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline *** understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of *** spanning~2,087 *** assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric *** genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years *** genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A *** further identified four specific alkali-induced phosphate transporter genes in ***;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline *** work highlights the significance of *** as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

关键词： Sesbania cannabina alkaline stress telomere-to-telomere genome legume green manure phosphate transporter allotetraploid

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Can DyeCycling break the photobleaching limit in single-molecule FRET?

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Nano Research 2022年第11期15卷 9818-9830页

作者： Benjamin Vermeer Sonja Schmid NanoDynamicslab Laboratory of BiophysicsWageningen UniversityStippeneng 46708WE WageningenThe Netherlands

Biomolecular systems,such as proteins,crucially rely on dynamic processes at the *** biomolecular nanodynamics is therefore key to obtaining a mechanistic understanding of the energies and molecular driving forces that controlbiomolecular ***-molecule fluorescence resonance energy transfer(smFRET)is a powerful technique to observe inreal-time how a single biomolecule proceeds through its functional cycle involving a sequence of distinct structural ***,this technique is fundamentally limited by irreversible photobleaching,causing the untimely end of the experiment andthus,a narrow temporal bandwidth of≤3 orders of ***,we introduce“DyeCycling”,a measurement scheme withwhich we aim to break the photobleaching limit in *** introduce the concept of spontaneous dye replacement bysimulations,and as an experimental proof-of-concept,we demonstrate the intermittent observation of a single biomolecule forone hour with a time resolution of ***,DyeCycling can provide>100-fold more information per singlemolecule than conventional *** discuss the experimental implementation of DyeCycling,its current and fundamentallimitations,and specific biological use *** its general simplicity and versatility,DyeCycling has the potential torevolutionize the field of time-resolved smFRET,where it may serve to unravel a wealth of biomolecular dynamics by bridgingfrom milliseconds to the hour range.

关键词： biomolecular dynamics single-molecule fluorescence resonance energy transfer(smFRET) photobleaching conformational changes single-molecule kinetics

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Comparative analysis of SIMILAR to RCD ONE(SRO)family from tetraploid cotton species and their diploid progenitors depict their significance in cotton growth and development

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Journal of Cotton Research 2024年第1期7卷 45-57页

作者： SHABAN Muhammad TABASSUM Riaz RANA Iqrar Ahmad ATIF Rana Muhammad AZMAT Muhammad Abubakkar IQBAL Zubair MAJEED Sajid AZHAR Muhammad Tehseen Department of Plant Breeding and Genetics University of Agriculture FaisalabadSub-Campus BurewalaVehari 61010Pakistan Department of Chemistry and Biochemistry University of AgricultureFaisalabad 38400Pakistan Centre of Agricultural Biochemistry and Biotechnology University of AgricultureFaisalabad 38400Pakistan Department of Plant Breeding and Genetics University of AgricultureFaisalabad 38400Pakistan Precision Agriculture and Analytics lab National Centre in Big Data and Cloud ComputingCentre for Advanced Studies in Agriculture and Food SecurityUniversity of Agriculture FaisalabadFaisalabad 38400Pakistan Department of Plant Pathology University of CaliforniaDavisCA 95616USA State Key laboratory of Cotton Biology Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan 455000China Federal seed Certification and Registration Department Ministry of National Food Security and ResearchIslamabad 44090Pakistan School of Agriculture Sciences Zhengzhou UniversityZhengzhou 450000China

Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental ***,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so *** A total of 36 SRO genes were identified from four cotton *** analysis divided these genes into three groups with distinct *** and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,*** duplication analysis revealed the presence of six duplicated gene pairs among GhSRO *** promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and *** miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO ***-specific expression profiling demonstrated the roles of GhSRO genes in one or more *** addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental *** The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.

关键词： Cotton SRO miRNAs Gene duplications Gene expression Ovule development

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DNA methylation in poultry:a review

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Journal of Animal Science and Biotechnology 2024年第2期15卷 509-518页

作者： Xing Ju Zhijun Wang Danfeng Cai Semiu Folaniyi Bello Qinghua Nie State Key laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong Provincial Key lab of Agro‑Animal Genomics and Molecular Breeding and Key lab of Chicken Genetics Breeding and ReproductionMinistry of AgricultureGuangzhouGuangdong 510642China College of Animal Science and Technology Zhejiang Agriculture and Forestry University666 Wusu RoadLin’an 311300China

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome *** DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological *** paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

关键词： CpG islands Differentially methylated genes Differentially methylated regions DNA methylation Poultry

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