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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 quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We 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 responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating 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

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CRISPR/CasΦ2-mediated gene editing in wheat and rye

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Journal of Integrative Plant Biology 2024年第4期66卷 638-641页

作者： Sanzeng Zhao Xueying Han Yachen Zhu Yuwei Han Huiyun Liu Zhen Chen Huifang Li Dan Wang Chaofan Tian Yuting Yuan Yajie Guo Xiaomin Si Daowen Wang Xiang Ji State Key Laboratory of Wheat and maize Crop Science and Center for Crop Genome EngineeringCollege of AgronomyHenan Agricultural UniversityZhengzhou 450046China Collaborative Innovation Center of Henan Grain Crops College of AgronomyHenan Agricultural UniversityZhengzhou 450046China State Key Laboratory of Crop Stress Adaptation and Improvement College of AgronomyHenan UniversityKaifeng 475004China The Shennong Laboratory Zhengzhou 450002China

The recent advancements in developing the CRISPR/Cas9 system and various derivative tools(e.g.,base editors)have accelerated basic plant science research and crop improvement by creating multiple types of genetic vari... 详细信息

关键词： CRISPR/Cas9 CRISPR/Cas

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 combinations.We describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci Scan.Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions.Among GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation workload.Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time.In comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness functions.In 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

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Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

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Journal of Integrative Plant Biology 2024年第4期66卷 645-659页

作者： Lei Liang Yuancong Wang Yanbin Han Yicong Chen Mengfei Li Yibo Wu Zeyang Ma Han Zhao Rentao Song State Key Laboratory of maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100091China institute of Crop Germplasm and Biotechnology Jiangsu Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing 210014China Sanya institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China

ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time.Using MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 families.We also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation population.Using the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter line.The Mu-starter genome also improved the assignment of 117,689(54.5%)germinal insertions.The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions.These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two genomes.As a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

关键词： ChinaMu Mutator MuT-seq PPR gene Zea mays

The cytosolic isoform of triosephosphate isomerase,ZmTPI4,is required for kernel development and starch synthesis in maize(Zea mays L.)

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The Crop Journal 2024年第2期12卷 401-410页

作者： Wenyu Li Han Wang Qiuyue Xu Long Zhang Yan Wang Yongbiao Yu Xiangkun Guo Zhiwei Zhang Yongbin Dong Yuling Li State Key Laboratory of Wheat and maize Crop Science Collaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityLongzi Lake CampusZhengzhou 450046HenanChina

Triosephosphate isomerase(TPI)is an enzyme that functions in plant energy production,accumulation,and conversion.To understand its function in maize,we characterized a maize TPI mutant,zmtpi4.In comparison to the wild type,zmtpi4 mutants showed altered ear development,reduced kernel weight and starch content,modified starch granule morphology,and altered amylose and amylopectin content.Protein,ATP,and pyruvate contents were reduced,indicating ZmTPI4 was involved in glycolysis.Although subcellular localization confirmed ZmTPI4 as a cytosolic rather than a plastid isoform of TPI,the zmtpi4 mutant showed reduced leaf size and chlorophyll content.Overexpression of ZmTPI4 in Arabidopsis led to enlarged leaves and increased seed weight,suggesting a positive regulatory role of ZmTPI4 in kernel weight and starch content.We conclude that ZmTPI4 functions in maize kernel development,starch synthesis,glycolysis,and photosynthesis.

关键词： maize Kernel Starch Weight Photosynthesis

Orchestrating seed storage protein and starch accumulation toward overcoming yield–quality trade-off in cereal crops

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Journal of Integrative Plant Biology 2024年第3期66卷 468-483页

作者： Shuanghe Cao Bingyan Liu Daowen Wang Awais Rasheed Lina Xie Xianchun Xia Zhonghu He State Key Laboratory of Crop Gene Resources and Breeding/National Wheat Improvement Center Institute of Crop SciencesBeijing 100081China college of agronomy Henan Agricultural UniversityZhengzhou 450002China International maize and Wheat Improvement Center(CIMMYT)China Office Chinese Academy of Agricultural SciencesBeijing 100081China

Achieving high yield and good quality in crops is essential for human food security and health.However,there is usually disharmony between yield and quality.Seed storage protein(SSP)and starch,the predominant components in cereal grains,determine yield and quality,and their coupled synthesis causes a yield–quality trade-off.Therefore,dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality.Here,we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops,including maize,rice and wheat.We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights.We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding.Finally,future perspectives on major challenges are proposed.

关键词： cereal crops grain yield and quality seed storage protein starch synergistic regulation

TaRLK-6A promotes Fusarium crown rot resistance in wheat

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Journal of Integrative Plant Biology 2024年第1期66卷 12-16页

作者： Haijun Qi Xiuliang Zhu Wenbiao Shen Xia Yang Chaozhong Zhang Genying Li Feng Chen Xuening Wei Zengyan Zhang institute of Special Animal and Plant Sciences Chinese Academy of Agricultural SciencesChangchun 130000China The National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China college of Life Science Nanjing Agricultural UniversityNanjing 210095China agronomy college/National Key Laboratory of Wheat and maize Crop Science/CIMMYT‐China(Henan)Joint Center of Wheat and maize Henan Agricultural UniversityZhengzhou 450002China Department of Plant Sciences University of CaliforniaDavisCA 95616USA Crop research institute Shandong Academy of Agricultural SciencesJinan 250100China

Fusariumcrown rot(FCR),mainly caused by the soil‐borne fungus Fusarium pseudograminearum,is a devastatingdisease of wheat(Triticum aestivum(Ta)).Fusariumcrown rotcauses substantial yield losses and generates mycotoxins inwheat grains that can cause serious health problems in hu-mans and livestock(Powell et al.,2017).Identifying genes thatprovide resistance toF.pseudograminearumand character-izing the molecular mechanisms underlying such resistance arekey to breeding wheat varieties that are resistant to this dev-astating fungus.

关键词： aestivum breeding soil

N-cycle gene abundance determination of N mineralization rate following re-afforestation in the Loess Plateau of China

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Soil Ecology Letters 2024年第1期6卷 97-106页

作者： Yaping Zhao Yuqing Zhao Shuohong Zhang Yulin Xu Xinhui Han Gaihe Yang Chengjie Ren college of agronomy Northwest A&F UniversityYangling 712100China Shaanxi Engineering research Center of Circular Agriculture College of AgronomyNorthwest A&F UniversityYangling 712100China

Afforestation effectively improved soil microbial communities and significantly increased soil nitro-gen mineralization rate(Rm).Soil microorganisms drive Rm by regulating soil N-cycling genes.Soil nitrification genes had a major effect on soil Rm than denitrification genes after afforestation.Assessing the function of forest ecosystems requires an understanding of the mechanism of soil nitrogen mineralization.However,it remains unclear how soil N-cycling genes drive soil nitrogen mineralization during afforestation.In this study,we collected soil samples from a chrono-sequence of 14,20,30,and 45 years of Robinia pseudoacacia L.(RP14,RP20,RP30,and RP45)with a sloped farmland(FL)as a control.Through metagenomic sequencing analysis,we found significant changes in the diversity and composition of soil microbial communities involved in N-cycling along the afforestation time series,with afforestation effectively increasing the diversity(both alpha and beta diversity)of soil microbial communities.We conducted indoor culture experiments and analyzed correlations,which revealed a significant increase in both soil nitrification rate(Rn)and soil nitrogen mineralization rate(Rm)with increasing stand age.Furthermore,we found a strong correlation between soil Rm and soil microbial diversity(both alpha and beta diversity)and with the abundance of soil N-cycling genes.Partial least squares path modeling(PLS-PM)analysis showed that nitrification genes(narH,narY,nxrB,narG,narZ,nxrA,hao,pmoC-amoC)and denitrification genes(norB,nosZ,nirK)had a greater direct effect on soil Rm compared to their effect on soil microbial communities.Our results reveal the relationships between soil nitrogen mineralization rate and soil microbial communities and between the mineralization rate and functional genes involved in N-cycling,in the context of Robinia pseudoacacia L.restoration on the Loess Plateau.This study enriches the understanding of the effects of microorganisms on soil nitrogen mineralization rate during afforestation and provides a ne

关键词： afforestation soil N mineralization rate denitrification genes nitrification genes the Loess Plateau

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 maize.However,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype dependence.In 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 subpopulations.The low-REC germplasms displayed more abundant genetic diversity than the high-REC germplasms.By 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.These 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 loci.These 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 induction.Numerous 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