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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 *** 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 *** 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 ***,the SRS gene family was not reported in sesame *** 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 *** identified total six SiSRS genes on seven different linkage groups in the *** genome by comparing with the other species,including the model plant Arabidopsis *** SiSRS genes showed variation in their structure like2–5 exons and 1–4 *** other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'***,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of ***,***,and some other plant *** 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 *** 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 *** SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variabl

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

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Rice Heat Tolerance breeding: A Comprehensive Review and Forward Gaze

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Rice science 2024年第4期31卷 375-400,I0022页

作者： Ravindran Lalithambika VISAKH Sreekumar ANAND Sukumaran Nair ARYA Behera SASMITA Uday Chand JHA Rameswar Prasad SAH Radha BEENA Department of genetics and plant breeding College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India Crop Improvement Division Indian Council of Agricultural Research-National Rice Research InstituteCuttackOdisha 7530006India Department of plant breeding and genetics Indian Institute of Pulse ResearchKanpur 208024India Department of plant Physiology College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

关键词： genetic mechanism high-temperature stress molecular breeding genomics selection

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Genetic variation in a heat shock transcription factor modulates cold tolerance in maize

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Molecular plant 2024年第9期17卷 1423-1438页

作者： Lei Gao Lingling Pan Yiting Shi Rong Zeng Minze Li Zhuoyang Li Xuan Zhang Xiaoming Zhao Xinru Gong Wei Huang Xiaohong Yang Jinsheng Lai Jianru Zuo Zhizhong Gong Xiqing Wang Weiwei Jin Zhaobin Dong Shuhua Yang State Key Laboratory of plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesCenter for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijing 100193China State Key Laboratory of Maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingDepartment of Plant Geneticsand BreedingChinaAgricultural UniversityBeijingChina State Key Laboratory of plant Genomics and National plant Gene Research Center Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China

Understanding how maize(Zea mays)responds to cold stress is crucial for facilitating breeding programs of cold-tolerant *** extensive utilization of the genome-wide association study(GWAs)approach for exploring favorable natural alleles associated with maize cold tolerance,few studies have successfully identified candidate genes that contribute to maize cold *** this study,we used a diverse panel of inbred maize lines collected from different germplasm sources to perform a GWAS on var-iations in the relative injured area of maize true leaves during cold stress-a trait very closely correlated with maize cold *** identified HsF21,which encodes a B-class heat shock transcription factor(HSF)that positively regulates cold tolerance at both the seedling and germination *** varia-tions in the promoter of the cold-tolerant HSF21Hap1 allele led to increased HSF21 expression under cold stress by inhibiting binding of the basic leucine zipper bziP68 transcription factor,a negative regulator of cold *** integrating transcriptome deep sequencing,DNA affinity purification sequencing,and targeted lipidomic analysis,we revealed the function of HsF21 in regulating lipid metabolism homeo-stasis to modulate cold tolerance in *** addition,we found that HsF21 confers maize cold tolerance without incurring yield ***,this study establishes HsF21 as a key regulator that en-hances cold tolerance in maize,providing valuable genetic resources for breeding of cold-tolerant maize varieties.

关键词： heat shock factor HSF21 cold tolerance natural variation bZiP68 lipid metabolism maize

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Emerging technological developments to address pest resistance in Bt cotton

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Journal of Cotton Research 2024年第3期7卷 318-333页

作者： NAGARAJ Selvarani RAJASEKARAN Ravikesavan PALANIAPPAN Jayamani RANGASAMY Selvakumar NARAYANASAMY Chitra NARAYANAN Manikanda Booapathi Department of genetics and plant breeding Centre for Plant Breeding and Genetics(CPBG)Tamil Nadu Agricultural University(TNAU)Coimbatore 641003India Centre for plant breeding and genetics TNAUCoimbatore 641003India Department of Pulses CPBGTNAUCoimbatore 641003India Research and Development Centre Rasi Seeds(P)Ltd.SalemAttur 636102India Department of Cotton TNAUCoimbatore 641003India Department of plant Biotechnology Centre for Plant Molecular Biology and Biotechnology(CPMB&B)TNAUCoimbatore 641003India

Cotton plays a crucial role in shaping Indian economy and rural *** cotton crop is prone to numerous insect pests,necessitating insecticidal application,which increases production *** advent of the expression of Bacillus thuringiensis(Bt)insecticidal protein in cotton has significantly reduced the burden of pest without compromising environmental or human *** the introduction of transgenic cotton,the cultivated area expanded to 22 million hectares,with a 64% increase in adoption by farmers ***,Bt cotton accounts for 93% of the cultivated cotton area in ***,extensive use of Bt cotton has accelerated resistance development in pests like the pink ***,the overreliance on Bt cotton has reduced the use of broad-spectrum pesticides,favouring the emergence of secondary pests with significant *** emphasizes the urgent necessity for developing novel pest management *** high-dose and refuge strategy was initially effective for managing pest resistance in Bt cotton,but its implementation in India faced challenges due to misunderstandings about the use of non-Bt refuge *** gene pyramiding was introduced as a solution,combining mono toxin also led to instances of ***,there is a need for further exploration of biotechnological approaches to manage insect resistance in Bt *** biotechnological strategies,such as sterile insect release,RNA interference(RNAi)-mediated gene silencing,stacking Bt with RNAi,and genome editing using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein(CRISPR-Cas),offer promising tools for identifying and managing resistance genes in ***,CRISPR-mediated gene drives and the development of novel biopesticides present potential avenues for effective pest management in cotton *** innovative approaches could significantly enhance the sustainability and efficacy of

关键词： Bt Cotton Gene pyramiding RNAi Modified toxin Genome editing plant derived insecticidal protein Gene drive

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How we look:European wild moufon and feral domestic sheep hybrids

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Current Zoology 2024年第3期70卷 298-303页

作者： Nikica Šprem Elena Buzan Toni Safner faculty of Agriculture Department of FisheriesApicultureWildlife Management and Special ZoologyUniversity of ZagrebSvetošimunska cesta 2510000 ZagrebCroatia faculty of Mathematics Natural Sciences and Information TechnologiesUniversity of PrimorskaGlagoljaška 86000 KoperSlovenia faculty of Environmental Protection Trg mladosti 73320 VelenjeSlovenia faculty of Agriculture Department of Plant BreedingGenetics and BiometricsUniversity of ZagrebSvetošimunska cesta 2510000 ZagrebCroatia Centre of Excellence for Biodiversity and Molecular plant breeding(CroP-BioDiv) Svetošimunska cesta 2510000 ZagrebCroatia

Hybridization between wild animals and feral individuals from closely related domestic species can occur when they share the same *** events are generally regarded as a threat to the genetic integrity and survival of established wild *** aim of this study is to confrm a hybridization between European moufon and feral sheep on the Adriatic island Dugi Otok,where a group of individuals phenotypically indicative of a possible introgression was *** an ovine medium-density SNP array genotypes,we provided genetic evidence of recent gene admixture between the two *** ADMIXTURE analysis suggests that two hybrid individuals had 82.2%and 94.1%of their ancestry attributable to feral sheep,respectively,with the rest of the moufon in *** analysis estimated the combined probabilities for the putative hybrid individuals belonging to one of the hybrid classes at 87.0%and 90.1%,*** main phenotypic differences in the hybrids were observed in the shape of the horns,a stronger horn circumference than in the moufon and weaker than for the sheep,pronounced horn rings,a shorter tail,and intermediate *** therefore recommend constant monitoring of the purity of the moufon population to maintain its genetic *** addition,all feral sheep should be removed from the wild,and released sheep raised in semi-wild conditions should be better controlled.

关键词： crossbreeding gene introgression livestock Ovis gmelinimusimon SNPs

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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

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Leveraging the potential of big genomic and phenotypic data for genome-wide association mapping in wheat

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The Crop Journal 2024年第3期12卷 803-813页

作者： Moritz Lell Yusheng Zhao Jochen C.Reif Leibniz Institute of plant genetics and Crop plant Research(IPK) Corrensstraße 3D-06466 SeelandGermany

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant *** number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly *** these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of *** this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading *** explored strategies for integrating these data and subsequently the resulting potential for *** interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic *** this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our *** to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental ***,the predictive power based on the marker-trait associations of the integrated data set was higher across data ***,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in *** results encourage further efforts to standardize and share data in the plant breeding community.

关键词： Big Data Genome-wide association study Data integration Genomic prediction Wheat

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ATM is a Prognostic Biomarker of Survival in Head and Neck Squamous Cell Carcinoma Patients

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Proceedings of Anticancer Research 2024年第5期8卷 121-135页

作者： Muhammad Umair Abid Department of plant breeding and genetics University of Agriculture FaisalabadFaisalabadPakistan

This review examines the role of ATM expression in head and neck squamous cell carcinoma(HNSCC).Analysis revealed significant overexpression of ATM in HNSCC cells compared to normal control samples,suggesting its involvement in cancer *** expression was notably upregulated across various clinical parameters,including different stages of cancer,racial groups,genders,and age groups,highlighting its role in cancer *** using the GEPIA2 tool confirmed strong ATM expression throughout all four stages of HNSCC,with the highest levels in stage II and the lowest in stage *** methylation analysis of ATM showed distinct patterns across different demographics and cancer stages,reinforcing its *** study also explored the relationship between ATM expression and patient outcomes using the KM plotter tool,finding that high ATM expression was associated with better overall survival(OS),while low ATM expression correlated with better disease-free survival(DFS).Genetic mutation analysis via cBioPortal identified minimal ATM mutations in HNSCC,including in-frame,splice,truncating,and missense mutations,suggesting their role in ATM *** STRING tool was used to construct a protein-protein interaction(PPI)network,revealing that the ATM gene interacts with ten key genes(NBN,ATR,CHEK2,MDC1,MSH2,MSH6,MRE11,TP53,TP53BP1,BRCA1),indicating its involvement in various biological *** annotation of differentially expressed genes(DEGs)through the DAVID web server revealed their participation in critical biological processes,including double-strand break repair,cellular response to DNA damage,and DNA damage *** pathway analysis further linked DEGs to cellular senescence,platinum drug resistance,homologous recombination,p53 signaling,and the cell cycle,underscoring ATM’s multifaceted role in HNSCC.

关键词： Head and neck squamous cell carcinoma Diagnosis Treatment Biomarker

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

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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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Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize

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Molecular plant 2024年第5期17卷 788-806页

作者： Tao Yang Yunqin Huang Longyu Liao Shanshan Wang Haoyu Zhang Jingying Pan Yongcai Huang Xiaoling Li Di Chen Tao Liu Xiaoduo Lu Yongrui Wu State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130SichuanChina National Key Laboratory of plant Molecular genetics CAS Center for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China Institute of Molecular breeding for Maize Qilu Normal UniversityJinanChina

During maize endosperm filling,sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this ***,the molecular mechanisms underlying sucrose and endosperm filling are poorly *** this study,we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2(O2),coordinating with storage-reserve *** showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation,but sucrose can release this *** assays revealed that SnRK1a1 phosphorylates O2 at serine 41(S41),negatively affecting its protein stability and transactivation *** observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves,while overexpression of SnRK1a1 causes the opposite *** of the native O2(O2-OE),phospho-dead(O2-SA),and phospho-mimetic(O2-SD)variants all increased 100-kernel *** O2-SA seeds exhibit smaller kernel size,they have higher accumulation of starch and proteins,resulting in larger vitreous endosperm and increased test weight.O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight.O2-OE seeds show elevated kernel dimensions and nutrient storage,like a mixture of O2-SA and O2-SD ***,our study discovers a novel regulatory mechanism of maize endosperm *** of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.

关键词： maize Opaque2 SnRK1 endosperm phosphorylation sucrose

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