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Analyzing Nitrogen Effects on Rice Panicle Development by Panicle Detection and Time-Series Tracking

Plant Phenomics 2023年第2期5卷 253-267页

作者： Qinyang Zhou Wei Guo Na Chen Ze Wang Ganghua Li Yanfeng Ding Seishi Ninomiya Yue Mu College of Agriculture Academy for Advanced Interdisciplinary StudiesCollaborative Innovation Center for Modern Crop Production co-sponsored by Province and MinistryNanjing Agricultural UniversityNanjing 210095China Graduate School of Agricultural and Life Sciences The University of Tokyo1-1-1 Midori-choNishi-TokyoTokyo 188-0002Japan

Detailed observation of the phenotypic changes in rice panicle substantially helps us to understand the yield *** recent studies,phenotyping of rice panicles during the heading–flowering stage still lacks comprehensive analysis,especially of panicle development under different nitrogen *** this work,we proposed a pipeline to automatically acquire the detailed panicle traits based on time-series images by using the YOLO v5,ResNet50,and DeepSORT *** with field observation data,the proposed method was used to test whether it has an ability to identify subtle differences in panicle developments under different nitrogen *** result shows that panicle counting throughout the heading–flowering stage achieved high accuracy(R^(2)=0.96 and RMSE=1.73),and heading date was estimated with an absolute error of 0.25 *** addition,by identical panicle tracking based on the time-series images,we analyzed detailed flowering phenotypic changes of a single panicle,such as flowering duration and individual panicle flowering *** rice population,with an increase in the nitrogen application:panicle number increased,heading date changed little,but the duration was slightly extended;cumulative flowering panicle number increased,rice flowering initiation date arrived earlier while the ending date was later;thus,the flowering duration became *** a single panicle,identical panicle tracking revealed that higher nitrogen application led to earlier flowering initiation date,significantly longer flowering days,and significantly longer total duration from vigorous flowering beginning to the end(total DBE).However,the vigorous flowering beginning time showed no significant differences and there was a slight decrease in daily DBE.

关键词： heading identical flowering

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Variations in OsSPL10 confer drought tolerance by directly regulating OsNAC2 expression and ROS production in rice

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Journal of Integrative Plant Biology 2023年第4期65卷 918-933页

作者： Yingxiu Li Shichen Han Xingming Sun Najeeb Ullah Khan Qun Zhong Zhanying Zhang Hongliang Zhang Feng Ming Zichao Li Jinjie Li State Key laboratory of Agrobiotechnology/Beijing Key laboratory of Crop Genetic Improvement College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Shanghai Key laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China Sanya Institute of China Agricultural University Sanya 572025China

Drought is a major factor restricting the production of rice(Oryza sativa L.).The identification of natural variants for drought stress-related genes is an important step toward developing genetically improved rice ***,we characterized a member of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)family,OsSPL10,as a transcription factor involved in the regulation of drought tolerance in ***10 appears to play a vital role in drought tolerance by controlling reactive oxygen species(ROS)production and stomatal *** and allele frequency analyses of OsSPL10 indicated that most upland rice and improved lowland rice varieties harbor the OsSPL10Hap1allele,whereas the OsSPL10Hap2allele was mainly present in lowland and landrace rice ***,we demonstrated that the varieties with the OsSPL10Hap1allele showed low expression levels of OsSPL10 and its downstream gene,OsNAC2,which decreases the expression of OsAP37 and increases the expression of OsCOX11,thus preventing ROS accumulation and programmed cell death(PCD).Furthermore,the knockdown or knockout of OsSPL10 induced fast stomatal closure and prevented water loss,thereby improving drought tolerance in *** on these observations,we propose that OsSPL10 confers drought tolerance by regulating OsNAC2 expression and that OsSPL10Hap1could be a valuable haplotype for the genetic improvement of drought tolerance in rice.

关键词： drought tolerance haplotype OsNAC2 OsSPL10 ROS

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SEC1A and SEC6 synergistically regulate pollen tube polar growth

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Journal of Integrative Plant Biology 2023年第7期65卷 1717-1733页

作者： Tingting Fan Yuemin Fan Yang Yang Dong Qian Yue Niu Lizhe An Yun Xiang MOE Key laboratory of Cell Activities and Stress Adaptations School of Life SciencesLanzhou UniversityLanzhou 730000China

Pollen tube polar growth is a key physiological activity for angiosperms to complete double fertilization, which is highly dependent on the transport of polar substances mediated by secretory *** exocyst and Sec1/Munc18(SM) proteins are involved in the regulation of the tethering and fusion of vesicles and plasma membranes, but the molecular mechanism by which they regulate pollen tube polar growth is still unclear. In this study, we found that loss of function of SEC1A, a member of the SM protein family in Arabidopsis thaliana, resulted in reducing pollen tube growth and a significant increase in pollen tube width. SEC1A was diffusely distributed in the pollen tube cytoplasm, and was more concentrated at the tip of the pollen tube. Through coimmunoprecipitation-mass spectrometry screening,protein interaction analysis and in vivo microscopy,we found that SEC1A interacted with the exocyst subunit SEC6, and they mutually affected the distribution and secretion rate at the tip of the pollen tube. Meanwhile, the functional loss of SEC1A and SEC6 significantly affected the distribution of the SNARE(soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex member SYP125 at the tip of the pollen tube, and led to the disorder of pollen tube cell wall components. Genetic analysis revealed that the pollen tube-related phenotype of the sec1a sec6 double mutant was significantly enhanced compared with their respective single mutants. Therefore, we speculated that SEC1A and SEC6 cooperatively regulate the fusion of secretory vesicles and plasma membranes in pollen tubes, thereby affecting the length and the width of pollen tubes.

关键词： pollen tube SEC1A SEC6 SYP125 vesicle secretory

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ZmbZIP27 regulates nitrogen-mediated leaf angle by modulating lignin deposition in maize

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The Crop Journal 2024年第5期12卷 1404-1413页

作者： Huan Chen Xiaoping Gong Yu Guo Jingjuan Yu Wen-Xue Li Qingguo Du State Key laboratory of Crop Gene Resources and Breeding National Engineering Laboratory for Crop Molecular BreedingInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China State Key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100193China

In grain crops such as maize(Zea mays),leaf angle(LA)is a key agronomic trait affecting light interception and thus planting density and ***(N)affects LA in plants,but we lack a good understanding of how N regulates ***,we report that N deficiency enhanced lignin deposition in the ligular region of maize *** situ hybridization showed that the bZIP transcription factor gene ZmbZIP27 is mainly expressed in the phloem of maize vascular *** N-sufficient conditions,transgenic maize overexpressing ZmbZIP27 showed significantly smaller LA compared with wild type(WT).By contrast,zmbzip27_(ems)mutant showed larger LA under both N-deficient and N-sufficient conditions compared with *** of ZmbZIP27 enhanced lignin deposition in the ligular region of maize in the *** further demonstrated that ZmbZIP27 could directly bind the promoters of the microRNA genes ZmMIR528a and ZmMIR528b and negatively regulate the expression levels of ***528 knockdown transgenic maize displayed erect architecture in the field by increasing lignin content in the ligular region of *** together,these results indicate that ZmbZIP27 regulates N-mediated LA size by regulating the expression of ZmmiR528 and modulating lignin deposition in maize.

关键词： Maize Nitrogen Leaf angle Ligular region Lignin deposition

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Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid

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The Crop Journal 2022年第6期10卷 1705-1716页

作者： Hui You Sundus Zafar Fan Zhang Shuangbing Zhu Kai Chen Congcong Shen Xiuqin Zhao Wenzhong Zhang Jianlong Xu Rice Research Institute Shenyang Agricultural UniversityShenyang 110866LiaoningChina The National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120GuangdongChina hainan yazhou bay seed lab/National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024HainanChina

Development of hybrid rice with high yield and grain quality is a goal of rice *** investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice,QTL mapping was conducted using 1061 recombinant inbred lines(RILs)derived from a cross of the xian rice cultivars Quan 9311B(Q9311B)and Wu-shan-si-miao(WSSM),and a backcross F_(1)(BC_(1)F_(1)) population developed by crossing the RILs with Quan 9311A(Q9311A),combined with phenotyping in two *** F_(1) hybrid(Q9311A×WSSM)showed various degrees of heterosis for milling and appearance quality.A total of 142 main-effect QTL(M-QTL)and 407 pairs of epistatic QTL(E-QTL)were identified for five milling and appearance quality traits and grain yield per plant(GYP)in the RIL,BC_(1)F_(1) and mid-parental heterosis(H_(MP)) *** detection of QTL in three populations revealed that most additive loci detected in the RILs did not show heterotic effects,but some of them did contribute to BC_(1)F_(1) trait *** heterosis of GYP,single-locus overdominance and epistasis were the main contributors to heterosis for milling and appearance *** contributed more to the heterosis for milling quality than to that for appearance ***(four)QTL regions harboring opposite(consistent)directions of favorable allele effects for GYP and grain quality were identified,indicating the presence of partial genetic overlaps between GYP and grain *** strategies are proposed to develop hybrid rice with high yield and good grain quality:1)pyramiding favorable alleles with consistent directions of gene effects for GYP and grain quality at the M-QTL on different chromosomes;2)introgressing favorable alleles for GYP and grain quality into the parents and then pyramiding and fixing these additive effects in hybrids;and 3)pyramiding overdominant and dominant loci and minimizing or eliminating underdominant loci from the parents.

关键词： Milling and appearance quality Quantitative trait locus/loci(QTL) Heterosis Hybrid rice Pyramiding breeding

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Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

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Molecular Plant 2023年第1期16卷 43-63页

作者： Shuangqian Shen Chuansong Zhan Chenkun Yang Alisdair R.Fernie Jie Luo Sanya Nanfan Research Institute of hainan University Hainan Yazhou Bay Seed LaboratorySanya 572025China College of Tropical Crops Hainan UniversityHaikou 570228China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival *** is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and *** ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of *** is usually performed by targeting either a specific cell,a specific tissue,or the entire *** advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end ***,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic *** addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics ***,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

关键词： metabolomics multi-omics high-throughput metabolic profiling bioactive markers

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Molecular cloning and functional analysis of the pepper resistance gene Me3 to root-knot nematode

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Horticultural Plant Journal 2023年第1期9卷 133-144页

作者： Yang Liu Hongyi Cao Jian Ling Yuhong Yang Yan Li Bingyan Xie Jianlong Zhao Zhenchuan Mao Institute of Vegetables and Flowers Chinese Academy of Agricultural ScienceBeijing 100081China

Root-knot nematodes(RKNs)cause severe diseases in peppers annually around the *** pepper,the Me3 gene provides a heat-stable and broad-spectrum resistance to *** this study,several simple sequence repeat(SSR)markers and insertion/deletion(In Del)markers were developed to fine map the Me3 *** of 2272 individuals(F2progenies)revealed that Me3 was located in a 45-kb DNA region between markers SSR784 and SSR339,in which there were three candidate *** them,as a novel nucleotide binding site and leucine rich repeat(NBS-LRR)family gene,the DNA sequence of Capana09g000163 of pepper line‘HDA149’was 6348 bp in length,with a 2802-bp open reading frame encoding 933 amino acids,including NB-ARC and LRR *** transient expression assays demonstrated that expression of Capana09g000163 triggered a hypersensitive response(HR)in Nicotiana benthamiana *** localization results showed that the Capana09g000163 protein was localized in the cell *** expression of Capana09g000163 in Arabidopsis significantly increased resistance against Meloidogyne incognita compared with the wild-type(WT)***,*** was almost unable to develop in transgenic Arabidopsis expressing *** together,we cloned the Me3 gene and verified that it induced resistance against *** with the methods of map-based cloning and transgenic technology,which may be of great significance to pepper breeding for resistance against RKNs.

关键词： Capsicum annuum L Meloidogyne incognita Nematode-resistant gene Fine mapping Transgenic technology

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DNNGP, a deep neural network-based method for genomic prediction using multi-omics data in plants

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Molecular Plant 2023年第1期16卷 279-293页

作者： Kelin Wang Muhammad Ali Abid Awais Rasheed Jose Crossa Sarah Hearne Huihui Li Institute of Crop Sciences Chinese Academy of Agricultural Sciences(CAAS)CIMMYT-China Office12 Zhongguancun South StreetBeijing 100081China Nanfan Research Institute CAASSanyaHainan 572024China Department of Plant Sciences Quaid-i-Azam UniversityIslamabad 45320Pakistan International Maize and Wheat Improvement Center(CIMMYT) Apdo.Postal 6-641TexcocoD.F.06600Mexico

Genomic prediction is an effective way to accelerate the rate of agronomic trait improvement in *** methods typically use linear regression models with clear assumptions;such methods are unable to capture the complex relationships between genotypes and ***-linear models(e.g.,deep neural networks)have been proposed as a superior alternative to linear models because they can capture complex non-additive *** we introduce a deep learning(DL)method,deep neural network genomic prediction(DNNGP),for integration of multi-omics data in *** trained DNNGP on four datasets and compared its performance with methods built with five classic models:genomic best linear unbiased prediction(GBLUP);two methods based on a machine learning(ML)framework,light gradient boosting machine(LightGBM)and support vector regression(SVR);and two methods based on a DL framework,deep learning genomic selection(DeepGS)and deep learning genome-wide association study(DLGWAS).DNNGP is novel in five ***,it can be applied to a variety of omics data to predict ***,the multilayered hierarchical structure of DNNGP dynamically learns features from raw data,avoiding overfitting and improving the convergence rate using a batch normalization layer and early stopping and rectified linear activation(rectified linear unit)***,when small datasets were used,DNNGP produced results that are competitive with results from the other five methods,showing greater prediction accuracy than the other methods when large-scale breeding data were ***,the computation time required by DNNGP was comparable with that of commonly used methods,up to 10 times faster than ***,hyperparameters can easily be batch tuned on a local *** with GBLUP,LightGBM,SVR,DeepGS and DLGWAS,DNNGP is superior to these existing widely used genomic selection(GS)***,DNNGP can generate robust assessments from diverse datasets,including omics data

关键词： deep learning genomic selection multi-omics data prediction method

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Time-Series Field Phenotyping of Soybean Growth Analysis by Combining Multimodal Deep Learning and Dynamic Modeling

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Plant Phenomics 2024年第2期6卷 323-334页

作者： Hui Yu Lin Weng Songquan Wu Jingjing He Yilin Yuan Jun Wang Xiaogang Xu Xianzhong Feng Key laboratory of Soybean Molecular Design Breeding State Key Laboratory of Black Soils Conservation and UtilizationNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchun 130102China Zhejiang lab Hangzhou 310012China Yanbian University Yanji 133002China

The rate of soybean canopy establishment largely determines photoperiodic sensitivity,subsequently influencing yield ***,assessing the rate of soybean canopy development in large-scale field breeding trials is both laborious and ***-throughput phenotyping methods based on unmanned aerial vehicle(UAV)systems can be used to monitor and quantitatively describe the development of soybean canopies for different *** this study,high-resolution and time-series raw data from field soybean populations were collected using UAVs.

关键词： analysis learning modeling dynamic growth field deep combining multimodal phenotyping

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A highly conserved amino acid in high molecular weight glutenin subunit 1Dy12 contributes to gluten functionality and processing quality in wheat

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Journal of Genetics and Genomics 2023年第11期50卷 909-912页

作者： Changfeng Yang Qian Chen Mingming Xin Zhenqi Su Jinkun Du Weilong Guo Zhaorong Hu Jie Liu Huiru Peng Zhongfu Ni Qixin Sun Yingyin Yao Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Bread wheat(Triticum aestivum L.)is one of the most commonly consumed staples worldwide,with widespread uses in foods such as breads,noodles,cakes,and cookies(Veraverbeke and Delcour,2002).The specific cooking properties of wheat products are mainly conferred by the gluten proteins contained in wheat grains(Delcour et al.,2012).High molecular weight glutenin subunits(HMW-GSs)are important constituents of wheat gluten proteins,largely determining gluten elasticity and processing quality(Branlard and Dardevet,1985;Payne et al.,1988).

关键词： weight wheat gluten

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