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1.
Nat Commun ; 11(1): 4928, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004791

RESUMO

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.


Assuntos
Aclimatação/genética , Cromatina/metabolismo , Grupos Étnicos/genética , Redes Reguladoras de Genes , Modelos Genéticos , Altitude , Doença da Altitude/etnologia , Doença da Altitude/genética , Doença da Altitude/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Hipóxia Celular/genética , Células Cultivadas , Cromatina/genética , Sequenciamento de Cromatina por Imunoprecipitação , Resistência à Doença/genética , Feminino , Regulação da Expressão Gênica , Células Endoteliais da Veia Umbilical Humana , Humanos , Hipóxia/genética , Hipóxia/metabolismo , Oxigênio/metabolismo , Polimorfismo de Nucleotídeo Único , Gravidez , Cultura Primária de Células , RNA-Seq , Elementos Reguladores de Transcrição/genética , Seleção Genética , Tibet/etnologia , Fatores de Transcrição/metabolismo , Sequenciamento Completo do Genoma
2.
Phytopathology ; 110(10): 1721-1726, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32915112

RESUMO

Stem rust is an important disease of cultivated oat (Avena sativa) caused by Puccinia graminis f. sp. avenae. In North America, host resistance is the primary strategy to control this disease and is conferred by a relatively small number of resistance genes. Pg2 is a widely deployed stem rust resistance gene that originates from cultivated oat. Oat breeders wish to develop cultivars with multiple Pg genes to slow the breakdown of single gene resistance, and often require DNA markers suited for marker-assisted selection. Our objectives were to (i) construct high density linkage maps for a major oat stem rust resistance gene using three biparental mapping populations, (ii) develop Kompetitive allele-specific PCR (KASP) assays for Pg2-linked single-nucleotide polymorphisms (SNPs), and (iii) test the prediction accuracy of those markers with a diverse panel of spring oat lines and cultivars. Genotyping-by-sequencing SNP markers linked to Pg2 were identified in an AC Morgan/CDC Morrison recombinant inbred line (RIL) population. Pg2-linked SNPs were then analyzed in an AC Morgan/RL815 F2 population and an AC Morgan/CDC Dancer RIL population. Linkage analysis identified a common location for Pg2 in all three populations on linkage group Mrg20 of the oat consensus genetic map. The most predictive markers were identified and converted to KASP assays for use in oat breeding programs. When used in combination, the KASP assays for the SNP loci avgbs2_126549.1.46 and avgbs_cluster_23819.1.27 were highly predictive of Pg2 status in panel of 54 oat breeding lines and cultivars.


Assuntos
Avena/genética , Basidiomycota , Mapeamento Cromossômico , Resistência à Doença/genética , Ligação Genética , Humanos , América do Norte , Doenças das Plantas , Polimorfismo de Nucleotídeo Único/genética
3.
Nat Commun ; 11(1): 4447, 2020 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-32895382

RESUMO

Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the 'Longjing 43' cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.


Assuntos
Camellia sinensis/genética , Resistência à Doença/genética , Evolução Molecular , Genoma de Planta/genética , Melhoramento Vegetal , Domesticação , Perfilação da Expressão Gênica , Genômica , Filogenia , Polimorfismo de Nucleotídeo Único
4.
Nat Commun ; 11(1): 4393, 2020 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-32879321

RESUMO

Rcr3 is a secreted protease of tomato that is targeted by fungal effector Avr2, a secreted protease inhibitor of the fungal pathogen Cladosporium fulvum. The Avr2-Rcr3 complex is recognized by receptor-like protein Cf-2, triggering hypersensitive cell death (HR) and disease resistance. Avr2 also targets Rcr3 paralog Pip1, which is not required for Avr2 recognition but contributes to basal resistance. Thus, Rcr3 acts as a guarded decoy in this interaction, trapping the fungus into a recognition event. Here we show that Rcr3 evolved > 50 million years ago (Mya), whereas Cf-2 evolved <6Mya by co-opting the pre-existing Rcr3 in the Solanum genus. Ancient Rcr3 homologs present in tomato, potato, eggplants, pepper, petunia and tobacco can be inhibited by Avr2 with the exception of tobacco Rcr3. Four variant residues in Rcr3 promote Avr2 inhibition, but the Rcr3 that co-evolved with Cf-2 lacks three of these residues, indicating that the Rcr3 co-receptor is suboptimal for Avr2 binding. Pepper Rcr3 triggers HR with Cf-2 and Avr2 when engineered for enhanced inhibition by Avr2. Nicotiana benthamiana (Nb) is a natural null mutant carrying Rcr3 and Pip1 alleles with deleterious frame-shift mutations. Resurrected NbRcr3 and NbPip1 alleles were active proteases and further NbRcr3 engineering facilitated Avr2 inhibition, uncoupled from HR signalling. The evolution of a receptor co-opting a conserved pathogen target contrasts with other indirect pathogen recognition mechanisms.


Assuntos
Cladosporium , Resistência à Doença/genética , Peptídeo Hidrolases/genética , Imunidade Vegetal/genética , Solanum , Tabaco , Cladosporium/genética , Cladosporium/metabolismo , Cladosporium/patogenicidade , Evolução Molecular , Proteínas Fúngicas/metabolismo , Genes de Plantas , Interações Hospedeiro-Parasita , Peptídeo Hidrolases/metabolismo , Filogenia , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Inibidores de Proteases/metabolismo , Solanum/genética , Solanum/metabolismo , Solanum/microbiologia , Tabaco/genética , Tabaco/metabolismo , Tabaco/microbiologia
5.
PLoS Biol ; 18(9): e3000783, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32925907

RESUMO

Plant nucleotide-binding (NB) leucine-rich repeat (LRR) receptor (NLR) proteins function as intracellular immune receptors that perceive the presence of pathogen-derived virulence proteins (effectors) to induce immune responses. The 2 major types of plant NLRs that "sense" pathogen effectors differ in their N-terminal domains: these are Toll/interleukin-1 receptor resistance (TIR) domain-containing NLRs (TNLs) and coiled-coil (CC) domain-containing NLRs (CNLs). In many angiosperms, the RESISTANCE TO POWDERY MILDEW 8 (RPW8)-CC domain containing NLR (RNL) subclass of CNLs is encoded by 2 gene families, ACTIVATED DISEASE RESISTANCE 1 (ADR1) and N REQUIREMENT GENE 1 (NRG1), that act as "helper" NLRs during multiple sensor NLR-mediated immune responses. Despite their important role in sensor NLR-mediated immunity, knowledge of the specific, redundant, and synergistic functions of helper RNLs is limited. We demonstrate that the ADR1 and NRG1 families act in an unequally redundant manner in basal resistance, effector-triggered immunity (ETI) and regulation of defense gene expression. We define RNL redundancy in ETI conferred by some TNLs and in basal resistance against virulent pathogens. We demonstrate that, in Arabidopsis thaliana, the 2 RNL families contribute specific functions in ETI initiated by specific CNLs and TNLs. Time-resolved whole genome expression profiling revealed that RNLs and "classical" CNLs trigger similar transcriptome changes, suggesting that RNLs act like other CNLs to mediate ETI downstream of sensor NLR activation. Together, our genetic data confirm that RNLs contribute to basal resistance, are fully required for TNL signaling, and can also support defense activation during CNL-mediated ETI.


Assuntos
Arabidopsis/imunologia , Proteínas NLR/fisiologia , Imunidade Vegetal/genética , Receptores Imunológicos/fisiologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/fisiologia , Resistência à Doença/genética , Resistência à Doença/imunologia , Regulação da Expressão Gênica de Plantas , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/fisiologia , Família Multigênica/genética , Família Multigênica/fisiologia , Proteínas NLR/genética , Doenças das Plantas/genética , Doenças das Plantas/imunologia , Plantas Geneticamente Modificadas , Receptores Imunológicos/genética , Transdução de Sinais/genética , Transdução de Sinais/imunologia , Transcriptoma
6.
PLoS One ; 15(8): e0236674, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32756600

RESUMO

In Sub-Saharan Africa cassava (Manihot esculenta Crantz) is one of the most important food crops where more than 40% of the population relies on it as their staple carbohydrate source. Biotic constraints such as viral diseases, mainly Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD), and arthropod pests, particularly Cassava Green Mite (CGM), are major constraints to the realization of cassava's full production potential in Africa. To address these problems, we aimed to map the quantitative trait loci (QTL) associated with resistance to CBSD foliar and root necrosis symptoms, foliar CMD and CGM symptoms in a full-sib mapping population derived from the genotypes AR40-6 and Albert. A high-density linkage map was constructed with 2,125 SNP markers using a genotyping-by-sequencing approach. For phenotyping, clonal evaluation trials were conducted with 120 F1 individuals for two consecutive field seasons using an alpha-lattice design at Chambezi and Naliendele, Tanzania. Previously identified QTL for resistance to CBSD foliar symptoms were corroborated, and a new putative QTL for CBSD root necrosis identified (qCBSDRNc14AR) from AR40-6. Two QTL were identified within the region of the previously recognized CMD2 locus from this population in which both parents are thought to possess the CMD2 locus. Interestingly, a minor but consistent QTL, qCGM18AR, for CGM resistance at 3 months after planting stage was also detected and co-localized with a previously identified SSR marker, NS346, linked with CGM resistance. Markers underlying these QTL may be used to increase efficiencies in cassava breeding programs.


Assuntos
Resistência à Doença/genética , Manihot/genética , Doenças das Plantas/genética , Locos de Características Quantitativas/genética , Cruzamento , Testes Genéticos , Genótipo , Manihot/fisiologia , Manihot/virologia , Doenças das Plantas/virologia , Potyviridae/genética , Potyviridae/patogenicidade , Estresse Fisiológico/genética , Tanzânia
7.
Infect Genet Evol ; 84: 104498, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32771700

RESUMO

New coronavirus SARS-CoV-2 is capable to infect humans and cause a novel disease COVID-19. Aiming to understand a host genetic component of COVID-19, we focused on variants in genes encoding proteases and genes involved in innate immunity that could be important for susceptibility and resistance to SARS-CoV-2 infection. Analysis of sequence data of coding regions of FURIN, PLG, PRSS1, TMPRSS11a, MBL2 and OAS1 genes in 143 unrelated individuals from Serbian population identified 22 variants with potential functional effect. In silico analyses (PolyPhen-2, SIFT, MutPred2 and Swiss-Pdb Viewer) predicted that 10 variants could impact the structure and/or function of proteins. These protein-altering variants (p.Gly146Ser in FURIN; p.Arg261His and p.Ala494Val in PLG; p.Asn54Lys in PRSS1; p.Arg52Cys, p.Gly54Asp and p.Gly57Glu in MBL2; p.Arg47Gln, p.Ile99Val and p.Arg130His in OAS1) may have predictive value for inter-individual differences in the response to the SARS-CoV-2 infection. Next, we performed comparative population analysis for the same variants using extracted data from the 1000 Genomes project. Population genetic variability was assessed using delta MAF and Fst statistics. Our study pointed to 7 variants in PLG, TMPRSS11a, MBL2 and OAS1 genes with noticeable divergence in allelic frequencies between populations worldwide. Three of them, all in MBL2 gene, were predicted to be damaging, making them the most promising population-specific markers related to SARS-CoV-2 infection. Comparing allelic frequencies between Serbian and other populations, we found that the highest level of genetic divergence related to selected loci was observed with African, followed by East Asian, Central and South American and South Asian populations. When compared with European populations, the highest divergence was observed with Italian population. In conclusion, we identified 4 variants in genes encoding proteases (FURIN, PLG and PRSS1) and 6 in genes involved in the innate immunity (MBL2 and OAS1) that might be relevant for the host response to SARS-CoV-2 infection.


Assuntos
Infecções por Coronavirus/genética , Resistência à Doença/genética , Predisposição Genética para Doença , Interações Hospedeiro-Patógeno/genética , Metagenômica , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Glicoproteína da Espícula de Coronavírus/genética , Alelos , Betacoronavirus/imunologia , Betacoronavirus/patogenicidade , Infecções por Coronavirus/imunologia , Proteínas do Olho/genética , Proteínas do Olho/imunologia , Furina/genética , Furina/imunologia , Frequência do Gene , Variação Genética , Genoma Humano , Interações Hospedeiro-Patógeno/imunologia , Humanos , Imunidade Inata , Lectina de Ligação a Manose/genética , Lectina de Ligação a Manose/imunologia , Glicoproteínas de Membrana/genética , Glicoproteínas de Membrana/imunologia , Pandemias , Peptidil Dipeptidase A/imunologia , Plasminogênio/genética , Plasminogênio/imunologia , Pneumonia Viral/imunologia , Ligação Proteica , Glicoproteína da Espícula de Coronavírus/imunologia , Tripsina/genética , Tripsina/imunologia
8.
Plant Dis ; 104(10): 2658-2664, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32749944

RESUMO

There has not been a major wheat stem rust epidemic worldwide since the 1970s, but the emergence of race TTKSK of Puccinia graminis f. sp. tritici in 1998 presented a great threat to the world wheat production. Single disease-resistance genes are usually effective for only several years before the pathogen changes genetically to overcome the resistance. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most common and persistent wheat diseases worldwide. The development of varieties with multiple resistance is the most economical and effective strategy for preventing stripe rust and stem rust, the two main rust diseases constraining wheat production. Plateau 448 has been widely used in the spring wheat growing region in northwest China, but it has become susceptible to stripe rust and is susceptible to TTKSK. To produce more durable resistance to race TTKSK as well as to stripe rust, four stem rust resistance genes (Sr33, Sr36, Sr-Cad, and Sr43) and three stripe rust resistance genes (Yr5, Yr18, and Yr26) were simultaneously introgressed into Plateau 448 to improve its stem rust (Ug99) and stripe rust resistance using a marker-assisted backcrossing strategy combined with phenotypic selection. We obtained 131 BC1F5 lines that pyramided two to four Ug99 resistance genes and one to two Pst resistance genes simultaneously. Thirteen of these lines were selected for their TTKSK resistance, and all of them exhibited near immunity or high resistance to TTKSK. Among the 131 pyramided lines, 95 showed high resistance to mixed Pst races. Nine lines exhibited not only high resistance to TTKSK and Pst but also better agronomic traits and high-molecular-weight glutenin subunit compositions than Plateau 448.


Assuntos
Basidiomycota , Doenças das Plantas/genética , Cruzamento , China , Resistência à Doença/genética , Humanos
9.
PLoS One ; 15(8): e0237741, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32804977

RESUMO

Region-specific local landraces represent a germplasm diversity adapted and acclimatized to local conditions, and are ideal to breed for targeted market niches while maintaining the variability of heirloom traits. A collection of 180 pepper accessions, collected from 62 diverse locations across six Balkan countries, were characterized and evaluated for phenotypic and biochemical variation during a multi-year environment. An assortment of 32 agro-morphological, fruit quality, and virus resistance traits were evaluated, and the top 10% accessions were identified. A wide range of trait variation concerning plant architecture, inflorescence and fruit traits, yield and fruit quality was observed, and appreciable variation was noticed. According to hierarchical clustering, six distinct clusters were established based on pre-defined varietal groups. Divergence among accessions for phenotypic and fruit compositional variability was analyzed, and eight principal components were identified that contributed ~71% of the variation, with fruit shape, width, wall thickness, weight, and fruit quality traits being the most discriminant. Evaluation of the response to tobacco mosaic virus (TMV) and pepper mild mottle mosaic virus (PMMoV) showed that 24 and 1 accession were resistant, respectively while no tomato spotted wilt virus (TSWV) resistance was found. Considerable diversity for agro-bio-morphological traits indicates the Balkan pepper collection as good gene sources for pre-breeding and cultivar development that are locally adapted.


Assuntos
Capsicum/genética , Resistência à Doença/genética , Melhoramento Vegetal , Locos de Características Quantitativas/genética , Península Balcânica , Capsicum/química , Capsicum/virologia , Frutas/química , Frutas/genética , Frutas/virologia , Variação Genética , Fenótipo , Tobamovirus/patogenicidade , Tospovirus/patogenicidade
10.
PLoS One ; 15(8): e0238148, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32822425

RESUMO

Root treatment with oxathiapiprolin, benthiavalicarb or their mixture Zorvec-Endavia [ZE (3+7, w/w)] was shown to provide prolonged systemic protection against foliar oomycete pathogens attacking cucumber, tomato and basil. Here we report that these fungicides can effectively protect potato plants against late blight when applied to the soil in which such potato plants are grown. In two field experiments, performed in 2019 and 2020, potato plants grown in 64 L containers were treated with a soil drench of oxathiapiprolin, benthiavalicarb or ZE at 12.5, 25 or 50 mg ai/five plants in a container. Artificial inoculations with Phytophthora infestans revealed that such treated plants were protected against late blight in a dose-dependent manner all along the season. Interestingly, oxathiapiprolin persisted in the treated soil for at least 139 days, providing systemic protection against late blight to the following potato crops grown in that treated soils. Potato plants grown in loess soil in the field were either sprayed or drenched with ZE. Plants treated via the soil were significantly better protected against late blight compared to the plants treated by a spray. The data demonstrate a new strategy for season-long protection of potato against late blight by a single soil application of ZE. The systemic nature of oxathiapiprolin and benthiavalicarb composing ZE assures the translocation to the foliage of two fungicides with different modes of action. This shall minimize the risk of developing resistance against either fungicide in the treated crops.


Assuntos
Hidrocarbonetos Fluorados/administração & dosagem , Hidrocarbonetos Fluorados/farmacologia , Doenças das Plantas/prevenção & controle , Pirazóis/administração & dosagem , Pirazóis/farmacologia , Resistência à Doença/genética , Fungicidas Industriais/farmacologia , Phytophthora infestans/efeitos dos fármacos , Phytophthora infestans/patogenicidade , Raízes de Plantas/efeitos dos fármacos , Plantas Geneticamente Modificadas/efeitos dos fármacos , Solo , Solanum tuberosum/microbiologia
11.
Nat Commun ; 11(1): 3849, 2020 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-32737300

RESUMO

Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR = 5.71(1.58-7.12)), HIV positivity (OR = 2.22(1.32-3.73)) and living in a more rural area (OR = 1.38(1.01-1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p = 6.64 × 10-09). For EBV, associations are identified for VCA (rs71542439, p = 1.15 × 10-12). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p = 5.24 × 10-44) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission.


Assuntos
Anticorpos Antivirais/biossíntese , Resistência à Doença/genética , Infecções por Vírus Epstein-Barr/genética , Infecções por Henipavirus/genética , Interações Hospedeiro-Patógeno/genética , Sarcoma de Kaposi/genética , Adolescente , Adulto , Antígenos Virais/genética , Antígenos Virais/imunologia , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/imunologia , Coinfecção , Infecções por Vírus Epstein-Barr/epidemiologia , Infecções por Vírus Epstein-Barr/imunologia , Infecções por Vírus Epstein-Barr/virologia , Antígenos Nucleares do Vírus Epstein-Barr/genética , Antígenos Nucleares do Vírus Epstein-Barr/imunologia , Feminino , Expressão Gênica , Estudo de Associação Genômica Ampla , HIV/genética , HIV/imunologia , HIV/patogenicidade , Cadeias alfa de HLA-DQ/genética , Cadeias alfa de HLA-DQ/imunologia , Infecções por Henipavirus/epidemiologia , Infecções por Henipavirus/imunologia , Infecções por Henipavirus/virologia , Herpesvirus Humano 4/genética , Herpesvirus Humano 4/imunologia , Herpesvirus Humano 4/patogenicidade , Herpesvirus Humano 8/genética , Herpesvirus Humano 8/imunologia , Herpesvirus Humano 8/patogenicidade , Interações Hospedeiro-Patógeno/imunologia , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , População Rural , Sarcoma de Kaposi/epidemiologia , Sarcoma de Kaposi/imunologia , Sarcoma de Kaposi/virologia , Uganda/epidemiologia , População Urbana
12.
Immunol Rev ; 296(1): 205-219, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32658335

RESUMO

This article provides a review of studies evaluating the role of host (and viral) genetics (including variation in HLA genes) in the immune response to coronaviruses, as well as the clinical outcome of coronavirus-mediated disease. The initial sections focus on seasonal coronaviruses, SARS-CoV, and MERS-CoV. We then examine the state of the knowledge regarding genetic polymorphisms and SARS-CoV-2 and COVID-19. The article concludes by discussing research areas with current knowledge gaps and proposes several avenues for future scientific exploration in order to develop new insights into the immunology of SARS-CoV-2.


Assuntos
Betacoronavirus/imunologia , Infecções por Coronavirus/imunologia , Resistência à Doença/genética , Predisposição Genética para Doença , Interações Hospedeiro-Patógeno/genética , Pneumonia Viral/imunologia , Animais , Betacoronavirus/patogenicidade , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/genética , Infecções por Coronavirus/virologia , Interações Hospedeiro-Patógeno/imunologia , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/imunologia , Coronavírus da Síndrome Respiratória do Oriente Médio/patogenicidade , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/genética , Pneumonia Viral/virologia , Vírus da SARS/imunologia , Vírus da SARS/patogenicidade , Síndrome Respiratória Aguda Grave/genética , Síndrome Respiratória Aguda Grave/virologia
13.
PLoS Pathog ; 16(7): e1008595, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32628727

RESUMO

Sarocladium zeae is a fungal endophyte of maize and can be found co-inhabiting a single seed with Fusarium verticillioides, a major mycotoxigenic food safety threat. S. zeae produces pyrrocidines A and B that inhibit the growth of F. verticillioides and may limit its spread within the seed to locations lacking S. zeae. Although coinhabiting single seeds, the fungi are generally segregated in separate tissues. To understand F. verticillioides' protective physiological response to pyrrocidines we sequenced the F. verticillioides transcriptome upon exposure to purified pyrrocidine A or B at sub-inhibitory concentrations. Through this work we identified a F. verticillioides locus FvABC3 (FVEG_11089) encoding a transporter critical for resistance to pyrrocidine. We also identified FvZBD1 (FVEG_00314), a gene directly adjacent to the fumonisin biosynthetic gene cluster that was induced several thousand-fold in response to pyrrocidines. FvZBD1 is postulated to act as a genetic repressor of fumonisin production since deletion of the gene resulted in orders of magnitude increase in fumonisin. Further, pyrrocidine acts, likely through FvZBD1, to shut off fumonisin biosynthesis. This suggests that S. zeae is able to hack the secondary metabolic program of a competitor fungus, perhaps as preemptive self-protection, in this case impacting a mycotoxin of central concern for food safety.


Assuntos
Acremonium , Fumonisinas/metabolismo , Fusarium/genética , Micoses/microbiologia , Doenças das Plantas/microbiologia , Zea mays/microbiologia , Hidrocarbonetos Aromáticos com Pontes/metabolismo , Hidrocarbonetos Aromáticos com Pontes/farmacologia , Coinfecção , Resistência à Doença/genética , Genes Fúngicos , Micoses/metabolismo , Pirrolidinonas/metabolismo , Pirrolidinonas/farmacologia
14.
PLoS One ; 15(7): e0235018, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32673321

RESUMO

Common scab disease in potato has become a widespread issue in major potato production areas, leading to increasing economic losses. Varietal resistance is seen as a viable and long-term scab management strategy. However, the genes and mechanisms of varietal resistance are unknown. In the current study, a comparative RNA transcriptome sequencing and differential gene signaling and priming sensitization studies were conducted in two potato cultivars that differ by their response to common scab (Streptomyces scabies), for unraveling the genes and pathways potentially involved in resistance within this pathosystem. We report on a consistent and contrasted gene expression pattern from 1,064 annotated genes differentiating a resistant (Hindenburg) and a susceptible (Green Mountain) cultivars, and identified a set of 273 co-regulated differentially expressed genes in 34 pathways that more likely reflect the genetic differences of the cultivars and metabolic mechanisms involved in the scab pathogenesis and resistance. The data suggest that comparative transcriptomic phenotyping can be used to predict scab lesion phenotype in breeding lines using mature potato tuber. The study also showed that the resistant cultivar, Hindenburg, has developed and maintained a capacity to sense and prime itself for persistent response to scab disease over time, and suggests an immune priming reaction as a mechanism for induced-resistance in scab resistant potato cultivars. The set of genes identified, described, and discussed in the study paves the foundation for detailed characterizations towards tailoring and designing procedures for targeted gene knockout through gene editing and phenotypic evaluation.


Assuntos
Perfilação da Expressão Gênica , Solanum tuberosum/imunologia , Streptomyces/imunologia , Resistência à Doença/genética , Resistência à Doença/imunologia , Suscetibilidade a Doenças/imunologia , Regulação da Expressão Gênica de Plantas , Doenças das Plantas/imunologia , Escabiose/microbiologia , Solanum tuberosum/microbiologia , Especificidade da Espécie , Streptomyces/patogenicidade
15.
PLoS One ; 15(7): e0235089, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32673346

RESUMO

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.


Assuntos
Resistência à Doença/genética , Estudo de Associação Genômica Ampla , Soja/genética , Tylenchoidea/patogenicidade , Animais , Biomassa , Genes de Plantas , Marcadores Genéticos , Genoma de Planta , Doenças das Plantas/genética , Polimorfismo de Nucleotídeo Único , Infecções por Secernentea/prevenção & controle , Soja/parasitologia
16.
PLoS One ; 15(6): e0235482, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603342

RESUMO

Fusarium head blight (FHB) is one of the most devastating fungal diseases affecting grain crops and Fusarium graminearum is the most aggressive causal species. Several evidences shown that stomatal closure is involved in the first line of defence against plant pathogens. However, there is very little evidence to show that photosynthetic parameters change in inoculated plants. The aim of the present study was to study the role of stomatal regulation in wheat after F. graminearum inoculation and explore its possible involvement in FHB resistance. RT-qPCR revealed that genes involved in stomatal regulation are induced in the resistant Sumai3 cultivar but not in the susceptible Rebelde cultivar. Seven genes involved in the positive regulation of stomatal closure were up-regulated in Sumai3, but it is most likely, that two genes, TaBG and TaCYP450, involved in the negative regulation of stomatal closure, were strongly induced, suggesting that FHB response is linked to cross-talk between the genes promoting and inhibiting stomatal closure. Increasing temperature of spikes in the wheat genotypes and a decrease in photosynthetic efficiency in Rebelde but not in Sumai3, were observed, confirming the hypothesis that photosynthetic parameters are related to FHB resistance.


Assuntos
Resistência à Doença/genética , Fusariose/imunologia , Fotossíntese , Estômatos de Plantas , Triticum/imunologia , Fusarium/imunologia , Fusarium/patogenicidade , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Fotossíntese/genética , Fotossíntese/imunologia , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Imunidade Vegetal/genética , Estômatos de Plantas/genética , Estômatos de Plantas/imunologia , Estômatos de Plantas/fisiologia , Triticum/genética , Triticum/microbiologia
17.
PLoS One ; 15(7): e0222747, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32639982

RESUMO

Physiology-based differentiation of SH genes and Hemileia vastatrix races is the principal method employed for the characterization of coffee leaf rust resistance. Based on the gene-for-gene theory, nine major rust resistance genes (SH1-9) have been proposed. However, these genes have not been characterized at the molecular level. Consequently, the lack of molecular data regarding rust resistance genes or candidates is a major bottleneck in coffee breeding. To address this issue, we screened a BAC library with resistance gene analogs (RGAs), identified RGAs, characterized and explored for any SH related candidate genes. Herein, we report the identification and characterization of a gene (gene 11), which shares conserved sequences with other SH genes and displays a characteristic polymorphic allele conferring different resistance phenotypes. Furthermore, comparative analysis of the two RGAs belonging to CC-NBS-LRR revealed more intense diversifying selection in tomato and grape genomes than in coffee. For the first time, the present study has unveiled novel insights into the molecular nature of the SH genes, thereby opening new avenues for coffee rust resistance molecular breeding. The characterized candidate RGA is of particular importance for further biological function analysis in coffee.


Assuntos
Café/genética , Resistência à Doença/genética , Genoma de Planta , Sequência de Aminoácidos , Basidiomycota/fisiologia , Sítios de Ligação , Café/classificação , Biblioteca Gênica , Lycopersicon esculentum/classificação , Lycopersicon esculentum/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/microbiologia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Polimorfismo Genético , Alinhamento de Sequência , Fatores de Virulência/genética , Fatores de Virulência/metabolismo , Vitis/classificação , Vitis/genética
18.
Plant Dis ; 104(9): 2411-2417, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32658634

RESUMO

Chinese wheat landrace Youbailan has excellent resistance to powdery mildew caused by Blumeria graminis f. sp. tritici. In the present study, genetic analysis indicated that a recessive gene, tentatively designated pmYBL, was responsible for the powdery mildew resistance of Youbailan. pmYBL was located in the 695-to-715-Mb genomic region of chromosome 7BL, with 19 gene-linked single-nucleotide polymorphism (SNP) markers. It was flanked by SNP1-12 and SNP1-2 with genetic distances of 0.6 and 1.8 centimorgans, respectively. The disease reaction patterns of Youbailan and four cultivars (lines) carrying the powdery mildew (Pm) genes located on chromosome arm 7BL indicated that pmYBL may be allelic or closely linked to these genes. All of the SNP markers linked to pmYBL were diagnostic, indicating that these markers will be useful for pyramiding pmYBL using marker-assisted selection.


Assuntos
Resistência à Doença/genética , Triticum/genética , Mapeamento Cromossômico , Genes de Plantas , Humanos , Doenças das Plantas
19.
Plant Mol Biol ; 104(1-2): 113-136, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32627097

RESUMO

KEY MESSAGE: Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.


Assuntos
Basidiomycota/metabolismo , Resistência à Doença/genética , Genes de Plantas/genética , Genoma de Planta/genética , Histonas/genética , Doenças das Plantas/genética , Triticum/genética , Triticum/metabolismo , Imunoprecipitação da Cromatina , Metilação de DNA , Regulação da Expressão Gênica de Plantas , Ligação Genética , Histonas/metabolismo , Anotação de Sequência Molecular , Doenças das Plantas/microbiologia , Folhas de Planta/genética , Folhas de Planta/microbiologia , Regiões Promotoras Genéticas , Reprodutibilidade dos Testes , Alinhamento de Sequência , Análise de Sequência , Análise de Sequência de RNA , Transcrição Genética , Triticum/microbiologia
20.
PLoS One ; 15(7): e0236317, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702002

RESUMO

Heterodera avenae, as an obligate endoparasite, causes severe yield loss in wheat (Triticum aestivum). Investigation on the mechanisms how H. avenae perceives wheat roots is limited. Here, the attractiveness of root exudates from eight plant genotypes to H. avenae were evaluated on agar plates. Results showed that the attraction of H. avenae to the root exudates from the non-host Brachypodium distachyon variety Bd21-3 was the highest, approximately 50 infective second-stage juveniles (J2s) per plate, followed by that from three H. avenae-susceptible wheat varieties, Zhengmai9023, Yanmai84 and Xiangmai25, as well as the resistant one of Xinyuan958, whereas the lowest attractive activity was observed in the two H. avenae-resistant wheat varieties, Xianmai20 (approximately 12 J2s/plate) and Liangxing66 (approximately 11 J2s/plate). Then Bd21-3, Zhengmai9023 and Heng4399 were selected for further assays as their different attractiveness and resistance to H. avenae, and attractants for H. avenae in their root exudates were characterized to be heat-labile and low-molecular compounds (LM) by behavioral bioassay. Based on these properties of the attractants, a principle of identifying attractants for H. avenae was set up. Then LM of six root exudates from the three plants with and without heating were separated and analyzed by HPLC-MS. Finally, dihydroxyacetone (DHA), methylprednisolone succinate, embelin and diethylpropionin in the root exudates were identified to be putative attractants for H. avenae according to the principle, and the attraction of DHA to H. avenae was validated by behavioral bioassay on agar. Our study enhances the recognition to the orientation mechanism of H. avenae towards wheat roots.


Assuntos
Di-Hidroxiacetona/química , Doenças das Plantas/parasitologia , Raízes de Plantas/química , Triticum/química , Animais , Brachypodium/genética , Brachypodium/parasitologia , Di-Hidroxiacetona/fisiologia , Resistência à Doença/genética , Resistência à Doença/fisiologia , Genótipo , Doenças das Plantas/genética , Raízes de Plantas/genética , Raízes de Plantas/parasitologia , Raízes de Plantas/fisiologia , Triticum/genética , Triticum/parasitologia , Triticum/fisiologia , Tylenchoidea/genética , Tylenchoidea/patogenicidade
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