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1.
An Acad Bras Cienc ; 92(suppl 1): e20180426, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32159585

RESUMO

Effective microorganisms (EM) are inoculants formed by fungi and bacteria isolated from soil. EM are commonly used by farmers on agronomic crops to stimulate plant growth, but their composition and their benefits has been controverted. This study aimed to analyze the diversity of microorganisms growing in three EM inoculants, as well as to evaluate their efficiency in the germination of palisade grass seeds. The total DNA of the three EM inoculants was extracted, the 16S rRNA and ITS genes were amplified by PCR and sequenced on the Illumina MiSeq platform. Germination tests were conducted with three type of the EM, in three concentration and two times of the immersion. The bacterial group was the most abundant in EM, followed by fungi. Bacterial operational taxonomic units OTUs were shared by all EMs. Pre-treatments of palisade grass seeds with EMs resulted in a higher germination percentage (% G) and germination speed index (IVG) when EM was used at concentration of 1 or 2% in water. Seed immersion for 5 min was more efficient than immersion for 24 h. We can conclude that EM of different origin can share microbial groups and diversity of microorganisms, besides being an alternative to increase palisade grass seeds germination.


Assuntos
Inoculantes Agrícolas/genética , DNA Bacteriano/isolamento & purificação , DNA Fúngico/isolamento & purificação , Germinação/fisiologia , Poaceae/crescimento & desenvolvimento , Sementes/crescimento & desenvolvimento , Biodiversidade , Produtos Agrícolas/genética , Germinação/efeitos dos fármacos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sementes/efeitos dos fármacos , Análise de Sequência de DNA , Análise de Sequência de RNA , Ácidos Sulfúricos/farmacologia
3.
J Agric Food Chem ; 68(3): 703-711, 2020 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-31904950

RESUMO

In crop plants, the yield loss caused by drought exceeds the losses resulting from other adverse environment stresses. In numerous plant species, seedling establishment is positively correlated with the initial seed size under drought stress conditions. In intra- and interspecies, plants with large seeds can withstand water deficiency stresses, whereas those with small seeds are efficient colonizers as a result of their ability to produce more seeds. Therefore, larger initial seeds confer more drought resistance on germinating seedlings. Although this phenomenon has been observed by evolutionary biologists and ecologists, the correlation of initial seed size with the drought resistance of seedlings/plants is not well-reviewed and characterized. Furthermore, the related molecular mechanisms are unknown. Understanding these mechanisms will benefit future breeding or design strategies to increase crop yields. In the present review, we focus on recent research to analyze the genetic factors of plants/crops involved in the regulation of seed size and drought tolerance and their corresponding signal transduction pathways. Several signaling pathways that determine plant drought tolerance through influencing the initial seed size are identified. Such pathways include those that are involved in mitogen-activated protein kinase, abscisic acid, brassinosteroids, and several transcription factors and sugar signaling pathways.


Assuntos
Produtos Agrícolas/crescimento & desenvolvimento , Sementes/química , Produtos Agrícolas/classificação , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Secas , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Sementes/genética , Sementes/crescimento & desenvolvimento , Sementes/metabolismo , Água/análise , Água/metabolismo
4.
J Sci Food Agric ; 100(3): 904-914, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31612486

RESUMO

A huge amount of nitrogenous fertilizer is used to increase crop production. This leads to an increase in the cost of production, and to human and environmental problems. It is therefore necessary to improve nitrogen use efficiency (NUE) and to design agronomic, biotechnological and breeding strategies for better fertilizer use. Nitrogen use efficiency relies primarily on how plants extract, uptake, transport, assimilate, and remobilize nitrogen. Many plants use nitrate as a preferred nitrogen source. It acts as a signaling molecule in the various important physiological processes required for growth and development. As nitrate is the main source of nitrogen in the soil, root nitrate transporters are important subjects for study. The latest reports have also discussed how nitrate transporter and assimilation genes can be used as molecular tools to improve NUE in crops. The purpose of this review is to describe the mechanisms and functions of nitrate as a specific factor that can be addressed to increase NUE. Improving factors such as nitrate uptake, transport, assimilation, and remobilization through activation by signaling, sensing, and regulatory processes will improve plant growth and NUE. © 2019 Society of Chemical Industry.


Assuntos
Produtos Agrícolas/metabolismo , Nitratos/metabolismo , Proteínas de Transporte de Ânions/genética , Proteínas de Transporte de Ânions/metabolismo , Transporte Biológico , Produtos Agrícolas/genética , Produtos Agrícolas/crescimento & desenvolvimento , Fertilizantes/análise , Nitrogênio/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
5.
J Agric Food Chem ; 68(1): 48-58, 2020 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-31829629

RESUMO

Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are perfluorinated alkyl substances widely used in industrial and domestic products. The European Food Safety Authority and United States Environmental Protection Agency have recently lowered the reference doses (RfDs) for PFOA and PFOS 4-1800-fold. The recently lowered RfDs call for re-evaluation of potential human health risks from PFOA and PFOS via food consumption. Serious concerns arise because some intakes of PFOA and PFOS exceeded the RfDs. Innovative cultivation of low-accumulating crop varieties becomes an option to decrease human exposure. We present an up-to-date review on low-accumulating crop varieties for PFOA and PFOS in reference to toxic metals and other organic pollutants, including the variety identification, physiological-biochemical mechanisms, molecular uptake mechanisms, and molecular docking, to call for attention and research efforts to decrease human intakes of PFOA and PFOS via crop consumption.


Assuntos
Ácidos Alcanossulfônicos/análise , Caprilatos/análise , Produtos Agrícolas/química , Fluorcarbonetos/análise , Contaminação de Alimentos/prevenção & controle , Ácidos Alcanossulfônicos/metabolismo , Caprilatos/metabolismo , Qualidade de Produtos para o Consumidor , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Fluorcarbonetos/metabolismo , Contaminação de Alimentos/análise , Inocuidade dos Alimentos , Humanos , Melhoramento Vegetal
6.
Plant Sci ; 290: 110317, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31779910

RESUMO

Thaumatin-like protein kinases (TLPKs) are defense related proteins having antimicrobial property. Herein, we identified two TLPKs in the genome of Brachypodium distachyon and Oryza sativa, four in Hordeum vulgare and Sorghum bicolor, and 16 in Triticum aestivum. All the TLPKs were located at only one chromosome in each plant except T. aestivum, where they were located on chromosome 2 and chromosome 3. Paralogous analysis suggested the occurrence of one duplication event (DE) in each B. distachyon and O. sativa, two in H. vulgare while four DEs in T. aestivum genome during the evolution of TLPKs. The majority of TLPKs were intron less, while a few contains one or two introns. The introns were found in each 0, 1 and 2 phase. Protein structure analysis suggested the occurrence of a thaumatin and a kinase domain with a transmembrane (TM) helix in each TLPK. Further, a thaumatin family signature motif "GX[GF]XCXT[GA]DCX(1,2)GX(2,3)C", a "REDDD" motif and 16 cysteine residues were found conserved in the majority of TLPKs. Expression analysis indicated variable expression of TLPKs in various tissues of different cereal crops. They were high expressing in reproductive tissues in B. distachyon, while in leaves in T. aestivum. Modulated expression of TaTLPKs in the presence of fungal pathogen, and heat, drought and salt stress in T. aestivum suggested their roles in stress response. Co-expression analysis showed interaction of TLPKs with various development and stress related genes. The results indicated diverse roles of TLPKs, which can be utilized for the development of eco-friendly pest resistant crops in future.


Assuntos
Produtos Agrícolas/genética , Proteínas de Plantas/genética , Proteínas Quinases/genética , Transcrição Genética , Sequência de Aminoácidos , Produtos Agrícolas/metabolismo , Perfilação da Expressão Gênica , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Proteínas Quinases/química , Proteínas Quinases/metabolismo , Alinhamento de Sequência
7.
Food Chem ; 309: 125760, 2020 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-31787392

RESUMO

Molecular characterization of exogenous DNA integrations in host genome is a key aspect in risk assessment of bioengineered crops. However, gaining a clear understanding of the molecular characters of a bioengineered crop using conventional techniques remains a challenging task. Herein, we report the full molecular characterization of one new transgenic rice event G6H1 via a paired-end sequencing approach and bioinformatics analysis pipelines. Also, the molecular characterization reported was validated using conventional PCR, Sanger sequencing, and digital PCR. The results showed there is only one copy of the exogenous DNA inserted, which is located within chromosome 7 of the G6H1 genome. There is no other unintended integration of sequences from the transformation plasmid. These results indicated that the paired-end sequencing approach, combined with bioinformatics pipeline developed, is well suited to elucidate the molecular characteristics of bioengineered crops, and is efficient, low cost, and comprehensive.


Assuntos
Oryza/genética , Plantas Geneticamente Modificadas/genética , Mapeamento Cromossômico , Biologia Computacional/métodos , Produtos Agrícolas/genética , DNA/análise , DNA/metabolismo , Reação em Cadeia da Polimerase , Análise de Sequência de DNA
8.
PLoS One ; 14(12): e0222737, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31846458

RESUMO

The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.


Assuntos
Microbiota/genética , Rizoma/genética , Zea mays/genética , Archaea/genética , Bactérias/genética , Produtos Agrícolas/genética , Desnitrificação , Dinamarca , Europa (Continente) , Fungos/genética , Edição de Genes , Nitrito Redutases/metabolismo , Nitrogênio/metabolismo , Filogenia , Plantas Geneticamente Modificadas/genética , Reação em Cadeia da Polimerase/métodos , Eslováquia , Solo/química , Microbiologia do Solo , Espanha , Zea mays/crescimento & desenvolvimento
9.
Nature ; 575(7781): 109-118, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31695205

RESUMO

The current trajectory for crop yields is insufficient to nourish the world's population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests.


Assuntos
Produção Agrícola/métodos , Produção Agrícola/estatística & dados numéricos , Produtos Agrícolas/genética , Abastecimento de Alimentos/métodos , Abastecimento de Alimentos/estatística & dados numéricos , Aquecimento Global/estatística & dados numéricos , Desenvolvimento Sustentável/tendências , Aclimatação/genética , Aclimatação/fisiologia , Animais , Produtos Agrícolas/crescimento & desenvolvimento , Produtos Agrícolas/microbiologia , Produtos Agrícolas/virologia , Fertilizantes , Humanos , Doenças das Plantas/genética , Doenças das Plantas/prevenção & controle , Doenças das Plantas/estatística & dados numéricos , Chuva
11.
J Agric Food Chem ; 67(49): 13506-13508, 2019 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-31725270

RESUMO

Since 2011, the European Food Safety Authority (EFSA) has implemented combined difference and equivalence testing of agronomic, phenotypic, and composition data in the risk assessment of genetically modified crops. A short perspective is provided on misunderstandings that have shown up in published criticisms of the approach to equivalence testing, different viewpoints regarding the questions to be answered, and new developments in statistical modeling.


Assuntos
Produtos Agrícolas/química , Análise de Alimentos/métodos , Plantas Geneticamente Modificadas/química , Qualidade de Produtos para o Consumidor , Produtos Agrícolas/genética , Produtos Agrícolas/metabolismo , Inocuidade dos Alimentos , Alimentos Geneticamente Modificados , Humanos , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Medição de Risco
12.
Yi Chuan ; 41(11): 1060-1066, 2019 Nov 20.
Artigo em Chinês | MEDLINE | ID: mdl-31735708

RESUMO

With the completion of the whole genome sequencing of major important crops, researchers have an increasing demand for high-throughput, accurate and nondestructive phenotyping technologies. The Plant Phenomics Analysis Platform (PPAP) was established in 2017 at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. The platform has the most up-to-date comprehensive phenotyping analysis facility in China with a full spectrum of imaging systems consisting of eight units including visible light, infrared, near-infrared, root near-infrared, fluorescence, chlorophyll fluorescence, high spectral and lidar imaging. The platform has also specifically established phenotyping technologies for complex traits, such as root phenotype collection and analysis, spike and spikelet feature collection and analysis and responses under stress conditions. PPAP is dedicated to providing all-possible services for domestic and international academic communities and industrial partners engaged in plant sciences.


Assuntos
Produtos Agrícolas/genética , Fenótipo , Melhoramento Vegetal , China
13.
Nat Genet ; 51(10): 1549-1558, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31570895

RESUMO

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.


Assuntos
Ananas/genética , Produtos Agrícolas/genética , Domesticação , Genoma de Planta , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Característica Quantitativa Herdável , Ananas/crescimento & desenvolvimento , Bromelaínas/metabolismo , Produtos Agrícolas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Fenótipo , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Dinâmica Populacional , Açúcares/metabolismo
14.
BMC Genomics ; 20(1): 740, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31615400

RESUMO

BACKGROUND: Chinese wild grapevine (Vitis amurensis) has remarkable cold stress tolerance, exceeding that of the common cultivated grapevine (Vitis vinifera L.). RESULT: Here, we surveyed the expression dynamics of microRNAs (miRNAs) across Chinese wild grapevine (cv. Beibinghong) and cultivated grapevine (cv. Cabernet Sauvignon) under cold stress using high-throughput sequencing. We identified 186 known miRNAs in cultivated grape and 427 known miRNAs in Beibinghong. Of the identified miRNAs, 59 are conserved miRNAs orthologous in Cabernet Sauvignon and Beibinghong. In addition, 105 and 129 novel miRNAs were identified in Cabernet Sauvignon and Beibinghong, respectively. The expression of some miRNAs was related to cold stress both in Cabernet Sauvignon and Beibinghong. Many cold-related miRNAs in Cabernet Sauvignon and Beibinghong were predicted to target stress response-related genes such as MYB, WRKY, bHLH transcription factor genes, and heat shock protein genes. However, the expression tendency under cold treatment of many of these miRNAs was different between Cabernet Sauvignon and Beibinghong. Different modes of expression of cultivated and Chinese wild grape miRNAs were indicated in key pathways under cold stress by degradome, target prediction, GO, and KEGG analyses. CONCLUSION: Our study indicated three likely reasons that led to the different cold stress tolerance levels of Cabernet Sauvignon and Beibinghong. Specifically, there may be (1) differential expression of orthologous miRNAs between cultivated grapevine and Chinese wild grape; (2) species-specific miRNAs or target genes; or (3) different regulatory models of miRNAs in cultivated and Chinese wild grape in some key pathways.


Assuntos
Redes Reguladoras de Genes , Sequenciamento de Nucleotídeos em Larga Escala/métodos , MicroRNAs/genética , Vitis/crescimento & desenvolvimento , China , Resposta ao Choque Frio , Produtos Agrícolas/genética , Produtos Agrícolas/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , RNA de Plantas/genética , Análise de Sequência de RNA , Vitis/genética
15.
Int J Mol Sci ; 20(20)2019 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-31623139

RESUMO

The vacuolar H+-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of VHA-H genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 VHA-H genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these VHA-H genes shared exon-intron structures similar to those of Arabidopsis thaliana. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The VHA-H gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The VHA-H genes from six species of crops (Gossypium raimondii, Brassica napus, Glycine max, Solanum tuberosum, Triticum aestivum, and Zea mays) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven VHA-H genes in six species of crops (Gossypium raimondii, Hordeum vulgare, Solanum tuberosum, Setaria italica, Triticum aestivum, and Zea mays) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of VHA-H genes as eco-enzymes. The gene structural diversity and proteomic diversity of VHA-H genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.


Assuntos
Produtos Agrícolas/genética , Genoma de Planta , Estudo de Associação Genômica Ampla , Família Multigênica , Subunidades Proteicas/genética , ATPases Vacuolares Próton-Translocadoras/genética , Processamento Alternativo , Sequência de Aminoácidos , Produtos Agrícolas/classificação , Genômica/métodos , Motivos de Nucleotídeos , Filogenia , Regiões Promotoras Genéticas , ATPases Vacuolares Próton-Translocadoras/química , ATPases Vacuolares Próton-Translocadoras/metabolismo
16.
Nat Commun ; 10(1): 4135, 2019 09 12.
Artigo em Inglês | MEDLINE | ID: mdl-31515535

RESUMO

Perennial grasses are promising feedstocks for biofuel production, with potential for leveraging their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus). We sample leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identify core leaf taxa based on occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is an important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support crop production.


Assuntos
Biocombustíveis/microbiologia , Produtos Agrícolas/microbiologia , Microbiota/genética , Folhas de Planta/microbiologia , Estações do Ano , Archaea/genética , Bactérias/genética , Produtos Agrícolas/genética , Variação Genética , Análise Multivariada , Panicum/genética , Panicum/microbiologia , Filogenia , Análise de Sequência de DNA , Microbiologia do Solo , Fatores de Tempo
17.
Yi Chuan ; 41(9): 875-882, 2019 Sep 20.
Artigo em Chinês | MEDLINE | ID: mdl-31549685

RESUMO

The advances in high-throughput technologies have enabled high-speed accumulation of omics data, which contain a large amount of genetic variations and their functional information. The integration and deep utilization of those data will be a long-term and difficult task, which requires highly efficient data storage and powerful data analysis and mining tools. In the past several years, our group has conducted multi-level genomic analyses in several plants, including genome assembly and annotation, comparative and population genomic studies, through collaboration with other labs inside and outside of our institution. Meanwhile, we have integrated a large amount of rice germplasm information and omics data into a structural database and developed related data query, visual display and mining web tools. Here, we summarize some of those results and discuss our next goal to construct an integrated omics knowledgebase for crops to support functional genomics and molecular design breeding.


Assuntos
Produtos Agrícolas/genética , Genômica , Bases de Conhecimento , Oryza/genética
18.
Theor Appl Genet ; 132(12): 3399-3411, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31562567

RESUMO

KEY MESSAGE: We propose new methods to predict genotype × environment interaction by selecting relevant environmental covariates and using an AMMI decomposition of the interaction. Farmers are asked to produce more efficiently and to reduce their inputs in the context of climate change. They have to face more and more limiting factors that can combine in numerous stress scenarios. One solution to this challenge is to develop varieties adapted to specific environmental stress scenarios. For this, plant breeders can use genomic predictions coupled with environmental characterization to identify promising combinations of genes in relation to stress covariates. One way to do it is to take into account the genetic similarity between varieties and the similarity between environments within a mixed model framework. Molecular markers and environmental covariates (EC) can be used to estimate relevant covariance matrices. In the present study, based on a multi-environment trial of 220 European elite winter bread wheat (Triticum aestivum L.) varieties phenotyped in 42 environments, we compared reference regression models potentially including ECs, and proposed alternative models to increase prediction accuracy. We showed that selecting a subset of ECs, and estimating covariance matrices using an AMMI decomposition to benefit from the information brought by the phenotypic records of the training set are promising approaches to better predict genotype-by-environment interactions (G × E). We found that using a different kinship for the main genetic effect and the G × E effect increased prediction accuracy. Our study also demonstrates that integrative stress indexes simulated by crop growth models are more efficient to capture G × E than climatic covariates.


Assuntos
Interação Gene-Ambiente , Modelos Genéticos , Triticum/genética , Produtos Agrícolas/genética , Genótipo , Modelos Estatísticos , Fenótipo
19.
Nat Protoc ; 14(10): 2954-2971, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31534231

RESUMO

Exogenous biomolecule delivery into plants is difficult because the plant cell wall poses a dominant transport barrier, thereby limiting the efficiency of plant genetic engineering. Traditional DNA delivery methods for plants suffer from host-species limitations, low transformation efficiencies, tissue damage, or unavoidable and uncontrolled DNA integration into the host genome. We have demonstrated efficient plasmid DNA delivery into intact plants of several species with functionalized high-aspect-ratio carbon nanotube (CNT) nanoparticles (NPs), enabling efficient DNA delivery into a variety of non-model plant species (arugula, wheat, and cotton) and resulting in high protein expression levels without transgene integration. Herein, we provide a protocol that can be implemented by plant biologists and adapted to produce functionalized single-walled CNTs (SWNTs) with surface chemistries optimized for delivery of plasmid DNA in a plant species-independent manner. This protocol describes how to prepare, construct, and optimize polyethylenimine (PEI)-functionalized SWNTs and perform plasmid DNA loading. The authors also provide guidance on material characterization, gene expression evaluation, and storage conditions. The entire protocol, from the covalent functionalization of SWNTs to expression quantification, can be completed in 5 d.


Assuntos
DNA/genética , Técnicas de Transferência de Genes , Nanotubos de Carbono , Plantas/genética , Produtos Agrícolas/genética , Nanotubos de Carbono/química , Plantas Geneticamente Modificadas , Plasmídeos/genética , Polietilenoimina/química , Transgenes
20.
Theor Appl Genet ; 132(12): 3277-3293, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31535162

RESUMO

KEY MESSAGE: Established spatial models improve the analysis of agricultural field trials with or without genomic data and can be fitted with the open-source R package INLA. The objective of this paper was to fit different established spatial models for analysing agricultural field trials using the open-source R package INLA. Spatial variation is common in field trials, and accounting for it increases the accuracy of estimated genetic effects. However, this is still hindered by the lack of available software implementations. We compare some established spatial models and show possibilities for flexible modelling with respect to field trial design and joint modelling over multiple years and locations. We use a Bayesian framework and for statistical inference the integrated nested Laplace approximations (INLA) implemented in the R package INLA. The spatial models we use are the well-known independent row and column effects, separable first-order autoregressive ([Formula: see text]) models and a Gaussian random field (Matérn) model that is approximated via the stochastic partial differential equation approach. The Matérn model can accommodate flexible field trial designs and yields interpretable parameters. We test the models in a simulation study imitating a wheat breeding programme with different levels of spatial variation, with and without genome-wide markers and with combining data over two locations, modelling spatial and genetic effects jointly. The results show comparable predictive performance for both the [Formula: see text] and the Matérn models. We also present an example of fitting the models to a real wheat breeding data and simulated tree breeding data with the Nelder wheel design to show the flexibility of the Matérn model and the R package INLA.


Assuntos
Simulação por Computador , Produtos Agrícolas/genética , Melhoramento Vegetal , Análise Espacial , Teorema de Bayes , Modelos Estatísticos , Software , Triticum/genética
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