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1.
Cytogenet Genome Res ; 161(5): 272-277, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34289478

RESUMO

The genus Dracaena is the main source of dragon's blood, which is a plant resin and has been used as traditional medicine since ancient times in different civilizations. However, the chromosome numbers and karyotypes present in this genus remain poorly understood. In this study, fluorescence in situ hybridization (FISH) using oligonucleotide probes for ribosomal DNAs (5S and 45S rDNA) and telomeric repeats (TTTAGGG)3 was applied to analyze 4 related species: Dracaena terniflora Roxb., Dracaena cambodiana Pierre ex Gagnep., Aizong (Dracaena sp.), and Dracaena cochinchinensis (Lour.) S.C. Chen. In all 4 species, both 5S and 45S rDNA showed hybridization signals in the paracentromeric region of a pair of chromosomes; the sizes of the 45S rDNA signals were larger than those of the 5S rDNA. Importantly, the telomeric repeat signals were located in the telomeric regions of almost all chromosomes. The results indicated that the chromosome number of all 4 Dracaena species is 2n = 40, and the lengths of the mitotic metaphase chromosomes range from 0.99 to 2.98 µm. Our results provide useful cytogenetic information, which will be beneficial to future studies in genome structure of the genus Dracaena.


Assuntos
Mapeamento Cromossômico/métodos , Cromossomos de Plantas/química , Dracaena/genética , Cariótipo , Centrômero , China , Dracaena/classificação , Hibridização in Situ Fluorescente/métodos , Cariotipagem/métodos , Filogeografia , RNA Ribossômico/genética , RNA Ribossômico 5S/genética , Telômero
2.
Int J Mol Sci ; 22(11)2021 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-34070753

RESUMO

In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simple method of in situ mapping of a short unique DNA sequences on plant chromosomes. We have carefully analyzed the critical steps of the Tyr-FISH to find out the reasons behind the flaws of this technique. The accurate visualization of markers/genes appeared to be significantly dependent on the means of chromosome slide preparation, probe design and labeling, and high stringency washing. Appropriate adjustment of these steps allowed us to detect a short DNA sequence of 1.6 Kb with a frequency of 51.6%. Based on our results, we developed a more reliable and simple protocol for dual-color Tyr-FISH visualization of unique short DNA sequences on plant chromosomes. This new protocol can allow for more accurate determination of the physical distance between markers and can be applied for faster integration of genetic and cytogenetic maps.


Assuntos
Mapeamento Cromossômico/métodos , Cromossomos de Plantas/química , Genoma de Planta , Hibridização in Situ Fluorescente , Cebolas/genética , Coloração e Rotulagem/métodos , Cromossomos de Plantas/metabolismo , Sondas de DNA/síntese química , Sondas de DNA/metabolismo , DNA de Plantas/genética , DNA de Plantas/metabolismo , Ligação Genética , Marcadores Genéticos , Cebolas/metabolismo , Transcriptoma
3.
Nat Commun ; 12(1): 1036, 2021 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-33589621

RESUMO

Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.


Assuntos
Cromossomos de Plantas/química , Genes Mitocondriais , Genes de Plantas , Infertilidade das Plantas/genética , RNA Mensageiro/genética , Triticum/genética , Sequência de Bases , Mapeamento Cromossômico , Citoplasma/genética , Citoplasma/metabolismo , Melhoramento Vegetal/métodos , Células Vegetais/química , Células Vegetais/metabolismo , Plantas Geneticamente Modificadas , Pólen/genética , Pólen/metabolismo , RNA Mensageiro/metabolismo , Triticum/metabolismo
4.
Genes (Basel) ; 11(7)2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32708324

RESUMO

Plants are under strong evolutionary pressure to maintain surveillance against pathogens. One major disease resistance mechanism is based on NB-LRR (NLR) proteins that specifically recognize pathogen effectors. The cluster organization of the NLR gene family could favor sequence exchange between NLR genes via recombination, favoring their evolutionary dynamics. Increasing data, based on progeny analysis, suggest the existence of a link between the perception of biotic stress and the production of genetic diversity in the offspring. This could be driven by an increased rate of meiotic recombination in infected plants, but this has never been strictly demonstrated. In order to test if pathogen infection can increase DNA recombination in pollen meiotic cells, we infected Arabidopsis Fluorescent Tagged Lines (FTL) with the virulent bacteria Pseudomonas syringae. We measured the meiotic recombination rate in two regions of chromosome 5, containing or not an NLR gene cluster. In all tested intervals, no significant difference in genetic recombination frequency between infected and control plants was observed. Although it has been reported that pathogen exposure can sometimes increase the frequency of recombinant progeny in plants, our findings suggest that meiotic recombination rate in Arabidopsis may be resilient to at least some pathogen attack. Alternative mechanisms are discussed.


Assuntos
Recombinação Homóloga , Meiose , Doenças das Plantas/genética , Arabidopsis , Cromossomos de Plantas/química , Cromossomos de Plantas/genética , Corantes Fluorescentes/química , Proteínas NLR/genética , Doenças das Plantas/microbiologia , Pólen/genética , Pólen/microbiologia , Pseudomonas syringae/patogenicidade
5.
Biosci Biotechnol Biochem ; 83(4): 666-674, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30585123

RESUMO

Asparagus (Asparagus officinalis) has several traits that make it a useful model for cytogenetic studies, however, few studies of the meiosis process have been made in asparagus. Here, we present in detail an atlas of male meiosis in asparagus, from preleptotene to telophase II. The meiosis process in asparagus is largely similar to those of the well-characterized model plants Arabidopsis thaliana, Zea mays, and Oryza sativa. However, most asparagus prophase I meiotic chromosomes show a strongly aggregated morphology, and this phenotype persists through the pachytene stage, highlighting a property in the control of chromosome migration and distribution in asparagus. Further, we observed no obvious banding of autofluorescent dots between divided nuclei of asparagus meiocytes, as one would expect in Arabidopsis. This description of wild-type asparagus meiosis will serve as a reference for the analyses of meiotic mutants, as well as for comparative studies among difference species. Abbreviations: DAPI: 4',6-diamidino-2-phenylindole; FISH: fluorescence in situ hybridization; PBS: phosphate-buffered saline; PMC: pollen mother cell; SEM: Scanning Electron Microscope.


Assuntos
Asparagus/ultraestrutura , Cromossomos de Plantas/ultraestrutura , Meiose , Células Vegetais/ultraestrutura , Pólen/ultraestrutura , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/ultraestrutura , Asparagus/genética , Asparagus/crescimento & desenvolvimento , Núcleo Celular/metabolismo , Núcleo Celular/ultraestrutura , Cromossomos de Plantas/química , Flores/genética , Flores/crescimento & desenvolvimento , Flores/ultraestrutura , Hibridização in Situ Fluorescente , Microscopia Eletrônica de Varredura , Células Vegetais/metabolismo , Pólen/genética , Pólen/crescimento & desenvolvimento
6.
G3 (Bethesda) ; 8(1): 123-130, 2018 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-29122849

RESUMO

Autosomal drivers violate Mendel's law of segregation in that they are overrepresented in gametes of heterozygous parents. For drivers to be polymorphic within populations rather than fixing, their transmission advantage must be offset by deleterious effects on other fitness components. In this paper, we develop an analytical model for the evolution of autosomal drivers that is motivated by the neocentromere drive system found in maize. In particular, we model both the transmission advantage and deleterious fitness effects on seed viability, pollen viability, seed to adult survival mediated by maternal genotype, and seed to adult survival mediated by offspring genotype. We derive general, biologically intuitive conditions for the four most likely evolutionary outcomes and discuss the expected evolution of autosomal drivers given these conditions. Finally, we determine the expected equilibrium allele frequencies predicted by the model given recent estimates of fitness components for all relevant genotypes and show that the predicted equilibrium is within the range observed in maize land races for levels of drive at the low end of what has been observed.


Assuntos
Centrômero/química , Cromossomos de Plantas/química , Evolução Molecular , Modelos Genéticos , Zea mays/genética , Alelos , Quimera/genética , Segregação de Cromossomos , Frequência do Gene , Heterozigoto , Meiose , Pólen/genética , Sementes/genética
7.
Methods Mol Biol ; 1653: 125-135, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28822130

RESUMO

Naturally occurring genetic variation in plants can be very useful to dissect the complex regulation of primary metabolism as well as of physiological traits such as photosynthesis and photorespiration. The physiological and genetic mechanisms underlying natural variation in closely related species or accessions may provide important information that can be used to improve crop yield. In this chapter we describe in detail the use of a population of introgression lines (ILs), with the Solanum pennellii IL population as a study case, as a tool for the identification of genomic regions involved in the control of photosynthetic efficiency.


Assuntos
Regulação da Expressão Gênica de Plantas , Genes de Plantas , Variação Genética , Fotossíntese/genética , Característica Quantitativa Herdável , Solanum/genética , Dióxido de Carbono/análise , Dióxido de Carbono/metabolismo , Quimera , Clorofila/metabolismo , Clorofila A , Mapeamento Cromossômico , Cromossomos de Plantas/química , Cruzamentos Genéticos , Fluorescência , Marcadores Genéticos , Genótipo , Imagem Óptica/métodos , Oxigênio/análise , Oxigênio/metabolismo , Consumo de Oxigênio/genética , Fenótipo , Melhoramento Vegetal , Folhas de Planta/genética , Folhas de Planta/metabolismo , Locos de Características Quantitativas , Solanum/metabolismo
8.
Sci Rep ; 6: 38401, 2016 12 05.
Artigo em Inglês | MEDLINE | ID: mdl-27917903

RESUMO

Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs. T0 DRGs, which suggested that 32 °C might be a more intense external stimulus than 18 °C resulting in more changes in the DNA methylation status of cultured microspores. Additionally, 32 °C treatment for 6 h led to increased CHG differential methylations of transposons (DMTs), which were mainly constituted by overlaps between the hypomethylated differentially methylated regions (hypo-DMRs) and transposon elements (TEs). Further analysis demonstrated that the DRGs and their paralogs exhibited differential methylated/demethylated patterns. To summarize, the present study is the first methylome analysis of cultured microspores in response to STHS and may provide valuable information on the roles of DNA methylation in heat response.


Assuntos
Brassica napus/genética , Metilação de DNA , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Pólen/genética , Brassica napus/metabolismo , Mapeamento Cromossômico , Cromossomos de Plantas/química , Cromossomos de Plantas/metabolismo , Elementos de DNA Transponíveis , Ontologia Genética , Loci Gênicos , Resposta ao Choque Térmico/genética , Temperatura Alta , Anotação de Sequência Molecular , Proteínas de Plantas/metabolismo , Pólen/metabolismo
9.
J Genet ; 95(3): 691-704, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27659341

RESUMO

Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro-exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka/Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.


Assuntos
Alumínio/toxicidade , Cromossomos de Plantas/química , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Proteínas de Transporte de Cátions Orgânicos/genética , Proteínas de Plantas/genética , Zea mays/efeitos dos fármacos , Sequência de Aminoácidos , Sequência Conservada , Éxons , Perfilação da Expressão Gênica , Ontologia Genética , Íntrons , Anotação de Sequência Molecular , Família Multigênica , Motivos de Nucleotídeos , Proteínas de Transporte de Cátions Orgânicos/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Duplicações Segmentares Genômicas , Seleção Genética , Sintenia , Zea mays/classificação , Zea mays/genética
10.
BMC Genomics ; 17(1): 614, 2016 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-27515663

RESUMO

BACKGROUND: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression in both mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored. RESULTS: In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover, coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes. CONCLUSIONS: Together, these results suggest that lincRNAs have potential functional roles in potato defence responses. Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.


Assuntos
Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Interações Hospedeiro-Patógeno , Pectobacterium carotovorum/patogenicidade , RNA Longo não Codificante/genética , RNA de Plantas/genética , Solanum tuberosum/genética , Cromossomos de Plantas/química , Éxons , Biblioteca Gênica , Ontologia Genética , Anotação de Sequência Molecular , Pectobacterium carotovorum/crescimento & desenvolvimento , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Imunidade Vegetal/genética , Caules de Planta/genética , Caules de Planta/imunologia , Caules de Planta/microbiologia , RNA Longo não Codificante/classificação , RNA Longo não Codificante/imunologia , RNA de Plantas/classificação , RNA de Plantas/imunologia , Solanum tuberosum/imunologia , Solanum tuberosum/microbiologia
11.
Chromosoma ; 120(4): 409-22, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21594600

RESUMO

Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.


Assuntos
Beta vulgaris , Centrômero/química , Cromossomos de Plantas/química , DNA Satélite/química , Epigenômica/métodos , Eucromatina/química , Heterocromatina/química , RNA Interferente Pequeno/química , Beta vulgaris/genética , Beta vulgaris/metabolismo , Southern Blotting , Centrômero/genética , Centrômero/metabolismo , Cromossomos de Plantas/genética , Cromossomos de Plantas/metabolismo , Análise por Conglomerados , Metilação de DNA , DNA Satélite/genética , DNA Satélite/metabolismo , Eucromatina/genética , Eucromatina/metabolismo , Heterocromatina/genética , Heterocromatina/metabolismo , Histonas/genética , Histonas/metabolismo , Hibridização in Situ Fluorescente , RNA Interferente Pequeno/genética , Análise de Sequência de DNA , Bibliotecas de Moléculas Pequenas/química
12.
Chromosoma ; 112(7): 342-9, 2004 May.
Artigo em Inglês | MEDLINE | ID: mdl-15138769

RESUMO

A multidisciplinary study was carried out to analyse the chromosome doubling process during the early stages of in vitro maize microspore embryogenesis. The main stages (microspore derivatives) that were formed in the course of the culture were analysed. Chromosome number was determined from squashed cells, and DNA content was measured by cytometry. In parallel, an ultrastructural analysis of the microspore derivatives demonstrated the occurrence of a nuclear fusion process. It seems likely that nuclear fusion ensures chromosome doubling at early stages of induced microspore embryogenesis. It occurs precisely at the 5/7 day stage in the embryonic domain and probably leads to polyploidy in the endosperm domain of the microspore derivatives. As a conclusion a scheme summarises the results and proposes an interpretation of the sequence of chromosome doubling events during early maize microspore embryogenesis. Understanding of this process will be important for future efforts to increase the percentage of homozygous plants for crop improvement.


Assuntos
Núcleo Celular/ultraestrutura , Cromossomos de Plantas/genética , Diploide , Pólen/embriologia , Zea mays/embriologia , Zea mays/genética , Fusão Celular , Núcleo Celular/metabolismo , Células Cultivadas , Cromossomos de Plantas/química , Pólen/metabolismo , Pólen/ultraestrutura , Fatores de Tempo , Zea mays/ultraestrutura
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