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LociScan,a tool for screening genetic marker combinations for plant variety discrimination

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The Crop Journal 2024年第2期12卷 583-593页

作者： Yang Yang Hongli Tian Hongmei Yi Zi Shi Lu Wang Yaming Fan Fengge Wang Jiuran Zhao Beijing Key Laboratory of maize DNA Fingerprinting and Molecular Breeding Maize Research InstituteBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China

To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker *** describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci ***-based variety discrimination power provided the largest optimization space among multiple fitness *** GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation *** algorithm afforded the same optimization depth as GA but vastly increased calculation *** comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness *** large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.

关键词： Plant variety discrimination Genetic marker combination Variety discrimination power Genetic algorithm

Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2196-2210页

作者： Hui Fang Xiuyi Fu Hanqiu Ge Mengxue Jia Jie Ji Yizhou Zhao Zijian Qu Ziqian Cui Aixia Zhang Yuandong Wang Ping Li Baohua Wang Scientific Observing and Experimental Station of maize in Plain Area of Southern Region Ministry of Agriculture and Rural Affairs/School of Life SciencesNantong UniversityNantong 226019China maize research institute Beijing Academy of Agriculture and Forestry Sciences(BAAFS)Beijing 100097China

Soil salinization poses a threat to maize production worldwide,but the genetic mechanism of salt tolerance in maize is not well ***,identifying the genetic components underlying salt tolerance in maize is of great *** the current study,a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related *** total,125 QTLs were detected using a high-density genetic bin map,with one to five QTLs explaining 6.05–32.02%of the phenotypic variation for each *** total phenotypic variation explained(PVE)by all detected QTLs ranged from 6.84 to 63.88%for each *** all 125 QTLs,only three were major QTLs distributed in two genomic regions on chromosome 6,which were involved in three salt tolerance-related *** addition,10 pairs of epistatic QTLs with additive effects were detected for eight traits,explaining 0.9 to 4.44%of the phenotypic ***,18 QTL hotspots affecting 3–7 traits were *** one hotspot(L5),a gene cluster consisting of four genes(ZmNSA1,SAG6,ZmCLCg,and ZmHKT1;2)was found,suggesting the involvement of multiple pleiotropic ***,two important candidate genes,Zm00001d002090 and Zm00001d002391,were found to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association ***00001d002090 encodes a calcium-dependent lipid-binding(CaLB domain)family protein,which may function as a Ca^(2+)sensor for transmitting the salt stress signal downstream,while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related *** findings provide valuable insights into the genetic basis of salt tolerance-related traits in maize and a theoretical foundation for breeders to develop enhanced salt-tolerant maize varieties.

关键词： maize salt tolerance-related traits QTL mapping region-based association analysis

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

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The Crop Journal 2024年第2期12卷 558-568页

作者： Junqiao Song Angela Pacheco Amos Alakonya Andrea S.Cruz-Morales Carlos Muoz-Zavala Jingtao Qu Chunping Wang Xuecai Zhang Felix San Vicente Thanda Dhliwayo College of Agronomy Henan University of Science and TechnologyLuoyang 471000HenanChina International maize and Wheat Improvement Center(CIMMYT) El BatanMexico Anyang Academy of Agricultural Sciences Anyang 455000HenanChina CIMMYT-China Specialty maize research Center Crop Breedingand Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201403China

maize stalk rot reduces grain yield and *** about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the *** prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted *** performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic *** favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred *** genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

关键词： maize stalk rot Genome-wide association mapping Haplotype analysis Genomic prediction G×E interaction

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2178-2195页

作者： Peng Liu Langlang Ma Siyi Jian Yao He Guangsheng Yuan Fei Ge Zhong Chen Chaoying Zou Guangtang Pan Thomas Lübberstedt Yaou Shen State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/maize research institute Sichuan Agricultural UniversityChengdu 611130China Department of Agronomy Iowa State UniversityAmesIA 50011USA

Genetic transformation has been an effective technology for improving the agronomic traits of ***,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype *** this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three *** low-REC germplasms displayed more abundant genetic diversity than the high-REC *** integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated *** variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated *** genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC *** leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

关键词： maize genetic transformation embryonic callus selective signal association analysis

Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

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Journal of Integrative Agriculture 2024年第1期23卷 1-19页

作者： Atiqur Rahman Hasan Sofiur Rahman Shakil Uddin Naima Sultana Shirin Akhter Ujjal Kumar Nath Shamsun Nahar Begum Mazadul Islam Afroz Naznin Nurul Amin Sharif Ahmed Akbar Hossain Department of Genetics and Plant Breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Plant Breeding Division Bangladesh Institute of Nuclear AgricultureMymensingh 2202Bangladesh Tuber Crop research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Horticulture research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Biotechnology Division Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh International Rice research institute Bangladesh OfficeDhaka 1213Bangladesh Division of Soil Science Bangladesh Wheat and Maize Research InstituteDinajpur 5200Bangladesh

The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop *** methylation plays a part in the regulation of both the chromatin structure and gene expression,and the enzyme involved,DNA methyltransferase,executes the methylation process within the plant *** regulating crucial biological pathways,epigenetic changes actively contribute to the creation of the ***,epigenome editing may assist in overcoming some of the drawbacks of genome editing,which can have minor off-target consequences and merely facilitate the loss of a gene’s *** drawbacks include gene knockout,which can have such off-target *** review provides examples of several molecular characteristics of DNA methylation,as well as some plant physiological processes that are impacted by these epigenetic changes in the *** also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

关键词： DNA methylation epigenetics CMS male sterility chromatin architecture gene expression higher plants

A novel semi-dominant allele of the transmembrane NAC transcription factor ZmNTL2 reduces the size of multiple maize organs

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The Crop Journal 2024年第3期12卷 676-687页

作者： Chuan Li Yun Bai Yuwei Hou Siyu Wang Yue Xin Tao Yu Jing Wang Xiaowei Liu Hongyang Yi Chao Xia Hai Lan Moju Cao State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Jilin Engineering research Center for Crop Biotechnology Breeding College of Plant ScienceJilin UniversityChangchun 130012JilinChina

maize plant architecture influences planting density and,in turn,grain *** of the plant architecture-related traits can be described as organ *** describe a miniature maize mutant,Tiny plant 4(Tip4),which exhibits reduced size of multiple organs and exhibits a semi-dominant monofactorial inheritance *** cloning confirmed that a 4-bp deletion in the NAC TF with transmembrane motif 1-Like(NTL)gene ZmNTL2,denoted as ZmNTL2^(Δ),confers the Tip4 ***-PCR showed that ZmNTL2 was expressed in all tested ***2 functions as a transcriptional activator and is located in both the nucleus and *** mutation does not affect the mRNA abundance of ZmNTL2 locus,but it does result in the loss of transmembrane domain and confines the ZmNTL2^(Δ)protein to the *** out ZmNTL2 has no effect on maize organ size development,indicating that the 4-bp deletion might be a gain-of-function mutation in organ size *** transcriptome sequencing with cytokinin and auxin content determination suggests that the decreased organ size may be possibly mediated by changes in hormone homeostasis.

关键词： Organ size c-ray mutagenesis Membrane-bound NAC TF Hormone homeostasis maize

Striking a growth–defense balance:Stress regulators that function in maize development

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Journal of Integrative Plant Biology 2024年第3期66卷 424-442页

作者： Shiyi Xie Hongbing Luo Wei Huang Weiwei Jin Zhaobin Dong maize Engineering and Technology research Center of Hunan Province College of AgronomyHunan Agricultural UniversityChangsha 410128China State Key Laboratory of maize Bio-breeding National Maize Improvement CenterFrontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijing 100193China Tianjin Key Laboratory of Intelligent Breeding of Major Crops Fresh Corn Research Center of BTHCollege of Agronomy&Resources and EnvironmentTianjin Agricultural UniversityTianjin 300384China

maize(Zea mays)cultivation is strongly affected by both abiotic and biotic stress,leading to reduced growth and *** has recently become clear that regulators of plant stress responses,including the phytohormones abscisic acid(ABA),ethylene(ET),and jasmonic acid(JA),together with reactive oxygen species(ROS),shape plant growth and *** their well established functions in stress responses,these molecules play crucial roles in balancing growth and defense,which must be finely tuned to achieve high yields in crops while maintaining some level of *** this review,we provide an in-depth analysis of recent research on the developmental functions of stress regulators,focusing specifically on *** unraveling the contributions of these regulators to maize development,we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.

关键词： stress regulators maize development ABA ET JA ROS

Application of CRISPR/Cas12i.3 for targeted mutagenesis in broomcorn millet(Panicum miliaceum L.)

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Journal of Integrative Plant Biology 2024年第8期66卷 1544-1547页

作者： Yuhe Bai Shengnan Liu Yan Bai Zhisong Xu Hainan Zhao Haiming Zhao Jinsheng Lai Ya Liu Weibin Song State Key Laboratory of maize Bio-breeding Key Laboratory of Genome Editing Research and ApplicationMinistry of Agriculture and Rural AffairsDepartment of Plant Genetics and BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China National Agricultural Technology Extension&Service Center Beijing 100125China Beijing Key Laboratory of maize DNA Fingerprinting and Molecular Breeding Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

As the global human population continues to grow and is predicted to reach 10 billion by 2050,the demand for food volume and quality raises a tremendous challenge(OECD/FAO,2017).The worldwide arable land area is decre... 详细信息

关键词： arable continue raise

Multi-omics analysis reveals the pivotal role of phytohormone homeostasis in regulating maize grain water content

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The Crop Journal 2024年第4期12卷 1081-1092页

作者： Yuanliang Liu Manman Li Jianju Liu Suining Deng Yan Zhang Yuanfeng Xia Baoshen Liu Mingliang Xu State Key Laboratory of Plant Environmental Resilience/College of Agronomy and Biotechnology/National maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China College of Agronomy/State Key Laboratory of Crop Biology Shandong Agricultural UniversityTai’an 271018ShandongChina institute of Agricultural Biotechnology Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina maize research institute Jilin Academy of Agricultural SciencesGongzhuling 136100JilinChina

Grain water content(GWC)is a key determinant for mechanical harvesting of maize(Zea mays).In our previous research,we identified a quantitative trait locus,qGWC1,associated with GWC in ***,we examined near-isogenic lines(NILs)NILL and NILH that differed at the qGWC1 *** GWC in NILL was primarily attributed to reduced grain water weight(GWW)and smaller fresh grain size,rather than the accumulation of dry *** difference in GWC between the NILs became more pronounced approximately 35 d after pollination(DAP),arising from a faster dehydration rate in *** an integrated analysis of the transcriptome,proteome,and metabolome,coupled with an examination of hormones and their derivatives,we detected a marked decrease in JA,along with an increase in cytokinin,storage forms of IAA(IAA-Glu,IAA-ASP),and IAA precursor IPA in immature NILL *** kernel development,genes associated with sucrose synthases,starch biosynthesis,and zein production in NILL,exhibited an initial up-regulation followed by a gradual down-regulation,compared to those in *** discovery highlights the crucial role of phytohormone homeostasis and genes related to kernel development in balancing GWC and dry matter accumulation in maize kernels.

关键词： Grain water content maize kernel Phytohormone homeostasis