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Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng Agricultural genomics Institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw *** advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea ***,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress ***,a considerable gap remains between pea functional genomics and molecular *** review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

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

Natural parasites in conjunction with behavioral and color traits explain male agonistic behaviors in a lizard

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Current Zoology 2024年第1期70卷 59-69页

作者： Rodrigo Megia-Palma Dhanashree Paranjpe Robert D.Cooper Pauline Blaimont Barry Sinervo Department of Biomedicine and Biotechnology Parasitology UnitUniversidad de Alcala(UAH)E-28805Alcala de HenaresSpain CIBio Centro de Investigagao em Biodiversidade e Recursos GeneticosInBIO Laboratorio AssociadoCampus de VairaoUniversidade do PortoP-4485-661 VairaoPortugal biopolis program in genomics Biodiversity and Land PlanningCIBIOCampus de VairaoP-4485-661 VairaoPortugal Rupa Rahul Bajaj Center for Environment and Art Empress Botanical GardensKavade MalaPuneIndia Department of Ecology and Evolutionary Biology University of CaliforniaLos AngelesCA 90095USA Department of Biology University of Houston Downtown1Main St.HoustonTX 77002USA Department of Ecology and Evolutionary Biology University of CaliforniaSanta CruzCA 95064USA

Male competition conforms to a cost-benefit model,because while aggression may increase reproductive prospects,it can also increase the risk of *** hypothesize that an additional cost in aggressive males would be an increase in parasite load associated with a high energy investment into sexual *** of these infections,in turn,may downmodulate the level of host aggression via energetic *** staged dyadic male contests in the lab to investigate the relationships of multiple parasites with the agonistic behavior of lizard hosts,Sceloporus *** also included both color and behavioral traits from opponents in the analyses because(1)color patches of lizards may serve as intraspecific signals used by conspecifics to assess the quality of opponents,and(2)contests between male lizards fit classical models of escalated aggression,where lizards increase aggression displays in response to an opponent's *** results conform to our hypothesis because male lizards displayed more pushups when they had more ***,some parasites may modulate the levels of aggression because lizards infected by hematic coccidians performed fewer ***,lizards also displayed fewer pushups when both the chroma and size of the opponent's blue patch were *** results thus also supported the role of the blue patch of *** as a sexual armament,because it contributed to the deterrence of aggression from opponent *** revealed that natural parasitic infections in lizard hosts can contribute to their agonistic *** encourage future studies to account for parasites in behavioral testswithlizards.

关键词： Ixodes pacificus Lankesterella sexual selection social interactions ticks

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

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

Guardian of the rice:Unveiling OsSSP1 for broad-spectrum disease resistance

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Molecular Plant 2024年第7期17卷 996-998页

作者： You-Jin Lim Yong-Hwan Lee Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Republic of Korea interdisciplinary program in Agricultural genomics Center for Fungal Genetic ResourcesPlant Immunity Research Centerand Center for Plant Microbiome ResearchSeoul National UniversitySeoul 08826Republic of Korea

Plants are continuously exposed to numerous biotic stresses throughout their *** arms race-driven coevolution with pathogens,plants have developed sophisticated immune systems,including pathogen-associated molecular pattern(PAMP)-triggered immunity(PTI)and effector-triggered immunity(ETI).PTI is initiated by the binding of danger signals to extracellular membrane-localized receptors calledpattern recognition receptors(PRRs).PTI triggers responses,including reactive oxygen species(ROS)bursts and the expression of defenseassociated ***,pathogens adapted to PTl secrete virulence proteins,effectors,to aid colonization,and ETl is then triggered by the recognition of these effectors by resistance proteins with a nucleotide-binding domain leucinerich repeat receptor(NLR).To circumvent this immune response,pathogens secrete various effectors into the host intracellular region and induce effector-triggered susceptibility(Zhou and Zhang.,2020).Currently,research on plant immunity has been primarily focused on plasma membrane and cytoplasmlocalized proteins,including oligomeric NLRs,resistosomes,and the secretion mechanisms of cytoplasmic effectors.

关键词： immunity resistance Guard

Lack of evidence for germline WWP1 pathogenic variants in gastrointestinal polyposis and other phenotypes suggestive of PTEN-hamartoma-tumor syndrome

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Genes & Diseases 2024年第2期11卷 524-527页

作者： Noemi Gonzalez-Abuin Tirso Pons Teresa Fuster Isabel Quintana Mariona Terradas Gemma Aiza Joan Brunet Gabriel Capellá Heather Hampel Laura Valle Hereditary Cancer program Catalan Institute of OncologyOncobell ProgramIDIBELLHospitalet de LlobregatBarcelona 08908Spain Department of Immunology and Oncology National Center for BiotechnologySpanish National Research Council (CNB-CSIC)Madrid 28049Spain Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) Madrid 28029Spain Catalan Institute of Oncology IDIBGiGirona 17007Spain Division of Clinical Cancer genomics Department of Medical Oncology & Therapeutic ResearchCity of Hope National Cancer CenterDuarteCA 91010USA

Germline activating variants in WWP1,which encodes an E3 ubiquitin ligase that antagonizes PTEN tumor suppressive function,have been proposed as an alternative mechanism of PTEN inactivation in PTEN-hamartoma-tumor syndrome(PHTS)-like patients with wildtype PTEN.1 More specifically,heterozygous,potentially activating wwP1 variants were first identified by Lee et al in patients affected with gastrointestinal oligopolyposis,including adenomatous,hyperplastic/serrated,and hamartomatous polyps,and occasionally with colorectal cancer(Table 1).Subsequently,based on the PHTS phenotypic features,wWP1 mutational screening was performed in patients with thyroid nodules,2 or normocephalic autism spectrum disorder(ASD),3 where germline WWP1 variants were also identified(Table S1).

关键词： WWP1 gastrointestinal polyposis

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

Praseodymium metal nanorods as a 5-fluorouracil carrier

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Journal of Rare Earths 2024年第7期42卷 1328-1336,I0005页

作者： Varnitha Manikantan Govindaraj Sri Varalakshmi Ujma Ashapak Tamboli Archana Sumohan Pillai Aleyamma Alexander Anushka Lucas Bose Allben Akash Israel V.M.V.Enoch Centre for Nanoscience and genomics Karunya Institute of Technology and Sciences(Deemed University)Coimbatore641114Tamil NaduIndia Department of Applied Chemistry Karunya Institute of Technology and Sciences(Deemed University)Coimbatore641114Tamil NaduIndia

Interest in metal nanoparticles as nanoscale drug-carrying vehicles has been *** such an aspect,lanthanide metal nanoparticles are particularly ***,we report praseodymium nanoparticles as a novel anticancer therapeutic transporting *** material was made as a composite with the supramolecular host polymer,poly-β-*** praseodymium nanorods were characterized using standard analytical techniques,including X-ray diffraction(XRD),X-ray photoelectron spectroscopy(XPS),and thermogravimetric analysis(TGA).In addition,they were imaged using transmission electron *** nanostructures are a long rod-shaped material with 2.0±0.1μm in length and 230±10 nm in *** material shows a saturation magnetization value above 30 emu/g with a coercivity value of 130 *** nanocarrier is freighted with the drug 5-fluorouracil,and the encapsulation efficiency is 76.09%.The drug release is continuous from the nanocarrier(polymer-containing praseodymium nanoparticles)and proceeds for above 250 *** in vitro cytotoxicities of the blank nanocarrier and the 5-fluorouracil-loaded one are deduced by testing them on MCF-7 and Vero(non-cancerous)cell *** cytotoxicity on the cancerous cell lines is observed,whereas the non-cancerous cells are *** IC_(50)values on the cell lines are reported.

关键词： Metal nanoparticles Praseodymium Poly-cyclodextrin Drug delivery Anticancer activity Rare earths