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Advances in Remote Sensing 2024年第1期13卷 1-17页

作者： Rosimara Barboza Bispo Maria Do Socorro Bezerra Araújo Antônio André da Silva Alencar Cláudia Pombo Sudré Rosana Rodrigues plant breeding Laboratory Darcy Ribeiro North Fluminense State University Campos dos Goytacazes Brazil plant breeding Laboratory University of the State of Mato Grosso Cáceres Brazil

The present work investigated the efficiency of leaf reflectance indices in the identification of Capsicum annuum L. var. annuum resistant to anthracnose in the fruit. Twenty-five F5:6 families originating from contrasting parents were assessed;the parents were accession UENF 2285 (susceptible to anthracnose) and accession UENF 1381, a hot pepper resistant to anthracnose in the fruit. The experiment was carried out in an experimental field in Campos dos Goytacazes, Rio de Janeiro, Brazil, between May and October of 2021. The treatments were arranged in a randomized block design, with three replications and five plants per plot. Fifteen LRIs were estimated using a CI-710 portable mini leaf spectrometer. The assessments covered all plant growth after flowering, and a total of six assessments were performed at 15-days intervals, beginning at 35 and ending 120 days after flowering (DAFs). Analysis of variance in a split-plot scheme was performed, as were tests of mean groupings and principal components analysis (PCA). The best period for evaluating leaf reflectance indices in C. annuum var. annuum is 120 days after flowering. The leaf reflectance indices PRI, CNDVI and Ctr2 stood out as effective in distinguishing between resistant and susceptible genotypes.

关键词： Phenotyping Bell Pepper CI-710 Colletotrichum scovillei

Computational tools for plant genomics and breeding

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Science China(Life Sciences) 2024年第8期67卷 1579-1590页

作者： Hai Wang Mengjiao Chen Xin Wei Rui Xia Dong Pei Xuehui Huang Bin Han 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 100193China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China State Key Laboratory of Tree Genetics and breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China Shanghai Key Laboratory of plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Horticulture South China Agricultural UniversityGuangzhou 510640China National Center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200233China

plant genomics and crop breeding are at the intersection of biotechnology and information *** by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome *** advances further revolutionized three directions of *** is genetic dissection of complex traits in crops,along with genomic prediction and *** second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant *** third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic *** three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

关键词： bioinformatics plant genomics breeding by design

Genomic selection in plant breeding:Key factors shaping two decades of progress

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Molecular plant 2024年第4期17卷 552-578页

作者： Admas Alemu Johanna Astrand Osval A.Montesinos-López Julio Isidro y Sanchez Javier Fernandez-Gónzalez Wuletaw Tadesse Ramesh R.Vetukuri Anders S.Carlsson Alf Ceplitis JoséCrossa Rodomiro Ortiz Aakash Chawade Department of plant breeding Swedish University of Agricultural SciencesAlnarpSweden Lantmannen Lantbruk SvalövSweden Facultad de Telematica University de ColimaColimaColima 28040Mexico Centro de Biotecnología y Genómica de plantas(CBGP UPM-INIA)Universidad Politécnica de Madrid(UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo-UPM28223 MadridSpain International Center for Agricultural Research in the Dry Areas(ICARDA) RabatMorocco International Maize and Wheat Improvement Center(CIMMYT) Km 45Carretera México-VeracruzTexcocoMéxico 52640Mexico

Genomic selection,the application of genomic prediction(GP)models to select candidate individuals,has significantly advanced in the past two decades,effectively accelerating genetic gains in plant *** article provides a holistic overview of key factors that have influenced GP in plant breeding during this *** delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP *** emphasis was placed on optimizing training population *** explored its benefits and the associated diminishing returns beyond an optimum *** was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization *** density and distribution of single-nucleotide polymorphisms,level of linkage disequilibrium,genetic complexity,trait heritability,statistical machine-learning methods,and non-additive effects are the other vital *** wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various *** search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various *** hypothesize that with ultra-high sizes of genotypic and phenotypic datasets,effective training population optimization methods and support from other omics approaches(transcriptomics,metabolomics and proteomics)coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy,making genomic selection an effective tool in plant breeding.

关键词： genomic selection genetic gain genomic prediction optimization deep learning training population optimization

Exploring the molecular basis of heterosis for plant breeding

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Journal of Integrative plant Biology 2020年第3期62卷 287-298页

作者： Jie Liu Mengjie Li Qi Zhang Xin Wei Xuehui Huang Shanghai Key Laboratory of plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China

Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis(hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and *** and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

关键词： breeding crops heterosis

META-R:A software to analyze data from multi-environment plant breeding trials

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The Crop Journal 2020年第5期8卷 745-756页

作者： Gregorio Alvarado Francisco M.Rodríguez Angela Pacheco Juan Burgueño JoséCrossa Mateo Vargas Paulino Pérez-Rodríguez Marco A.Lopez-Cruz Biometrics and Statistics Unit International Maize and Wheat Improvement Center(CIMMYT)MexicoDF 6-64106600Mexico Centro de Investigación en Matemáticas(CIMAT)A.C. Jalisco S/NCol.ValencianaGuanajuatoGto 40236023Mexico Universidad Autónoma Chapingo Carretera Federal México-Texcoco km 38.5TexcocoMéxico 6356230Mexico Colegio de Postgraduados Carretera México-Texcoco Km.36.5MontecilloTexcoco 6356231Mexico Department of plant Soil and Microbial SciencesMichigan State University1066 Bogue StEast LansingMI 48824USA

META-R(multi-environment trial analysis in R)is a suite of R scripts linked by a graphical user interface(GUI)designed in Java *** objective of META-R is to accurately analyze multi-environment plant breeding trials(METs)by fitting mixed and fixed linear models from experimental designs such as the randomized complete block design(RCBD)and the alpha-lattice/lattice ***-R simultaneously estimates the best linear and unbiased estimators(BLUEs)and the best linear and unbiased predictors(BLUPs).Additionally,it computes the variance-covariance parameters,as well as some statistical and genetic parameters such as the least significant difference(LSD)at 5%significance,the coefficient of variation in percentage(CV),the genetic variance,and the broad-sense *** parameters are very important in the selection of top performing genotypes in plant ***-R also computes the phenotypic and genetic correlations among environments and between traits,as well as their statistical *** genetic correlations between environments or traits can be visualized in a biplot graph or a tree diagram(dendrogram).Genetic correlations are very important for identifying environments with similar behavior or making indirect selection and identifying the most highly associated ***-R performs multi-environment analyses by using the residual maximum likelihood(REML)method;these analyses can be done by environment,across environments by grouping factors(stress conditions,nitrogen content,etc.)and across environments;the analyses across environments can be done with a pre-defined degree of heritability.

关键词： environments breeding variance

Investigation of CRISPR/Cas9-induced SD1 rice mutants highlights the importance of molecular characterization in plant molecular breeding

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Journal of Genetics and Genomics 2020年第5期47卷 273-280页

作者： Sukumar Biswas Jiaqi Tian Rong Li Xiaofei Chen Zhijing Luo Mingjiao Chen Xiangxiang Zhao Dabing Zhang Staffan Persson Zheng Yuan Jianxin Shi Joint International Research Laboratory of Metabolic&Developmental Sciences Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and HealthState Key Laboratory of Hybrid RiceSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China Key Laboratory of Crop Marker-Assisted breeding of Huaian Municipality Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental ProtectionHuaian223300China School of Biosciences University of MelbourneParkville VIC3010MelbourneAustralia

Although Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR)/CRISPR-associated 9(Cas9)system has been widely used for basic research in model plants,its application for applied breeding in crops has faced strong regulatory obstacles,due mainly to a poor understanding of the authentic output of this system,particularly in higher *** this study,different from any previous studies,we investigated in detail the molecular characteristics and production performance of CRISPR/Cas9-generated SD1(semi-dwarf 1)mutants from T2 to T4 generations,of which the selection of T1 and T2 was done only by visual phenotyping for semidwarf *** data revealed not only on-and off-target mutations with small or lager indels but also exogenous elements in T2 *** indel mutants passed stably to T3 or T4 without additional modifications independent on the presence of Cas9,while some lines displayed unexpected hereditary patterns of Cas9 or some exogenous *** addition,effects of various SD1 alleles on rice height and yield differed depending on genetic *** together,our data showed that the CRISPR/Cas9 system is effective in producing homozygous mutants for functional analysis,but it may be not as precise as expected in rice,and that early and accurate molecular characterization and screening must be carried out for generations before transitioning of the CRISPR/Cas9 system from laboratory to field.

关键词： CRISPR/Cas9 plant height Oryza sativa Semi-dwarf 1 Yield

Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based plant Height Dynamics for breeding

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Rice science 2024年第5期31卷 617-628,I0066-I0070页

作者： HONG Weiyuan LI Ziqiu FENG Xiangqian QIN Jinhua WANG Aidong JIN Shichao WANG Danying CHEN Song State Key Laboratory of Rice Biology and breeding China National Rice Research InstituteHangzhou 311400China College of Computer Science and Technology Zhejiang Sci-Tech UniversityHangzhou 310018China College of Agriculture Yangtze UniversityJingzhou 434025China plant Phenomics Research Centre Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China

Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. plant height(PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle(UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading(IH) and full heading(FH), and panicle initiation(PI), and growth period after transplanting(GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model(DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest(RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th(R^(2) = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features(CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI(R^(2) = 0.834, RMSE = 4.344 d), IH(R^(2) = 0.877, RMSE = 2.721 d), and FH(R^(2) = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

关键词： phenological date plant height unmanned aerial vehicle machine learning rice breeding

Expression changes of mi RNA-regulated genes associated with the formation of the leafy head in cabbage

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Horticultural plant Journal 2024年第4期10卷 1007-1019页

作者： Jorge Aleman-Baez Jose Fernando Acevedo-Zamora Johan Bucher Chengcheng Cai Roeland E.Voorrips Guusje Bonnema plant breeding Wageningen University and ResearchWageningenThe Netherlands

The vegetative development of cabbage(Brassica oleracea ***)passes through seedling,rosette,folding and heading *** that form the rosette are large and mostly *** the following developmental stages,the plants produce leaves that curve inward to produce the leafy *** microRNAs and their target genes have been described participating in leaf development and leaf *** aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading *** compared the mi RNA and gene abundances between emerging rosette and heading *** remove transcripts(miRNAs and genes)whose regulation was most likely associated with plant age rather than the change from rosette to heading stage,we utilized a non-heading collard green(*** ***)morphotype as *** resulted in 33 DEMs and 1998 DEGs with likely roles in the transition from rosette to heading stage in *** these 1998 DEGs,we found enriched GO terms related to DNA-binding transcription factor activity,transcription regulator activity,iron ion binding,and *** predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed(1998DEGs)between rosette and heading stage leaves to construct mi RNA-target gene interaction *** main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORs 3(GRF3)and 4(GRF4)in pointed cabbage head formation.

关键词： Brassica oleracea var.capitata RNA sequencing miRNA-target gene network leafy head formation

Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The Laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

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