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1.
Medicine (Baltimore) ; 98(38): e17225, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31567982

RESUMO

The present study is to analyze the difference of gene methylation in early cervical adenocarcinoma and to find molecular markers for predicting the occurrence and development of cervical adenocarcinoma.A total of 15 cases of primary cervical adenocarcinoma and 10 cases of primary cervical squamous cell carcinoma at stages IB1 or IIA1 were included in the study. Infinium MethylationEPIC BeadChip (850K) was used to screen specifically expressed genes in cervical adenocarcinoma tissues. Bisulfite sequencing polymerase chain reaction (BSP) and quantitative real-time polymerase chain reaction (qRT-PCR) were used to verify the methylation levels in cervical adenocarcinoma, cervical squamous cell carcinoma, and normal cervical tissues.Sex determining region Y-box 1 (SOX1) and cyclin D1 (CCND1) genes participated in multiple signaling pathways, being the central nodes of gene regulatory networks. SOX1 gene, but not CCND1 gene, was a specifically methylated gene in cervical adenocarcinoma according to BSP. According to qRT-PCR, methylation level of SOX1 in cervical adenocarcinoma tissues is significantly different from that in cervical squamous cell carcinoma tissues or normal cervical tissues, and the methylation level of CCND1 in cervical adenocarcinoma tissues or cervical squamous cell carcinoma tissues is significantly different from that in normal cervical tissues.The present study demonstrates that tumor-suppressor gene SOX1 is a methylation-specific expression gene of cervical adenocarcinoma and is expected to become a specific molecular marker for the diagnosis of cervical adenocarcinoma. However, CCND1 gene was not proven to be a specific methylation expression gene in cervical adenocarcinoma in the present study.


Assuntos
Adenocarcinoma/genética , Metilação de DNA/genética , Fatores de Transcrição SOXB1/genética , Neoplasias do Colo do Útero/genética , Adenocarcinoma/metabolismo , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/metabolismo , Colo do Útero/metabolismo , Ciclina D1/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes/genética , Marcadores Genéticos/genética , Humanos , Reação em Cadeia da Polimerase em Tempo Real , Neoplasias do Colo do Útero/metabolismo
2.
An Acad Bras Cienc ; 91(3): e20180209, 2019 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-31482993

RESUMO

Twig girdlers have a short adult life and a long larval stage (up to one year in some species). This fact, together with lack of morphological traits to identify the species from the larval stage, poses obstacles for the taxonomic identification and characterization of the many twig girdlers found in the wild. To solve this matter, Random Amplified Polymorphic DNA (RAPD) molecular markers have been applied to identify some insect species and to determine species boundaries. The aim of this study was to identify three species of Oncideres using the RAPD technique. Adults and larvae of O. saga, O. ocularis and O. ulcerosa were collected in Minas Gerais, Brazil. Two RAPD primers were used (OPA-05 and OPB-13), which produced different electrophoretic profiles that were used to construct a UPGMA phenogram. Three groups identified in the analyses accurately separated the three species, based on individuals in two different stages of development (adults and larvae): I: O. saga, II: O. ulcerosa, and III: O. ocularis. Molecular markers, such as RAPD, are valuable tools that help taxonomists in species identification.


Assuntos
Besouros/genética , Marcadores Genéticos/genética , Animais , Besouros/classificação , Técnica de Amplificação ao Acaso de DNA Polimórfico , Especificidade da Espécie
3.
Adv Exp Med Biol ; 1178: 175-206, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31493228

RESUMO

A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.


Assuntos
Envelhecimento , Epigênese Genética , Marcadores Genéticos , Envelhecimento/genética , Animais , Ilhas de CpG/genética , Metilação de DNA , Epigenômica , Marcadores Genéticos/genética , Longevidade
4.
Braz Oral Res ; 33: e058, 2019 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-31432925

RESUMO

Cementum is the mineralized tissue covering the tooth root that functions in tooth attachment and post-eruptive adjustment of tooth position. It has been reported to be highly similar to bone in several respects but remains poorly understood in terms of development and regeneration. Here, we investigate whether cementocytes, the residing cells in cellular cementum, have the potential to be protagonist in cementum homeostasis, responding to endocrine signals and directing local cementum metabolism. Cells from healthy erupted human teeth were isolated using sequential collagenase/EDTA digestions, and maintained in standard cell culture conditions. A cementocyte-like cell line was cloned (HCY-23, for human cementocyte clone 23), which presented a cementocyte compatible gene expression signature, including the expression of dentin matrix protein 1 ( DMP1 ), sclerostin ( SOST ), and E11/gp38/podoplanin ( E11 ). In contrast, these cells did not express the odontoblast/dentin marker dentin sialoprotein ( DSPP ). HCY-23 cells produced mineral-like nodules in vitro under differentiation conditions, and were highly responsive to inorganic phosphate (Pi). Within the limits of the present study, it can be concluded that cementocytes are phosphate-responsive cells, and have the potential do play a key role in periodontal homeostasis and regeneration.


Assuntos
Técnicas de Cultura de Células/métodos , Cemento Dentário/citologia , Adolescente , Adulto , Análise de Variância , Proteínas Morfogenéticas Ósseas/análise , Proteínas Morfogenéticas Ósseas/genética , Linhagem Celular , Cemento Dentário/metabolismo , Proteínas da Matriz Extracelular/análise , Proteínas da Matriz Extracelular/genética , Feminino , Imunofluorescência , Expressão Gênica , Marcadores Genéticos/genética , Humanos , Masculino , Glicoproteínas de Membrana/análise , Glicoproteínas de Membrana/genética , Dente Molar/citologia , Fosfatos/farmacologia , Fosfoproteínas/análise , Fosfoproteínas/genética , Sialoglicoproteínas/análise , Sialoglicoproteínas/genética , Fatores de Tempo , Adulto Jovem
5.
Plant Dis ; 103(10): 2645-2651, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31453747

RESUMO

Chinese wheat landrace Dahongtou was resistant to 35 of 38 tested Chinese isolates of Blumeria graminis f. sp. tritici at the seedling stage. Genetic analysis of the F2 populations and their derived F2:3 families of crosses of Dahongtou with the susceptible varieties Mingxian 169 and Huixianhong indicated that the resistance of Dahongtou to B. graminis f. sp. tritici isolate E09 was conferred by a single recessive gene, tentatively designated as pmDHT. The gene was mapped to chromosome arm 7BL and flanked by markers Xwmc526/XBE443877 and Xgwm611/Xwmc511 at genetic distances of 0.8 and 0.3 cM, respectively. The chromosomal position of pmDHT was similar to the multi-allelic Pm5 locus on 7BL. Allelism tests with crosses of Dahongtou with Fuzhuang 30 (Pm5e) and Xiaobaidong (mlxbd) indicated that pmDHT was allelic to both Pm5e and mlxbd. However, pmDHT showed a different pattern of resistance to the 38 B. graminis f. sp. tritici isolates compared with wheat lines with Pm5a, Pm5b, Pm5e, mlxbd, and PmHYM and also differed from PmSGA. Thus, pmDHT was identified most likely as a new allele or at least a closely linked gene of the Pm5 locus. This gene can be transferred into susceptible wheat cultivars/lines and pyramided with other resistance genes through marker-assisted selection to improve powdery mildew resistance.


Assuntos
Ascomicetos , Resistência à Doença , Genes de Plantas , Triticum , Ascomicetos/fisiologia , Mapeamento Cromossômico , Resistência à Doença/genética , Genes de Plantas/genética , Marcadores Genéticos/genética , Doenças das Plantas/microbiologia , Triticum/genética , Triticum/microbiologia
6.
BMC Plant Biol ; 19(1): 296, 2019 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-31286893

RESUMO

BACKGROUND: Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin pheophorbide hydrolase (Pheophytinase, PPH) gene encodes a Chl degradation hydrolase. RESULTS: In this study, the coding, genomic and promoter sequences of wheat TaPPH-A gene were cloned. The corresponding lengths were 1467 bp, 4479 bp and 3666 bp, respectively. Sequence structure analysis showed that TaPPH-A contained five exons and four introns. After the multiple sequences alignment of TaPPH-A genome from 36 accessions in a wheat diversity panel, four SNPs and one 2-bp InDel were observed, which formed two haplotypes, TaPPH-7A-1 and TaPPH-7A-2. Based on the SNP at 1299 bp (A/G), a molecular marker TaPPH-7A-dCAPS was developed to distinguish allelic variation (A/G). Using the molecular markers, 13 SSR, and 116 SNP markers, a linkage map of chromosome 7A were integrated. TaPPH-A was mapped on the chromosome region flanked by Xwmc9 (0.94 cM) and AX-95634545 (1.04 cM) on 7A in a DH population. Association analysis between TaPPH-7A allelic variation and agronomic traits found that TaPPH-7A was associated with TGW in 11 of 12 environments and Chl content at grain-filling stage under drought stress using Population 1 consisted of 323 accessions. The accessions possessed TaPPH-7A-1 (A) had higher TGW and Chl content than those possessed TaPPH-7A-2 (G), thus TaPPH-7A-1 (A) was a favorable allelic variation. By analyzing the frequency of favorable allelic variation TaPPH-7A-1 (A) in Population 2 with 157 landraces and Population 3 with 348 modern cultivars, we found it increased from pre-1950 (0) to 1960s (54.5%), then maintained a relatively stable level about 56% from 1960s to 1990s. CONCLUSION: These results suggested the favorable allelic variation TaPPH-7A-1 (A) should be valuable in enhancing grain yield by improving the source (chlorophyll content) and sink (the developing grain) simultaneously. Furthermore, the newly developed molecular marker TaPPH-7A-dCAPS could be integrated into a breeding kit of screening high TGW wheat for marker-assisted selection.


Assuntos
Haplótipos/genética , Proteínas de Plantas/genética , Triticum/genética , Marcadores Genéticos/genética , Melhoramento Vegetal , Proteínas de Plantas/metabolismo , Triticum/metabolismo
7.
Plant Dis ; 103(9): 2359-2366, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31355733

RESUMO

In Ethiopia, breeding rust resistant wheat cultivars is a priority for wheat production. A stem rust epidemic during 2013 to 2014 on previously resistant cultivar Digalu highlighted the need to determine the effectiveness of wheat lines to multiple races of Puccinia graminis f. sp. tritici in Ethiopia. During 2014 and 2015, we evaluated a total of 97 bread wheat and 14 durum wheat genotypes against four P. graminis f. sp. tritici races at the seedling stage and in single-race field nurseries. Resistance genes were postulated using molecular marker assays. Bread wheat lines were resistant to race JRCQC, the race most virulent to durum wheat. Lines with stem rust resistance gene Sr24 possessed the most effective resistance to the four races. Only three lines with adult plant resistance possessed resistance effective to the four races comparable with cultivars with Sr24. Although responses of the wheat lines across races were positively correlated, wheat lines were identified that possessed adult plant resistance to race TTKSK but were relatively susceptible to race TKTTF. This study demonstrated the importance of testing wheat lines for response to multiple races of the stem rust pathogen to determine if lines possessed non-race-specific resistance. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.


Assuntos
Resistência à Doença , Triticum , Resistência à Doença/genética , Etiópia , Marcadores Genéticos/genética , Triticum/classificação , Triticum/microbiologia
8.
Mol Biol (Mosk) ; 53(3): 388-392, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31184603

RESUMO

The causative agent of tick-borne encephalitis (a neurotropic RNA virus from the Flavivirus genus) can cause both severe paralytic forms of the disease (meningoencephalitis, etc.) and milder nonparalytic forms (fever and meningitis). The organism response to viral infection (and, as a consequence, the nature and outcome of the disease) significantly depends on individual peculiarities of the human organism protective systems predetermined by genome structure. Human genetic predisposition to tick-borne encephalitis has been poorly studied. In the present work, the results of the search for new genes that predetermine the peculiarities and outcome of tick-borne encephalitis in humans are presented. The aim of the work was to verify the association between three previously detected (using the exome sequencing on a limited sample of tick-borne encephalitis patients with severe forms) SNPs: intronic rs3109675 (C/T) in the COL5A1 gene, intronic rs41554313 (A/G) in the POLRMT gene, and intergenic rs10006630 (C/A), and the predisposition to tick-borne encephalitis in a Russian population (using an extended sample of patients with different forms of tick-borne encephalitis). The association of the rs10006630 SNP located in chromosome 4 between the FABP2 and LINC01061 genes with a predisposition to tick-borne encephalitis was confirmed. This SNP can be considered as a new genetic marker of a human predisposition to severe forms of tick-borne encephalitis. The possible regulatory role of this SNP in the functioning of neighboring genes and a mechanism of its effect on the development of predisposition to severe forms of tick-borne encephalitis require further study.


Assuntos
Encefalite Transmitida por Carrapatos/genética , Predisposição Genética para Doença , Marcadores Genéticos/genética , Humanos , Polimorfismo de Nucleotídeo Único/genética , Federação Russa
9.
J Dairy Sci ; 102(8): 7237-7247, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31155255

RESUMO

Relatedness between reference and test animals has an important effect on the reliability of genomic prediction for test animals. Because genomic prediction has been widely applied in practical cattle breeding and bulls have been selected according to genomic breeding value without progeny testing, the sires or grandsires of candidates might not have phenotypic information and might not be in the reference population when the candidates are selected. The objective of this study was to investigate the decreasing trend of the reliability of genomic prediction given distant reference populations, using genomic best linear unbiased prediction (GBLUP) and Bayesian variable selection models with or without including the quantitative trait locus (QTL) markers detected from sequencing data. The data used in this study consisted of 22,242 bulls genotyped using the 54K SNP array from EuroGenomics. Among them, 1,444 Danish bulls born from 2006 to 2010 were selected as test animals. Different reference populations with varying relationships to test animals were created according to pedigree-based relationships. The reference individuals having a relationship with one or more test animals higher than 0.4 (scenario ρ < 0.4), 0.2 (ρ < 0.2), or 0.1 (ρ < 0.1, where ρ = relationship coefficient) were removed from reference sets; these represented the distance between reference and test animals being 2 generations, 3 generations, and 4 generations, respectively. Imputed whole-genome sequencing data of bulls from Denmark were used to conduct a genome-wide association study (GWAS). A small number of significant variants (QTL markers) from the GWAS were added to the array data. To compare the effects of different models, the basic GBLUP model, a Bayesian selection variable model, a GBLUP model with 2 components of genetic effects, and a Bayesian model with pooled array data and QTL markers were used for estimating genomic estimated breeding values (GEBV) of test animals. The reliability of genomic prediction decreased when the test animals were more generations away from the reference population. The reliability of genomic prediction was 0.461 for 1 generation away and 0.396 for 3 generations away, with the same number of individuals in the reference set, using a GBLUP model with chip markers only. The results showed that using the Bayesian method and QTL markers improved the reliability of genomic prediction in all scenarios of relationship between test and reference animals, in a range of 1.3% and 65.1% (4 generations away with only 841 individuals in the reference set). However, most gains were for predictions of milk yield and fat yield. There was little improvement for predictions of protein yield and mastitis, and no improvement for prediction of fertility, except for scenario ρ < 0.1, in which there was a large improvement for predictions of all traits. On the other hand, models including more than 10% polygenic effect decreased prediction reliability when the relationship between test and reference animals was distant.


Assuntos
Teorema de Bayes , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Mastite Bovina/genética , Leite/metabolismo , Locos de Características Quantitativas/genética , Animais , Cruzamento , Dinamarca , Feminino , Fertilidade/genética , Marcadores Genéticos/genética , Genômica , Genótipo , Masculino , Herança Multifatorial/genética , Linhagem , Fenótipo , Reprodutibilidade dos Testes
10.
J Dairy Sci ; 102(8): 7226-7236, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31202648

RESUMO

The mammalian Y chromosome gene families in the ampliconic region are expressed predominantly or exclusively in the testis, and their copy number variations (CNV) are significantly associated with male reproductive traits, suggesting they have important roles in spermatogenesis and testicular development. ZNF280AY (zinc finger protein 280A, Y-linked) is a member of the zinc finger protein family and has been identified as a bovid-specific Y-chromosome gene. The current study applied a reliable quantitative real-time PCR method to estimate the CNV of ZNF280AY in 715 bulls across 21 cattle breeds and to further investigate the association of the CNV of ZNF280AY with bull reproductive traits and ZNF280AY mRNA expression levels in adult testis. The results revealed that the median copy number of ZNF280AY was 47, and the copy number varied from 11 to 154, showing significant CNV between and within the investigated cattle breeds. In addition, all 715 bulls were classified into Y1, Y2, and Y3 lineage groups based on a rapid genotyping method described previously. Pairwise comparisons indicated that bulls belonging to the Y1 lineage had a significantly lower median copy number (40) than bulls belonging to the Y2 (52) and Y3 lineages (57). Association analysis revealed that the CNV of ZNF280AY was correlated negatively with the percentage of normal sperm and sperm concentration in Holstein bulls, whereas no significant correlation was observed with ejaculation volume, total sperm count, sperm motility, postthaw motility (PTM), and scrotal circumference in Holstein and Simmental bulls. Furthermore, no correlation was observed between ZNF280AY copy number and ZNF280AY mRNA expression levels in the testis. The current study suggests that the CNV of the ZNF280AY gene family is associated with male reproductive traits and may serve as a valuable marker for early bull fertility selection in Holstein breeding programs.


Assuntos
Bovinos/genética , Variações do Número de Cópias de DNA , Fertilidade/genética , Regulação da Expressão Gênica , Genes Ligados ao Cromossomo Y/genética , Reprodução/genética , Cromossomo Y/genética , Animais , Cruzamento , Bovinos/fisiologia , Marcadores Genéticos/genética , Genótipo , Masculino , Especificidade de Órgãos , Fenótipo , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Especificidade da Espécie , Contagem de Espermatozoides/veterinária , Motilidade Espermática/genética , Espermatogênese/genética , Testículo/fisiologia , Dedos de Zinco/genética
11.
Medicine (Baltimore) ; 98(21): e15796, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31124977

RESUMO

miRNAs and genes play significant roles in the etiology and pathogenesis of intervertebral disc degeneration (IDD). This study aimed to identify aberrantly expressed miRNAs, genes, and pathways in IDD through a comprehensive bioinformatics analysis.Data of miRNAs expression microarrays (GSE63492) and genes microarrays (GSE23130) were obtained from GEO database. Similarly, aberrantly expressed miRNAs and genes were obtained using GEO2R. In addition, functional and enrichment analyses of selected miRNAs and genes were performed using the DAVID database. Meanwhile, protein-protein interaction (PPI) network was constructed using STRING, and then visualized in Cytoscape.A total of 98 upregulated miRNAs were identified. They were enriched in biological processes of response to organelle, ion binding, cellular nitrogen compound metabolic process, biosynthetic process, small molecule metabolic process, cellular protein modification process, catabolic process, molecular function, neurotrophin TRK receptor signaling pathway, and protein complex. In addition, 1405 high expression protein genes were detected. It indicated enrichment in biological processes, such as translational initiation, nonsense-mediated decay, viral transcription, cell-cell adhesion, rRNA processing, translation, RP-dependent cotranslational protein targeting to membrane, nuclear-transcribed mRNA catabolic process, regulation of mRNA stability, and mRNA splicing via spliceosome and extracellular matrix organization. In addition, pathway analysis exhibited the common enrichment in focal adhesion, Hippo signaling pathway, ECM-receptor interaction, Wnt signaling pathway, PI3K-Akt signaling pathway, endocytosis, proteoglycans in cancer, and so on. The top 10 central genes of PPI network were POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A.In conclusion, our research proposed abnormally expressed miRNAs, genes, and pathways in IDD through bioinformatics methods, which may provide new insights into the pathogenesis of IDD. Thus, the Hub gene involving POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A may be biomarkers for accurate diagnosis and treatment of IDD in the future.


Assuntos
Mineração de Dados/métodos , Degeneração do Disco Intervertebral/genética , MicroRNAs/genética , Transdução de Sinais/genética , Revisão Sistemática como Assunto , Biologia Computacional/métodos , Ontologia Genética , Marcadores Genéticos/genética , Humanos , Análise em Microsséries , Mapas de Interação de Proteínas , Projetos de Pesquisa
12.
Plant Dis ; 103(7): 1738-1745, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31082329

RESUMO

Neofusicoccum parvum, causal fungus of the grapevine trunk disease Botryosphaeria dieback, attacks the wood of Vitis vinifera. Because lesions are internal, using putative host-based markers of infection from leaves for diagnosis is a nondestructive option. However, their specificity under drought stress is unknown. Potted 'Cabernet-Sauvignon' were inoculated with N. parvum in the greenhouse after wounding (IW), and with wounded and nonwounded noninoculated controls. At 2 weeks postinoculation (WPI), half of the plants were severely stressed (SS), receiving 30% water volume of the well-watered (WW) plants. Larger lesions at 12 WPI among IW-SS plants, compared with all other treatments, revealed an interactive effect of inoculation and drought on lesion length. Expression of eight putative marker genes was analyzed in leaves by qPCR at the onset of drought stress, and at 8 and 12 WPI. One marker showed consistent over-expression at 8 WPI in IW plants, regardless of water treatment, suggesting specificity to infection. By 12 WPI, higher expression of seven genes in all SS plants (across inoculation treatments) revealed specificity to drought. Cross-reactivity of markers to drought, therefore, limits their utility for disease diagnosis in the field, where drought induced by climate and deficit irrigation is common.


Assuntos
Ascomicetos , Secas , Vitis , Ascomicetos/genética , Ascomicetos/fisiologia , Marcadores Genéticos/genética , Folhas de Planta/microbiologia , Vitis/genética , Vitis/microbiologia
13.
Planta ; 250(2): 507-518, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31098709

RESUMO

MAIN CONCLUSION: 'Petaloid' cytoplasmic male sterility is commonly used as a stable genetic mechanism in carrot hybrid breeding. Its introgression in tropical carrot showed morphometric changes and molecular markers were identified for detection at early stage. Cytoplasmic male sterility (CMS) is the only genetic mechanism in carrot for commercial exploitation of heterosis and production of low cost affordable hybrid seeds. The 'petaloid' CMS system is stable and commonly used in hybrid breeding in temperate carrot but there is no information available on existence of natural CMS system in tropical Asiatic carrot. Therefore, the present study was aimed to investigate morphometric traits and organizational features of cytoplasmic atp9 gene sequences in newly converted CMS lines (BC4-7) of tropical carrot. The CMS lines had root traits at par with fertile counterparts while floral traits had variation. Petal colour and length, petaloids colour and shape and style length showed differences among the CMS lines and with their maintainers. Molecular markers are effective to establish male sterility at genetic level, for this, six fixed and stable CMS lines were screened with seven novel primer combinations. Out of which five pairs produced clearly distinguishable bands in CMS lines and their fertile counterparts. The study confirmed that the region between 3' end of atp9-1/atp9-3 gene and 5' end of region of homology to Arabidopsis thaliana mtDNA is ideal for developing the trait specific markers. These new CMS lines have potential to use in hybrid development and molecular markers will be useful to confirm male sterility to rogue out fertile plants.


Assuntos
Daucus carota/genética , Infertilidade das Plantas/genética , Proteínas de Plantas/genética , Arabidopsis/anatomia & histologia , Arabidopsis/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Quimera , Citoplasma/genética , DNA Mitocondrial/genética , Daucus carota/anatomia & histologia , Daucus carota/fisiologia , Marcadores Genéticos/genética , ATPases Mitocondriais Próton-Translocadoras/genética , ATPases Mitocondriais Próton-Translocadoras/metabolismo , Melhoramento Vegetal , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas
14.
J Anim Sci ; 97(7): 2793-2802, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31087081

RESUMO

The objectives of this study were to identify informative genomic regions that affect the exterior traits of purebred Korean Yorkshire pigs and to investigate and compare the accuracy of genomic prediction for response variables. Phenotypic data on body height (BH), body length (BL), and total teat number (TTN) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and 2 types of deregressed EBVs-one including the parent average (DEBVincPA) and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods-with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)-were used to estimate SNP effects, through the genome-wide association study. The significance of genomic windows (1 Mb) was obtained at 1.0% additive genetic variance and was subsequently used to identify informative genomic regions. Furthermore, SNPs with a high model frequency (≥0.90) were considered informative. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). The number of identified informative windows (1 Mb) for BH, BL, and TTN was 4, 3, and 4, respectively. The number of significant SNPs for BH, BL, and TTN was 6, 4, and 5, respectively. Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for exterior traits than BayesC method in this study. In addition, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy values for BH, BL, and TTN were calculated to be 0.52, 0.60, and 0.51, respectively.


Assuntos
Estudo de Associação Genômica Ampla/veterinária , Genoma/genética , Genômica , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Suínos/genética , Animais , Cruzamento , Análise por Conglomerados , Confiabilidade dos Dados , Feminino , Marcadores Genéticos/genética , Testes Genéticos/veterinária , Genótipo , Masculino , Glândulas Mamárias Animais/anatomia & histologia , Fenótipo , Suínos/anatomia & histologia
15.
Int J Food Microbiol ; 299: 33-38, 2019 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-30952015

RESUMO

In order to determine the microbial safety of produce, conventional fecal indicator bacteria (CFIB) such as Escherichia coli and Enterococcus are quantified as a standard practice. Bacteroidales are also fecal indicators mostly used for water samples; however, their use and persistence in foods has been rarely studied. In this study, persistence of both CFIB and genetic markers of host-specific Bacteroidales was determined in artificially contaminated materials and vegetables with different textured surfaces under different storage conditions. Sterile feces were contaminated with E. coli, E. faecalis, Bacteroidesthetaiotaomicron (human origin), and Bacteroidales from porcine and bovine origin. Feces were applied to filters of mixed cellulose esters and tomatoes (smooth surface) and flat cork coupons and melons (rough surface) and stored at 10 °C/95% relative humidity (RH) and 25 °C/65%RH for up to 25 days. Bacteroidales markers were analyzed by real-time polymerase chain reaction (qPCR), whereas CFIB were plated onto selective agars. CFIB detection on filters and cork surfaces declined over time. E. coli decreased 2.9 log CFU and 1.2 log CFU per filter and cork, respectively, at 10 °C/95%RH and 5.8 log CFU and 1.8 log CFU per filter and cork, respectively, at 25 °C/65%RH. E. faecalis decreased 1.9 log CFU on filters and 1.3 log CFU on cork at 10 °C/95%RH and 2.6 log CFU/filter and cork under both storage conditions. Although E. coli levels in tomatoes slightly increased during storage, the levels decreased by the end of the assays. However, CFIB levels in melons stored at 10 °C/95%RH increased after 20 days; when stored at 25 °C/65%RH, these levels increased after five days. Bacteroidales levels (universal and host-specific markers) in inanimated material and produce did not show significant differences (P ≤ 0.01) over time. Stability and persistence of Bacteroidales genetic markers make them superior to CFIB as markers and are alternatives for determining the risk of exposure to feces-contaminated produce.


Assuntos
Bacteroidetes/fisiologia , Enterococcus/fisiologia , Escherichia coli/fisiologia , Microbiologia de Alimentos/métodos , Frutas/microbiologia , Animais , Bacteroidetes/genética , Bovinos , Cucurbitaceae/microbiologia , Enterococcus/genética , Escherichia coli/genética , Marcadores Genéticos/genética , Humanos , Lycopersicon esculentum/microbiologia , Reação em Cadeia da Polimerase em Tempo Real , Suínos
16.
BMC Genomics ; 20(1): 289, 2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30987602

RESUMO

BACKGROUND: Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D. villosum#4 still remains less studied. In particular, chromosomes of D. villosum#4 except 6V#4 have not been introduced into wheat by addition or substitution and translocation, which is an essential step to identify and apply the alien desired genes. RNA-seq technology can generate large amounts of transcriptome sequences and accelerate the development of chromosome-specific molecular markers and assisted selection of alien chromosome line. RESULTS: We obtained the transcriptome of D. villosum#4 via a high-throughput sequencing technique, and then developed 76 markers specific to each chromosome arm of D. villosum#4 based on the bioinformatic analysis of the transcriptome data. The D. villosum#4 sequences containing the specific DNA markers were expected to be involved in different genes, among which most had functions in metabolic processes. Consequently, we mapped these newly developed molecular markers to the homologous chromosome of barley and obtained the chromosome localization of these markers on barley genome. Then we analyzed the collinearity of these markers among D. villosum, wheat, and barley. In succession, we identified six types of T. aestivum-D. villosum#4 alien chromosome lines which had one or more than one D. villosum#4 chromosome in the cross and backcross BC3F5 populations between T. durum-D. villosum#4 amphidiploid TH3 and wheat cv. Wan7107 by employing the selected specific markers, some of which were further confirmed to be translocation or addition lines by genomic in situ hybridization (GISH). CONCLUSION: Seventy-six PCR markers specific to chromosomes of D. villosum#4 based on transcriptome data were developed in the current study and their collinearity among D. villosum, wheat, and barley were carried out. Six types of Triticum aestivum-D. villosum#4 alien chromosome lines were identified by using 12 developed markers and some of which were further confirmed by GISH. These novel T. aestivum-D. villosum#4 chromosome lines have great potential to be used for the introduction of desirable genes from D. villosum#4 into wheat by chromosomal translocation to breed new wheat varieties.


Assuntos
Cruzamento , Cromossomos de Plantas/genética , Perfilação da Expressão Gênica , Marcadores Genéticos/genética , Genômica , Poaceae/genética , Triticum/genética , Genoma de Planta/genética , Anotação de Sequência Molecular , Reação em Cadeia da Polimerase
17.
Biomed Res Int ; 2019: 5046958, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31016191

RESUMO

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos/genética , Sorghum/genética , Composição de Bases/genética , DNA de Cloroplastos/genética , Ordem dos Genes/genética , Marcadores Genéticos/genética , Genômica/métodos , Filogenia , Poaceae/genética , Análise de Sequência de DNA/métodos
18.
Plant Dis ; 103(6): 1166-1171, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30998448

RESUMO

The deployment of diverse sources of resistance in new cultivars underpins durable control of rust diseases. Aus27430 exhibited a moderate level of stripe rust resistance against Puccinia striiformis f. sp. tritici (Pst) pathotypes currently prevalent in Australia. Aus27430 was crossed with the susceptible parent Avocet S (AvS) and subsequent filial generations were raised. Monogenic segregation observed among Aus27430/AvS F3 families was confirmed through stripe rust screening of an F6 recombinant inbred line (RIL) population, and the resistance locus was temporarily named YrAW5. Selective genotyping using an Illumina iSelect 90K wheat SNP bead chip array located YrAW5 in chromosome 6A. Genetic mapping of the RIL population with linked 90K SNPs that were converted into PCR-based marker assays, as well as SSR markers previously mapped to chromosome 6A, confirmed the chromosomal assignment for YrAW5. Comparative analysis of other stripe rust resistance genes located in chromosome 6A led to the formal designation of YrAW5 as Yr81. Tests with a marker linked with Yr18 also demonstrated the presence of this gene in Aus27430. Yr18 interacted with Yr81 to produce stripe rust responses lower than those produced by RILs carrying these genes individually. Although gwm459 showed higher recombination with Yr81 compared with the other flanking marker KASP_3077, it amplified the AvS allele in 80 cultivars, whereas KASP_3077 amplified AvS allele in 67 cultivars. Both markers can be used in marker-assisted selection after confirming parental polymorphism.


Assuntos
Cromossomos de Plantas , Resistência à Doença , Triticum , Austrália , Basidiomycota/fisiologia , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Resistência à Doença/genética , Marcadores Genéticos/genética , Triticum/genética , Triticum/microbiologia
19.
Res Vet Sci ; 124: 284-292, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31005660

RESUMO

West Nile virus (WNV) is a mosquito-borne zoonotic neurotropic virus capable to cause lethal meningoencephalitis (WNE) in infected hosts such as birds, horses, and humans. Due to their sensitivity, horses serve as sentinel species in areas at risk. We studied a population of Camargue horses living in Southern France in two zones with endemic WNV circulation where WNV outbreaks were recorded in 2000 and 2003-4. Two sets of microsatellite markers located in MHC and Ly49 genomic regions were genotyped as well as multiple SNPs in ten immunity-related candidate gene regions. Associations between genetic polymorphisms and resistance/susceptibility to WNE were tested. While single marker associations were weak, compound two-gene genotypes of SNPs located within the MAVS, NCR2 and IL-10 genes and microsatellites HMS082 and CZM013 were associated with susceptibility to WNE. Combinations of microsatellite markers CZM009, ABGe17402 and ABGe9019 were associated with simple seroconversion without clinical signs of WNE (resistance). In addition, a distribution of polymorphic markers between WNV-IgG seropositive horses and a control group of WNV-IgG seronegative horses was tested. One SNP in the OAS1 gene (NC_009151.3:g.21961328A>G) was significantly associated with the seropositive phenotype (pcorr = 0.023; OR = 40.5 CI (4.28; 383.26); RR = 8.18 CI (1.27; 52.89) in the Camargue breed. In compound genotypes, SNP markers for SLC11A1, MAVS, OAS1, TLR4, ADAM17 and NCR2 genes and ten microsatellites showed non-random distribution between seropositive and seronegative groups of horses. Further analysis of associated markers could contribute to our understanding of anti-WNV defense mechanisms in horses.


Assuntos
Resistência à Doença/genética , Marcadores Genéticos/genética , Predisposição Genética para Doença/genética , Doenças dos Cavalos/genética , Polimorfismo Genético , Febre do Nilo Ocidental/veterinária , Animais , França/epidemiologia , Doenças dos Cavalos/virologia , Cavalos , Imunoglobulina G/imunologia , Repetições de Microssatélites , Polimorfismo de Nucleotídeo Único , Febre do Nilo Ocidental/genética , Febre do Nilo Ocidental/virologia , Vírus do Nilo Ocidental/fisiologia
20.
Nat Plants ; 5(5): 480-485, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30988404

RESUMO

Developing herbicide-tolerant varieties by genome editing holds great promise for addressing the worsening weed problems in wheat cultivation1. Here, we generated transgene-free wheat germplasms harbouring herbicide tolerance mutations that confer tolerance to sulfonylurea-, imidazolinone- and aryloxyphenoxy propionate-type herbicides by base editing the acetolactate synthase (ALS) and acetyl-coenzyme A carboxylase genes. These stackable herbicide tolerance traits provide a potentially powerful tool for weed management. In addition, we found that base editing at the wheat ALS Pro-174 codon (TaALS-P174) endowed wheat with sufficient resistance to nicosulfuron herbicide in MS growth medium to allow selection. When the TaALS-P174 editor was coupled with editors for other targets of interest, co-editing occurred in the nicosulfuron-resistant plants, and selection for resistance in growth medium enriched the frequency of coupled targets by several-fold. This selectable co-editing system has the potential to greatly bolster adoption of base editing for crop improvement applications.


Assuntos
Edição de Genes/métodos , Resistência a Herbicidas/genética , Triticum/genética , Acetolactato Sintase/genética , Acetolactato Sintase/metabolismo , Acetil-CoA Carboxilase/genética , Acetil-CoA Carboxilase/metabolismo , Alelos , Códon/genética , Marcadores Genéticos/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Característica Quantitativa Herdável , Alinhamento de Sequência , Triticum/efeitos dos fármacos , Triticum/enzimologia , Controle de Plantas Daninhas/métodos
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