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  1 / 16089 MEDLINE  
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[PMID]:29408396
[Au] Autor:Wang W; Zhang H; Wei X; Yang L; Yang B; Zhang L; Li J; Jiang YQ
[Ad] Endereço:State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China.
[Ti] Título:Functional characterization of calcium-dependent protein kinase (CPK) 2 gene from oilseed rape (Brassica napus L.) in regulating reactive oxygen species signaling and cell death control.
[So] Source:Gene;651:49-56, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Calcium-dependent protein kinases (CPKs), being Ser/Thr protein kinases found only in plants and some protozoans are calcium sensors that regulate diverse biological processes. However, the function and mode of CPKs in oilseed rape (Brassica napus) remain elusive. In this study, we identified CPK2 from oilseed rape as a novel regulator of reactive oxygen species (ROS) and cell death. BnaCPK2 was identified to be located at the endoplasmic reticulum membrane. Expression of BnaCPK2 was induced during Bax-induced cell death. Overexpression of the constitutively active form of BnaCPK2 led to significantly more accumulation of ROS and cell death than the full-length CPK2, which is supported by various measurements of physiological data. In addition, a quantitative RT-PCR survey revealed that the expression levels of a few marker genes are significantly changed as a result of CPK2 expression. Mating-based split ubiquitin system (mbSUS) and bimolecular fluorescence complementation (BiFC) were used to screen and confirm the BnaCPK2 interacting proteins. We identified and confirmed that CPK2 interacted with NADPH oxidase-like respiratory burst oxidase homolog D (RbohD), but not with RbohF. Based on its function and interacting partners, we propose that BnaCPK2 plays an important role in ROS and cell death control through interacting with RbohD.
[Mh] Termos MeSH primário: Brassica napus/genética
Morte Celular/genética
Proteínas de Plantas/genética
Proteínas Quinases/genética
Espécies Reativas de Oxigênio/metabolismo
[Mh] Termos MeSH secundário: Brassica napus/enzimologia
Clonagem Molecular
DNA de Plantas
Proteínas de Plantas/metabolismo
Proteínas Quinases/metabolismo
Análise de Sequência de DNA
Transdução de Sinais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant); 0 (Plant Proteins); 0 (Reactive Oxygen Species); EC 2.7.- (Protein Kinases); EC 2.7.1.- (calcium-dependent protein kinase)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180207
[St] Status:MEDLINE


  2 / 16089 MEDLINE  
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[PMID]:29351563
[Au] Autor:Ates D; Aldemir S; Alsaleh A; Erdogmus S; Nemli S; Kahriman A; Ozkan H; Vandenberg A; Tanyolac B
[Ad] Endereço:Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey.
[Ti] Título:A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.
[So] Source:PLoS One;13(1):e0191375, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). RESULTS: The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. CONCLUSION: This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
[Mh] Termos MeSH primário: Lens (Planta)/genética
[Mh] Termos MeSH secundário: Mapeamento Cromossômico/métodos
Sequência Consenso
DNA de Plantas/genética
Ligação Genética
Genoma de Planta
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180120
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191375


  3 / 16089 MEDLINE  
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[PMID]:29352281
[Au] Autor:Al-Harrasi I; Al-Yahyai R; Yaish MW
[Ad] Endereço:Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
[Ti] Título:Differential DNA methylation and transcription profiles in date palm roots exposed to salinity.
[So] Source:PLoS One;13(1):e0191492, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation. To achieve these, whole-genome bisulfite sequencing (WGBS) was employed and mRNA was sequenced from salinity-treated and untreated roots. The WGBS analysis included 324,987,795 and 317,056,091 total reads of the control and the salinity-treated samples, respectively. The analysis covered about 81% of the total genomic DNA with about 40% of mapping efficiency of the sequenced reads and an average read depth of 17-fold coverage per DNA strand, and with a bisulfite conversion rate of around 99%. The level of methylation within the differentially methylated regions (DMRs) was significantly (p < 0.05, FDR ≤ 0.05) increased in response to salinity specifically at the mCHG and mCHH sequence contexts. Consistently, the mass spectrometry and the enzyme-linked immunosorbent assay (ELISA) showed that there was a significant (p < 0.05) increase in the global DNA methylation in response to salinity. mRNA sequencing revealed the presence of 6,405 differentially regulated genes with a significant value (p < 0.001, FDR ≤ 0.05) in response to salinity. Integration of high-resolution methylome and transcriptome analyses revealed a negative correlation between mCG methylation located within the promoters and the gene expression, while a positive correlation was noticed between mCHG/mCHH methylation rations and gene expression specifically when plants grew under control conditions. Therefore, the methylome and transcriptome relationships vary based on the methylated sequence context, the methylated region within the gene, the protein-coding ability of the gene, and the salinity treatment. These results provide insights into interplay among DNA methylation and gene expression, and highlight the effect of salinity on the nature of this relationship, which may involve other genetic and epigenetic players under salt stress conditions. The results obtained from this project provide the first draft map of the differential methylome and transcriptome of date palm when exposed to an abiotic stress.
[Mh] Termos MeSH primário: Metilação de DNA
Phoeniceae/genética
Phoeniceae/metabolismo
Salinidade
[Mh] Termos MeSH secundário: Adaptação Fisiológica/genética
DNA de Plantas/genética
DNA de Plantas/metabolismo
Epigênese Genética
Perfilação da Expressão Gênica
Genes de Plantas
Anotação de Sequência Molecular
Phoeniceae/crescimento & desenvolvimento
Fotossíntese
Raízes de Plantas/genética
Raízes de Plantas/crescimento & desenvolvimento
Raízes de Plantas/metabolismo
Regiões Promotoras Genéticas
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA de Plantas/genética
RNA de Plantas/metabolismo
Sequenciamento Completo do Genoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (DNA, Plant); 0 (RNA, Messenger); 0 (RNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191492


  4 / 16089 MEDLINE  
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[PMID]:29342197
[Au] Autor:Talukder SK; Azhaguvel P; Chekhovskiy K; Saha MC
[Ad] Endereço:Noble Research Institute, LLC, Ardmore, OK, United States of America.
[Ti] Título:Molecular discrimination of tall fescue morphotypes in association with Festuca relatives.
[So] Source:PLoS One;13(1):e0191343, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute's core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. F. pratensis and F. arundinacea var. glaucescens, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and F. mairei (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both F. pratensis and F. mairei formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity.
[Mh] Termos MeSH primário: Cloroplastos/genética
Festuca/genética
[Mh] Termos MeSH secundário: DNA de Plantas/genética
Festuca/metabolismo
Variação Genética/genética
Genômica/métodos
Genótipo
Repetições de Microssatélites/genética
Filogenia
Poaceae/genética
Análise de Sequência de DNA/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180118
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191343


  5 / 16089 MEDLINE  
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[PMID]:28888790
[Au] Autor:Simpson L; Clements MA; Crayn DM; Nargar K
[Ad] Endereço:Australian Tropical Herbarium, Sir Robert Norman Building (E2), James Cook University, Cairns, PO Box 6811, QLD 4878, Australia; Centre for Tropical Biodiversity and Climate Change, James Cook University, Building 145, James Cook Drive, Townsville, QLD 4811, Australia. Electronic address: lalita.sim
[Ti] Título:Evolution in Australia's mesic biome under past and future climates: Insights from a phylogenetic study of the Australian Rock Orchids (Dendrobium speciosum complex, Orchidaceae).
[So] Source:Mol Phylogenet Evol;118:32-46, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Australian mesic biome spans c. 33° of latitude along Australia's east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary diversification and to predict the impact of future climate change on the distribution of species and genetic diversity within this biome, we inferred phylogenetic relationships within the Dendrobium speciosum complex (Orchidaceae) across its distribution and undertook environmental niche modelling (ENM) under past, contemporary and projected future climates. Neighbor Joining tree inference, NeighborNet and Structure analyses of Amplified Fragment Length Polymorphism (AFLP) profiles for D. speciosum sampled from across its distribution showed that the complex consists of two highly supported main groups that are geographically separated by the St. Lawrence gap, an area of dry sclerophyll forest and woodland. The presence of several highly admixed individuals identified by the Structure analysis provided evidence of genetic exchange between the two groups across this gap. Whereas previous treatments have recognised between one to eleven species, the molecular results support the taxonomic treatment of the complex as a single species with two subspecies. The ENM analysis supported the hypothesis that lineage divergence within the complex was driven by past climatic changes. The St. Lawrence gap represented a stronger biogeographic barrier for the D. speciosum complex during the cool and dry glacial climatic conditions of the Pleistocene than under today's interglacial conditions. Shallow genetic divergence was found within the two lineages, which mainly corresponded to three other biogeographic barriers: the Black Mountain Corridor, Glass House Mountains and the Hunter Valley. Our ENM analyses provide further support for the hypothesis that biogeographic barriers along Australia's east coast were somewhat permeable to genetic exchange due to past episodic range expansions and contractions caused by climatic change resulting in recurrent contact between previously isolated populations. An overall southward shift in the distribution of the complex under future climate scenarios was predicted, with the strongest effects on the northern lineage. This study contributes to our understanding of the factors shaping biodiversity patterns in Australia's mesic biome.
[Mh] Termos MeSH primário: Dendrobium/classificação
[Mh] Termos MeSH secundário: Análise do Polimorfismo de Comprimento de Fragmentos Amplificados
Austrália
Evolução Biológica
Mudança Climática
DNA de Plantas/química
DNA de Plantas/metabolismo
Dendrobium/genética
Ecossistema
Variação Genética
Filogenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170911
[St] Status:MEDLINE


  6 / 16089 MEDLINE  
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[PMID]:29293613
[Au] Autor:Silva JC; Carvalho CR; Clarindo WR
[Ad] Endereço:Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa-MG, Brazil.
[Ti] Título:Updating the maize karyotype by chromosome DNA sizing.
[So] Source:PLoS One;13(1):e0190428, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The karyotype is a basic concept regarding the genome, fundamentally described by the number and morphological features of all chromosomes. Chromosome class, centromeric index, intra- and interchromosomal asymmetry index, and constriction localization are important in clinical, systematic and evolutionary approaches. In spite of the advances in karyotype characterization made over the last years, new data about the chromosomes can be generated from quantitative methods, such as image cytometry. Therefore, using Zea mays L., this study aimed to update the species' karyotype by supplementing information on chromosome DNA sizing. After adjustment of the procedures, chromosome morphometry and class as well as knob localization enabled describing the Z. mays karyotype. In addition, applying image cytometry, DNA sizing was unprecedentedly measured for the arms and satellite of all chromosomes. This way, unambiguous identification of the chromosome pairs, and hence the assembly of 51 karyograms, were only possible after the DNA sizing of each chromosome, their arms and satellite portions. These accurate, quantitative and reproducible data also enabled determining the distribution and variation of DNA content in each chromosome. From this, a correlation between DNA amount and total chromosome length evidenced that the mean DNA content of chromosome 9 was higher than that of chromosome 8. The chromosomal DNA sizing updated the Z. mays karyotype, providing insights into its dynamic genome with regards to the organization of the ten chromosomes and their respective portions. Considering the results and the relevance of cytogenetics in the current scenario of comparative sequencing and genomics, chromosomal DNA sizing should be incorporated as an additional parameter for karyotype definition. Based on this study, it can be affirmed that cytogenetic approaches go beyond the simple morphological description of chromosomes.
[Mh] Termos MeSH primário: Cromossomos de Plantas
DNA de Plantas/genética
Cariotipagem
Zea mays/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190428


  7 / 16089 MEDLINE  
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[PMID]:29232688
[Au] Autor:Raskina O
[Ad] Endereço:Institute of Evolution, University of Haifa, Haifa, Israel.
[Ti] Título:Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in Aegilops speltoides Tausch (Poaceae, Triticeae).
[So] Source:Cytogenet Genome Res;153(2):105-116, 2017.
[Is] ISSN:1424-859X
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:In wild plant populations, chromosome rearrangements lead to the wide intraspecific polymorphisms in the abundance and patterns of highly repetitive DNA. However, despite the large amount of accumulated data, the impact of the complex repetitive DNA fraction on genome reorganization and functioning and the mechanisms balancing and maintaining the structural integrity of the genome are not fully understood. Homologous recombination is thought to play a key role in both genome reshuffling and stabilization, while the contribution of nonhomologous recombination seems to be undervalued. Here, tandem repeat patterns and dynamics during pollen mother cell development were addressed, with a focus on the meiotic recombination that determines chromosome/genome repatterning and stabilization under cross-pollination and artificial hybridization in wild goatgrass, Aegilops speltoides. Native plants from contrasting allopatric populations and artificially created intraspecific hybrids were investigated using a FISH approach. Cytogenetic analysis uncovered a wide spectrum of genotype- and cell-specific chromosomal rearrangements, suggesting intensive repatterning of both parental and hybrid genomes. The data obtained provide evidence that repetitive elements serve as overabundant and ubiquitous resources for maintaining chromosome architecture/genome integrity through homologous and nonhomologous recombination at the intraorganismal level, and genotype-specific repatterning underlies intrapopulation polymorphisms and intraspecific diversification in the wild.
[Mh] Termos MeSH primário: Cromossomos de Plantas/genética
DNA de Plantas/genética
Poaceae/genética
Sequências de Repetição em Tandem/genética
[Mh] Termos MeSH secundário: Cromossomos de Plantas/ultraestrutura
Cruzamentos Genéticos
Genoma de Planta
Genótipo
Recombinação Homóloga
Hibridização Genética
Hibridização in Situ Fluorescente
Meiose
Metagenômica
Polimorfismo Genético
Turquia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171213
[St] Status:MEDLINE
[do] DOI:10.1159/000484917


  8 / 16089 MEDLINE  
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[PMID]:29054811
[Au] Autor:Silva SR; Gibson R; Adamec L; Domínguez Y; Miranda VFO
[Ad] Endereço:Universidade Estadual Paulista (Unesp), Instituto de Biociências, Botucatu, São Paulo, Brazil; Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil.. Electronic address: saura.silva@gma
[Ti] Título:Molecular phylogeny of bladderworts: A wide approach of Utricularia (Lentibulariaceae) species relationships based on six plastidial and nuclear DNA sequences.
[So] Source:Mol Phylogenet Evol;118:244-264, 2018 Jan.
[Is] ISSN:1095-9513
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The carnivorous plant genus Utricularia L. (bladderwort) comprises about 240 species distributed worldwide and is traditionally classified into two subgenera (Polypompholyx and Utricularia) and 35 sections, based mainly on general and trap morphology. It is one out of the largest carnivorous genera, representing ca. 30% of all carnivorous plant species, and is also the most widely distributed. According to previous phylogenetic studies, most infrageneric sections are monophyletic, but there are several incongruences considering their relationships and also the dissenting position of some species as a result of a too few (mostly one or two) molecular markers analyzed. Thus, here we present a multilocus phylogeny for Utricularia species with a wide taxonomic sampling (78 species and 115 accessions) based on six plastid (rbcL, matK, rpl20-rps12, rps16, trnL-F) and nuclear DNA (ITS region) sequences. The aim is to reconstruct a well-resolved tree to propose evolutionary and biogeographic hypotheses for the radiation of lineages with inferences about the divergence times of clades using a molecular clock approach.
[Mh] Termos MeSH primário: DNA de Plantas/química
Lamiales/genética
Plastídeos/genética
[Mh] Termos MeSH secundário: Sequência de Bases
Teorema de Bayes
Evolução Biológica
Núcleo Celular/genética
DNA de Plantas/isolamento & purificação
DNA de Plantas/metabolismo
Lamiales/classificação
Filogenia
Proteínas de Plantas/classificação
Proteínas de Plantas/genética
Proteínas de Plantas/metabolismo
Ribulose-Bifosfato Carboxilase/classificação
Ribulose-Bifosfato Carboxilase/genética
Ribulose-Bifosfato Carboxilase/metabolismo
Alinhamento de Sequência
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant); 0 (Plant Proteins); EC 4.1.1.39 (RbcL protein, plastid); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171022
[St] Status:MEDLINE


  9 / 16089 MEDLINE  
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[PMID]:29338034
[Au] Autor:Geremew A; Stiers I; Sierens T; Kefalew A; Triest L
[Ad] Endereço:Laboratory of Plant Biology and Nature Management (APNA), Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
[Ti] Título:Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps.
[So] Source:PLoS One;13(1):e0190810, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m) in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low) were sampled for two years. We found that ramets under the high sedimentation regime (HSR) were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR). The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR) to phalanx (in HSR). Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80) as compared to the LSR (R = 0.48). Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.
[Mh] Termos MeSH primário: Cyperus/crescimento & desenvolvimento
Cyperus/genética
[Mh] Termos MeSH secundário: Aclimatação
Adaptação Fisiológica
Biodiversidade
Cyperus/fisiologia
DNA de Plantas/genética
Etiópia
Variação Genética
Genótipo
Sedimentos Geológicos
Repetições de Microssatélites
Solo
Zonas Úmidas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Plant); 0 (Soil)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190810


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[PMID]:29272307
[Au] Autor:Technow F; Gerke J
[Ad] Endereço:Maize Product Development/Systems and Innovation for Breeding and Seed Products, DuPont Pioneer, Tavistock, Ontario, Canada.
[Ti] Título:Parent-progeny imputation from pooled samples for cost-efficient genotyping in plant breeding.
[So] Source:PLoS One;12(12):e0190271, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The increased usage of whole-genome selection (WGS) and other molecular evaluation methods in plant breeding relies on the ability to genotype a very large number of untested individuals in each breeding cycle. Many plant breeding programs evaluate large biparental populations of homozygous individuals derived from homozygous parent inbred lines. This structure lends itself to parent-progeny imputation, which transfers the genotype scores of the parents to progeny individuals that are genotyped for a much smaller number of loci. Here we introduce a parent-progeny imputation method that infers individual genotypes from non-barcoded pooled samples of DNA of multiple individuals using a Hidden Markov Model (HMM). We demonstrate the method for pools of simulated maize double haploids (DH) from biparental populations, genotyped using a genotyping by sequencing (GBS) approach for 3,000 loci at 0.125x to 4x coverage. We observed high concordance between true and imputed marker scores and the HMM produced well-calibrated genotype probabilities that correctly reflected the uncertainty of the imputed scores. Genomic estimated breeding values (GEBV) calculated from the imputed scores closely matched GEBV calculated from the true marker scores. The within-population correlation between these sets of GEBV approached 0.95 at 1x and 4x coverage when pooling two or four individuals, respectively. Our approach can reduce the genotyping cost per individual by a factor up to the number of pooled individuals in GBS applications without the need for extra sequencing coverage, thereby enabling cost-effective large scale genotyping for applications such as WGS in plant breeding.
[Mh] Termos MeSH primário: Análise Custo-Benefício
Melhoramento Vegetal
[Mh] Termos MeSH secundário: DNA de Plantas/genética
Sequenciamento de Nucleotídeos em Larga Escala
Cadeias de Markov
Modelos Teóricos
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171223
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190271



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