基于GroIMP的水稻功能与结构仿真模型研究

为探索植物仿真模型构建方法及提高仿真模型构建效率,设计并实现了一个基于相关生长语法RGG及扩展L系统的植物模型构建语言XL的水稻秧苗功能与结构模型。该模型包含了光环境模块、植物结构模型、生理功能模型以及环境设置模块,从而能够在植物外部形态层面及内部生理功能层面同时来描述虚拟植物的生长过程,并通过对植物生理过程与形态结构及环境因子的交互作用的考虑,能够在开源及交互的建模平台GroIMP上实现对虚拟植物的生长状态进行综合预测与动态可视化。简要地介绍了模型中主要模块及子模型构建的主要方法及模型构建的关键步骤,并通过模型的图形、数据输出验证了模型的有效性。经过简单地扩展,构建的模型可以直接应用到水稻整个生长期的建模仿真研究中。

Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols

Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing,primarily as dietary antioxidants.Although numerous pre-and post-harvest factors can affect the composition of polyphenols in apples,genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars.Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography(HPLC)data with~100,000 single nucleotide polymorphisms(SNPs)from two diverse apple populations.We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars,and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci.Using GWAS,we identified candidate genes for the production of quercitrin,epicatechin,catechin,chlorogenic acid,4-O-caffeoylquinic acid and procyanidins B1,B2,and C1.Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through markerassisted breeding or gene editing.

Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple

Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’בPink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population.

In the name of the rose:a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process,but rather a starting point that opens up a whole set of new and exciting activities.Next to a high-quality genome sequence other genomic tools have also become available for rose,including transcriptomics data,a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids.Rose cultivars are highly heterogeneous and diverse.This vast diversity in cultivated roses can be explained through the genetic potential of the genus,introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders.We can now investigate how this diversity can best be exploited and refined in future breeding work,given the rich molecular toolbox now available to the rose breeding community.This paper presents possible lines of research now that rose has entered the genomics era,and attempts to partially answer the question that arises after the completion of any draft genome sequence:‘Now that we have“the”genome,what’s next?’.Having access to a genome sequence will allow both(fundamental)scientific and(applied)breeding-orientated questions to be addressed.We outline possible approaches for a number of these questions.

A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.

Diversity and selection of the continuous-flowering gene, RoKSN, in rose

Blooming seasonality is an important trait in ornamental plants and was selected by humans.Wild roses flower only in spring whereas most cultivated modern roses can flower continuously.This trait is explained by a mutation of a floral repressor gene,RoKSN,a TFL1 homologue.In this work,we studied the origin,the diversity and the selection of the RoKSN gene.We analyzed 270 accessions,including wild and old cultivated Asian and European roses as well as modern roses.By sequencing the RoKSN gene,we proposed that the allele responsible for continuous-flowering,RoKSN copia,originated from Chinese wild roses(Indicae section),with a recent insertion of the copia element.Old cultivated Asian roses with the RoKSN copia allele were introduced in Europe,and the RoKSN copia allele was progressively selected during the 19th and 20th centuries,leading to continuous-flowering modern roses.Furthermore,we detected a new allele,RoKSN A181,leading to a weak reblooming.This allele encodes a functional floral repressor and is responsible for a moderate accumulation of RoKSN transcripts.A transient selection of this RoKSN A181 allele was observed during the 19th century.Our work highlights the selection of different alleles at the RoKSN locus for recurrent blooming in rose.

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

The apple REFPOP—a reference population for genomics-assisted breeding in apple

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions.Here we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple breeding.The population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95.Based on the genotypic data,linkage disequilibrium was low and population structure was weak.Two well-studied phenological traits of horticultural importance were measured.We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,respectively.With decreasing SNP density,the detection of significant marker–trait associations varied depending on trait architecture.Regardless of the trait,10,000 SNPs sufficed to maximize genomic prediction ability.We confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

Morphological studies of rose prickles provide new in sights

Prickles are common structures in plants that play a key role in defense against herbivores.In the Rosa genus,prickles are widely present with great diversity in terms of form and density.For cut rose production,prickles represent an important issue,as they can damage the flower and injure workers.Our objectives were to precisely describe the types of prickles that exist in roses,their tissues of origin and their development.We performed a detailed histological analysis of prickle initiation and development in a rose F1 population.Based on the prickle investigation of 110 roses,we proposed the fi rst categorization of prickles in the Rosa genus.They are mainly divided into two categories,nonglandular prickles(NGPs)and glandular prickles(GPs),and subcategories were defined based on the presence/absence of hairs and branches.We demonstrated that NGPs and GPs both originate from multiple cells ofthe ground meristem beneath the protoderm.For GPs,the gland cells originate from the protoderm of the GP at the early developmental stage.Our findings clearly demonstrate that prickles are notmodified trichomes(which originate from the protoderm).These conclusions are different from the current mainstream hypothesis.These results provide a foundation for further studies on prickle initiation and development in plants.

Radiated Ultrashort High-Power Electromagnetic Pulses Induce ATP Release in B16F10 Murine Melanoma Cells

Ultrawideband electromagnetic pulses with high amplitude and short duration are reported to affect several aspects of cell physiology. They are usually delivered to the living material through electrodes in small dedicated chambers. Here we showed, using a totally different experimental setup, that radiated EM pulses illuminating the living material through a specialized antenna (without any direct contact) are able to trigger a rapid release of ATP in cultured murine cells that was concomitant with a drop of intracellular AEC. Despite this rapid and strong response, we found that cell viability and clonogenicity were only slightly affected by the EMF exposure.

The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Pedigree information is of fundamental importance in breeding programs and related genetics efforts.However,many individuals have unknown pedigrees.While methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive inbreeding.The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet cherry.HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops.These distributions were then used to estimate previously unknown relationships.Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data.For cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were confirmed.For apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree relationships.Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

Effects of flight parameters for plant protection UAV on droplets deposition rate based on a 3D simulation approach

With the development of aviation agricultural technology,the number of farmers adopting the use of drones in daily agricultural activities is growing rapidly in recent decades.Among these,a large portion constitutes agricultural drones being used in pest control and crop protection practices,e.g.agriculture spraying of pesticides.Spraying pesticides with drones have proven to be faster than other traditional methods.On the downside,flight time and range of Unmanned Aerial Vehicles(UAV)are often limited.Thus,a proper arrangement of flight height and velocity will greatly improve spraying efficiency.A new strategy to optimize the flight parameters,i.e.flight height and flight velocity,for fixed-wing UAV with a 3D simulation-based approach together with an automatic optimization algorithm was proposed in this study.To find the optimal parameters for a UAV to fly and spray under certain environmental conditions,a three-dimensional model of the target crop was established first,followed by a detailed simulation of droplet spraying.As a demonstration case,a grass model was developed and used as the target plant,and a physics-based method was used to simulate realistically the movement of the droplets in the air as well as the interaction between the droplets and the plant to obtain the droplet deposition rate under the specified operating parameters.Furthermore,the standard Particle Swarm Optimization(PSO)algorithm was used to optimize the UAV operating parameters to obtain the best operating parameters.The results indicate that using the standard PSO algorithm to optimize the operating parameters of the drone could significantly improve the deposition rate and find the best operating parameters.

GenoDrawing:An Autoencoder Framework for Image Prediction from SNP Markers

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species,providing an abundance of genotypic data for genomic analysis.Genomic selection and neural networks(NNs),particularly deep learning,have been developed to predict complex traits from dense genotypic data.Autoencoders,an NN model to extract features from images in an unsupervised manner,has proven to be useful for plant phenotyping.This study introduces an autoencoder framework,GenoDrawing,for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism(SNP)array,potentially useful in predicting traits that are difficult to define.GenoDrawing demonstrates proficiency in its task using a small dataset of shape-related SNPs.Results indicate that the use of SNPs associated with visual traits has substantial impact on the generated images,consistent with biological interpretation.While using substantial SNPs is crucial,incorporating additional,unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs.The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping,particularly beneficial for small to medium breeding companies to predict economically substantial heritable traits.Although GenoDrawing has limitations,it sets the groundwork for future research in image prediction from genomic markers.Future studies should focus on using stronger models for image reproduction,SNP information extraction,and dataset balance in terms of phenotypes for more precise outcomes.

Genetic causes of macrozoospermia and proposal for an optimized genetic diagnosis strategy based on sperm parameters

Macrozoospermia,characterized by the presence of largeheaded spermatozoa usually carrying several flagella,is one of the most severe phenotypes of male infertility.As in most cases,the gametes are chromosomally abnormal and cannot be used for assisted reproductive technologies(ART)(Ray et al.,2017).In 2007,subjects from consanguineous families were shown to carry the same homozygous deleterious AURKC variant(NM_001015878.2:c.144delC,later renamed c.145delC,p.Leu49TrpfsTer23),establishing AURKC as the first and main gene associated with macrozoospermia(Dieterich et al.,2007).Using flow cytometry,all spermatozoa from patients homozygous for the c.145delC variant were shown to be tetraploid,highlighting a cytokinesis blockage of the first meiotic divisions thus confirming that ART cannot be successful for these patients(Dieterich et al.,2009).

整合数量遗传信息的水稻虚拟生长模型研究进展

随着全球人口的持续增加和环境的恶化,粮食作物的高产作为解决粮食短缺必不可少的途径,一直受到科学家们的广泛关注.运用可视化技术和作物模型相结合的方法,来研究植物的基因型-表现型相互反馈是一种新型的研究手段.其中,运用植物功能与结构模型的方法,能够对作物株型研究和传统育种进行辅助,从而促进育种进程.本文以水稻的虚拟生长模型为例,从运用作物模型及功能与结构模型进行QTL定位研究出发,阐述了植物模型研究的研究现状.重点综述了水稻功能与结构模型应用于虚拟育种研究的进展,提出了目前运用水稻生长模型进行虚拟育种研究中存在的问题和弊端,并论述了可能的解决方案,最后进行了相关的讨论和展望.

FSPM-P： towards a general functional-structural plant model for robust and comprehensive model development

In the last decade, functional-structural plant modelling （FSPM） has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse （by modularisafion）, combination and comparison, and the enhancement of existing mod- els. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim （e.g., photosynthesis, organ formation and growth）. Simulation runs with several general parameter sets adopted from the literature show that the present prototype was able to reproduce a plausible output range for different crops （rapeseed, barley, etc.） in terms of both the dynamics and final values （at harvest time） of model state variables such as assimilate production, organ biomass, leaf area and architecture.

The ABA-Deficiency Suppressor Locus HAS2 Encodes the PPR Protein LOI1/MEF11 Involved in Mitochondrial RNA Editing

The hotABA-deficiency suppressor2 （has2） mutation increases drought tolerance and the ABA sensitivity of stomata closure and seed germination. Here we report that the HAS2 locus encodes the MITOCHONDRIAL EDITING FACTOR11 （MEF11）, also known as LOVASTATIN INSENSITIVE1. has21mef11 mutants exhibited phenotypes very similar to the ABA-hypersensitive mutant, hail-1 pp2ca-1 hab 1-1 abil-2, which is impaired in four genes encoding type 2C protein phosphatases （PP2C） that act as upstream negative regulators of the ABA signaling cascade. Like pp2c, mef11 plants were more resistant to progressive water stress and seed germination was more sensitive to paclobutrazol （a gibberellin biosynthesis inhibitor） as well as mannitol and NaCI, compared with the wild-type plants. Phenotypic alterations in mef11 were associated with the lack of editing of transcripts for the mitochondrial cytochrome c maturation FN2 （cCmFN2） gene, which encodes a cytochrome c-heme lyase subunit involved in cytochrome c biogenesis. Although the abundance of electron transfer chain complexes was not affected, their dysfunction could be deduced from increased respiration and altered production of hydrogen peroxide and nitric oxide in reef11 seeds. As minor defects in mitochondrial respiration affect ABA signaling, this suggests an essential role for ABA in mitochondrial retrograde regulation.

Physics-based algorithm to simulate tree dynamics under wind load

Rapid development in the different computer science fields during the recent decades has facilitated the creation of new applications in the area of dynamic simulation of plant development.Among these new applications,simulation of trees swaying in the wind is of great importance,as those computer graphics related areas,e.g.,computer games,tree cultivation and forest management simulations,help a lot in revealing the mechanisms of tree dynamics under wind load.However,it is a big challenge to balance the effect of visualization in real time and calculation efficiency for any simulation algorithm.A physics-based algorithm to simulate tree dynamics under wind load was proposed in this study.A mechanistic model simulating the bending of a cantilever beam was used within the algorithm to simulate deformation of stems,and the algorithm was integrated with a landscape model in which different types of trees were constructed with an L-system-based formalism.Simulation results show that realistic dynamic effects can be achieved with reasonably high computational efficiency.