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1.
Plant Mol Biol ; 104(1-2): 173-185, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32734417

RESUMEN

KEY MESSAGE: A novel and major QTL for the effective tiller number was identified on chromosomal arm 1BL and validated in two genetic backgrounds The effective tiller number (ETN) substantially influences plant architecture and the wheat yield improvement. In this study, we constructed a genetic map of the 2SY (20828/SY95-71) recombinant inbred line population based on the Wheat 55K array as well as the simple sequence repeat (SSR) and Kompetitive Allele Specific PCR (KASP) markers. A comparison between the genetic and physical maps indicated the marker positions were consistent in the two maps. Additionally, we identified seven tillering-related quantitative trait locus (QTLs), including Qetn-sau-1B.1, which is a major QTL localized to a 6.17-cM interval flanked by markers AX-89635557 and AX-111544678 on chromosome 1BL. The Qetn-sau-1B.1 QTL was detected in eight environments and explained 12.12-55.71% of the phenotypic variance. Three genes associated with the ETN were detected in the physical interval of Qetn-sau-1B.1. We used a tightly linked KASP marker, KASP-AX-110129912, to further validate this QTL in two other populations with different genetic backgrounds. The results indicated that Qetn-sau-1B.1 significantly increased the ETN by up to 23.5%. The results of this study will be useful for the precise mapping and cloning of Qetn-sau-1B.1.


Asunto(s)
Cromosomas de las Plantas , Sitios de Carácter Cuantitativo/genética , Triticum/genética , Bangladesh , Mapeo Cromosómico , Marcadores Genéticos/genética , Genotipo , Repeticiones de Microsatélite , Anotación de Secuencia Molecular , Fenotipo
2.
Medicine (Baltimore) ; 99(31): e21326, 2020 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-32756117

RESUMEN

Northern corn leaf blight (NCLB), a corn disease infected by Exserohilum turcicum, can cause loss of harvest and economy. Identification or evaluation of NCLB-resistant quantitative trait loci (QTL) and genes could improve maize breeds. This study aimed to identify novel QTLs for NCLB-resistance.Two maize strains (BB and BC) were utilized to generate B73 × B97 and B73 × CML322 and constructed the genetic linkage using high-throughput single nucleotide polymorphism (SNP) linkage map analysis of 170 (BB) and 163(BC) recombinant inbred line (RIL) genomic DNA samples. NCLB-resistant QTL was associated with phenotypic data from the field trial of 170 BB and 163 BC strains over two years using these 1100 SNPs to identify high-density NCLB-resistant QTLs.In BB, QTL of the NCLB resistance was on chromosome 1 and 3 (LOD scores between 2.74 and 5.44); in BC, QTL of NCLB resistance was on chromosome 1, 2, 4, 8, and 9 (LOD scores between 2.52 and 8.53). A number of genes or genetic information related to NCLB resistance in both BB and BC were identified with the maximum number of genes/NCLB resistance-related QTL on chromosome 3 for BB and on chromosome 1 for BC.This study successfully mapped and identified NCLB-resistant QTL and genes for these 2 different maize strains, which provides insightful information for future study of NCLB-resistance and selection of NCLB-resistant maize variants.


Asunto(s)
Enfermedades de las Plantas/genética , Zea mays/genética , Marcadores Genéticos , Inmunidad Innata , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo
3.
Nat Commun ; 11(1): 3475, 2020 07 21.
Artículo en Inglés | MEDLINE | ID: mdl-32694610

RESUMEN

Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80-93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93-98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89-98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.


Asunto(s)
ADN Tumoral Circulante/sangre , Detección Precoz del Cáncer/métodos , Neoplasias/sangre , Neoplasias/diagnóstico , Adulto , Anciano , Anciano de 80 o más Años , Biomarcadores de Tumor/sangre , China , Metilación de ADN , Epigenómica , Femenino , Marcadores Genéticos , Voluntarios Sanos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Estudios Longitudinales , Masculino , Persona de Mediana Edad , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Adulto Joven
4.
Nat Commun ; 11(1): 3730, 2020 07 24.
Artículo en Inglés | MEDLINE | ID: mdl-32709840

RESUMEN

Long-term follow up studies from Ebola virus disease (EVD) survivors (EBOV_S) are lacking. Here, we evaluate immune and gene expression profiles in 35 Guinean EBOV_S from the last West African outbreak, a median of 23 months (IQR [18-25]) after discharge from treatment center. Compared with healthy donors, EBOV_S exhibit increases of blood markers of inflammation, intestinal tissue damage, T cell and B cell activation and a depletion of circulating dendritic cells. All survivors have EBOV-specific IgG antibodies and robust and polyfunctional EBOV-specific memory T-cell responses. Deep sequencing of the genes expressed in blood reveals an enrichment in 'inflammation' and 'antiviral' pathways. Integrated analyses identify specific immune markers associated with the persistence of clinical symptoms. This study identifies a set of biological and genetic markers that could be used to define a signature of "chronic Ebola virus disease (CEVD)".


Asunto(s)
Ebolavirus/inmunología , Fiebre Hemorrágica Ebola/complicaciones , Fiebre Hemorrágica Ebola/inmunología , Enfermedades del Sistema Inmune/complicaciones , Enfermedades del Sistema Inmune/inmunología , Adulto , Anticuerpos Antivirales/sangre , Anticuerpos Antivirales/inmunología , Antivirales/farmacología , Linfocitos B/inmunología , Citocinas/sangre , Ebolavirus/efectos de los fármacos , Ebolavirus/genética , Femenino , Marcadores Genéticos , Fiebre Hemorrágica Ebola/tratamiento farmacológico , Fiebre Hemorrágica Ebola/virología , Humanos , Enfermedades del Sistema Inmune/genética , Inmunoglobulina G/sangre , Inmunoglobulina G/inmunología , Inflamación/genética , Activación de Linfocitos , Masculino , Sobrevivientes , Linfocitos T/inmunología , Transcriptoma , Adulto Joven
5.
PLoS One ; 15(7): e0233808, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32673320

RESUMEN

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.


Asunto(s)
Grupo de Ascendencia Continental Africana/genética , Grupo de Ascendencia Continental Europea/genética , Genoma Humano , Indios Sudamericanos/genética , Matrimonio , Linaje , Grupo de Ascendencia Continental Africana/etnología , Argentina , Colonialismo , ADN/genética , Esclavización , Grupo de Ascendencia Continental Europea/etnología , Marcadores Genéticos , Variación Genética , Genética de Población , Genotipo , Migración Humana , Humanos , Indios Sudamericanos/etnología , Modelos Genéticos
6.
Plant Dis ; 104(9): 2369-2376, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32689920

RESUMEN

Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide. Fhb1 is the most widely utilized and the only isolated gene for FHB resistance, while Sr2 is a durable stem rust resistance gene used in rust-prone areas. The two loci are closely linked on the short arm of chromosome 3B and the two genes are in repulsion phase among cultivars. With climate change and the shift in Fusarium populations, it is imperative to develop wheat cultivars resistant to both diseases. The present study was dedicated to developing wheat germplasm combining Fhb1 and Sr2 resistance alleles in the International Maize and Wheat Improvement Center (CIMMYT)'s elite cultivars' backgrounds. Four recombinant inbred lines (RILs) in Hartog background that have the resistant Fhb1 and Sr2 alleles in coupled phase linkage were crossed with seven CIMMYT bread wheat lines, resulting in 208 lines. Molecular markers for both genes were employed in addition to the use of pseudo-black chaff (PBC) as a phenotypic marker for the selection of Sr2. At various stages of the selection process, progeny lines were assessed for FHB index, Fusarium damaged kernels (FDK), stem rust, and PBC expression as well as other diseases of interest (stripe rust and leaf spotting diseases). The 25 best lines were selected for CIMMYT's wheat breeding program. In addition to expressing resistance to FHB, most of these 25 lines have an acceptable level of resistance to other tested diseases. These lines will be useful for wheat breeding programs worldwide and potentially speed up the resistance breeding efforts against FHB and stem rust.


Asunto(s)
Resistencia a la Enfermedad , Triticum/genética , Cromosomas de las Plantas , Marcadores Genéticos , Humanos , Enfermedades de las Plantas
7.
Medicine (Baltimore) ; 99(22): e20429, 2020 May 29.
Artículo en Inglés | MEDLINE | ID: mdl-32481444

RESUMEN

Determining the clinically optimal dose in methadone maintenance therapy (MMT) is a time-consuming procedure, which considers clinical signs and symptoms.To perform a quantitative trait locus association for identifying genetic variants for MMT dosage that underlie heroin addiction and methadone metabolism and then integrate several genotypic and phenotypic factors are potential predictors for clinically optimal MMT dose for personalized prescription.In total, 316 heroin-dependent patients undergoing MMT were recruited at the Addiction Center of the China Medical University Hospital. A multinomial logistic regression model was used to assess associations between genetic polymorphisms and MMT dosing. The data were randomly separated into training and testing sets. In order to enhance the prediction accuracy and the reliability of the prediction model, we used areas under the receiver operating characteristic curves to evaluate optimal MMT dose in both training and testing sets.Four single nucleotide polymorphisms, namely rs806368 in CNR1, s1386493 in TPH2, s16974799 in CYP2B6, and rs2229205 in OPRL1, were significantly associated with the maximum MMT dose (P < .05). The genetic risk score (GRS) was associated with maximum MMT dose, and after adjustments for age, sex, and body mass index, the GRS remained independently associated with the maximum MMT dose. The area under the receiver operating characteristic curve of the combined GRS and craving score was 0.77 for maximum MMT dose, with 75% sensitivity and 60% specificity.Integrating the GRS and craving scores may be useful in the evaluation of individual MMT dose requirements at treatment initiation. Optimal dose prediction allows clinicians to tailor MMT to each patient's needs.


Asunto(s)
Ansia , Dependencia de Heroína/tratamiento farmacológico , Dependencia de Heroína/genética , Metadona/administración & dosificación , Narcóticos/administración & dosificación , Medicina de Precisión , Adulto , Citocromo P-450 CYP2B6/genética , Femenino , Estudios de Asociación Genética , Marcadores Genéticos , Humanos , Masculino , Tratamiento de Sustitución de Opiáceos , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Receptor Cannabinoide CB1/genética , Receptores Opioides/genética , Sensibilidad y Especificidad , Índice de Severidad de la Enfermedad , Triptófano Hidroxilasa/genética
8.
PLoS One ; 15(6): e0234088, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32559183

RESUMEN

Bacterial blight (BB) and fungal blast diseases are the major biotic constraints that limit rice productivity. To sustain yield improvement in rice, it is necessary to developed yield potential of the rice varieties by incorporation of biotic stress resistance genes. Tellahamsa is a well-adapted popular high yielding rice variety in Telangana state, India. However, the variety is highly susceptible to BB and blast. In this study, simultaneous stepwise transfer of genes through marker-assisted backcross breeding (MABB) strategy was used to introgress two major BB (Xa21 and xa13) and two major blast resistance genes (Pi54 and Pi1) into Tellahamsa. In each generation (from F1 to ICF3) foreground selection was done using gene-specific markers viz., pTA248 (Xa21), xa13prom (xa13), Pi54MAS (Pi54) and RM224 (Pi1). Two independent BC2F1 lines of Tellahamsa/ISM (Cross-I) and Tellahamsa/NLR145 (Cross-II) possessing 92% and 94% recurrent parent genome (RPG) respectively were intercrossed to develop ICF1-ICF3 generations. These gene pyramided lines were evaluated for key agro-morphological traits, quality, and resistance against blast at three different hotspot locations as well as BB at two locations. Two ICF3 gene pyramided lines viz., TH-625-159 and TH-625-491 possessing four genes exhibited a high level of resistance to BB and blast. In the future, these improved Tellahamsa lines could be developed as mega varieties for different agro-climatic zones and also as potential donors for different pre-breeding rice research.


Asunto(s)
Resistencia a la Enfermedad/genética , Genoma de Planta , Oryza/genética , Enfermedades de las Plantas/genética , ADN de Plantas/metabolismo , Grano Comestible/fisiología , Marcadores Genéticos , Genotipo , Oryza/crecimiento & desarrollo , Enfermedades de las Plantas/microbiología
9.
PLoS One ; 15(6): e0234395, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32525930

RESUMEN

As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.


Asunto(s)
Oryza/genética , Sitios de Carácter Cuantitativo , Amilosa/análisis , Biofortificación/métodos , Productos Agrícolas/química , Productos Agrícolas/clasificación , Productos Agrícolas/genética , Alimentos Fortificados/análisis , Genes de Plantas , Marcadores Genéticos , Hierro/análisis , Valor Nutritivo , Oryza/química , Oryza/clasificación , Fenotipo , Fitomejoramiento/métodos , Proteínas de Vegetales Comestibles/análisis , Análisis de Regresión , Semillas/química , Semillas/genética , Zinc/análisis
10.
PLoS One ; 15(6): e0235215, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32598372

RESUMEN

Anthracnose (ANT) and angular leaf spot (ALS) caused by Colletotrichum lindemuthianum and Pseudocercospora griseola, respectively, are devastating diseases of common bean around the world. Therefore, breeders are constantly searching for new genes with broad-spectrum resistance against ANT and ALS. This study aimed to characterize the genetic resistance of California Dark Red Kidney (CDRK) to C. lindemuthianum races 73, 2047, and 3481 and P. griseola race 63-39 through inheritance, allelism testing, and molecular analyses. Genetic analysis of response to ANT and ALS in recombinant inbred lines (RILs) from a CDRK × Yolano cross (CY) showed that the resistance of CDRK cultivar is conferred by a single dominant loci, which we named CoPv01CDRK/PhgPv01CDRK. Allelism tests performed with race 3481showed that the resistance gene in CDRK is independent of the Co-1 and Co-AC. We conducted co-segregation analysis in genotypes of 110 CY RILs and phenotypes of the RILs in response to different races of the ANT and ALS pathogens. The results revealed that CoPv01CDRK and PhgPv01CDRK are coinherited, conferring resistance to all races. Genetic mapping of the CY population placed the CoPv01CDRK/PhgPv01CDRK loci in a 245 Kb genomic region at the end of Pv01. By genotyping 19 RILs from the CY population using three additional markers, we fine-mapped the CoPv01CDRK/PhgPv01CDRK loci to a smaller genomic region of 33 Kb. This 33 Kb region harbors five predicted genes based on the common bean reference genome. These results can be applied in breeding programs to develop bean cultivars with ANT and ALS resistance using marker-assisted selection.


Asunto(s)
Colletotrichum/fisiología , Resistencia a la Enfermedad/genética , Genes de Plantas , Ligamiento Genético , Marcadores Genéticos , Phaseolus/genética , Enfermedades de las Plantas/genética , California , Mapeo Cromosómico , Genotipo , Phaseolus/microbiología , Fenotipo , Enfermedades de las Plantas/microbiología
11.
PLoS One ; 15(6): e0234465, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32544194

RESUMEN

Obesity leads a crucial importance in metabolic disorders, as well as type 2 diabetes mellitus. Our present study was designed to assess the potential role of irisin, adiponectin, leptin and gene polymorphism of PNPLA3, leptin and adiponectin as predictive markers of diabetes associated with obesity. One hundred eighty subjects were distributed to three groups including; healthy non-diabetic non obese volunteers as a control group, diabetic non obese group, and diabetic obese group (n = 60 for each group). Fasting blood samples of all groups were collected to determine fasting blood glucose, insulin levels, insulin resistance, total cholesterol, high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), triacylglycerol, irisin, adiponectin, leptin; as well as, polymorphism of PNPLA3, adiponectin and leptin. The results showed that glucose, insulin resistance, total cholesterol, irisin, leptin, LDL-C, triacylglycerol concentrations were significantly increased, however, insulin, HDL-C, adiponectin were significantly decreased in diabetic obese patients in relation to diabetic non-obese patients as well as in healthy volunteers. The polymorphism of PNPLA3 rs738409 was linearly related to irisin and leptin but was not related with circulating concentrations of adiponectin. We concluded that increased irisin and leptin levels can predict the insulin resistance in obese patients. Moreover, patients who have mutant genotype of PNPLA3 I148 gene (rs738409) C>G, ADIPOQ gene (rs266729) G>C and LEP gene (rs2167270) G>A showed a significant higher susceptibility rate for DM in obese people than those with wild type. This could be considered as an adjustable retort to counter the impact of obesity on glucose homeostasis.


Asunto(s)
Adiponectina/genética , Diabetes Mellitus Tipo 2/etiología , Predisposición Genética a la Enfermedad , Resistencia a la Insulina/genética , Leptina/genética , Lipasa/genética , Proteínas de la Membrana/genética , Obesidad/complicaciones , Obesidad/genética , Adiponectina/sangre , Adulto , Femenino , Fibronectinas/sangre , Fibronectinas/genética , Marcadores Genéticos , Humanos , Leptina/sangre , Lipasa/sangre , Masculino , Proteínas de la Membrana/sangre , Polimorfismo Genético , Adulto Joven
12.
J Fish Biol ; 96(6): 1293, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32572953
13.
Mol Genet Genomics ; 295(5): 1197-1209, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32500265

RESUMEN

Growing evidence indicates that the development and progression of multiple complex diseases are influenced by microRNA (miRNA). Identifying more miRNAs as biomarkers for clinical diagnosis, treatment and prognosis is vital to promote the development of bioinformatics and medicine. Considering that the traditional biological experimental methods are generally time-consuming and expensive, high-efficient computational methods are encouraged to uncover potential disease-related miRNAs. In this paper, FCGCNMDA is presented to predict latent miRNA-disease associations by utilizing fully connected graph convolutional networks. Specially, our method first constructs a fully connected graph in which edge weights represent correlation coefficient between any two pairs of miRNA-disease pair, and then feeds this fully connected graph along with miRNA-disease pairs feature matrix into a two-layer graph convolutional networks (GCN) for training. At last, we utilize the trained network to predict the scores for unknown miRNA-disease pairs. As a result, FCGCNMDA achieves AUC value of [Formula: see text] and AUPRC value of [Formula: see text] in HMDD v2.0 based on five-fold cross validation. Moreover, case studies on Lymphoma, Breast Neoplasms and Prostate Neoplasms shown that 98%, 98%, 98% of the top 50 selected miRNAs were validated by recent experimental evidence. From above results, we can deduce that FCGCNMDA can be regarded as reliable method for potential miRNA-disease associations prediction.


Asunto(s)
Neoplasias de la Mama/genética , Biología Computacional/métodos , Estudios de Asociación Genética/métodos , Linfoma/genética , MicroARNs/genética , Neoplasias de la Próstata/genética , Algoritmos , Área Bajo la Curva , Aprendizaje Profundo , Diagnóstico Precoz , Femenino , Marcadores Genéticos , Predisposición Genética a la Enfermedad , Humanos , Masculino , Pronóstico
14.
Gene ; 756: 144912, 2020 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-32574760

RESUMEN

Assessment of existing diversity is the key for germplasm conservation and crop improvement. Wheat (Triticum aestivum L.) is among the most important cereal crop and consumed by two billion world's populations. DNA-based markers are predominantly used for diversity characterization because they are easy to develop and not influenced by environment. Among them microsatellites (simple sequence repeats, SSRs) are most suitable due to their genome-wide distribution, hypervariability and reproducibility for their applications in diversity, genetic improvement, and molecular breeding. bZIP transcription factors play major roles in plants in light and stress signalling, seed development, and defence. A total of 846 SSRs were identified from 370 wheat cDNA sequences and a sub-set of 35 polymorphic TabZIPMS (TriticumaestivumbZIP MicroSatellites) was used for diversity and genetic structure analysis of 92 Indian wheat varieties and related species. 114 SSR variants ranging from 2 to 5 per SSR locus were detected for 35 SSRs in the varieties. Average polymorphic information content (PIC) and observed heterozygosity was found to be 0.135 and 0.838, respectively. Thirty-four SSRs showed cross-transferability into different related species. Combined Bayesian model and Jaccard's similarity based genetic clustering analysis revealed two clusters of 80 bread wheat varieties and one separate cluster of related species. In this study, a total 35 novel bZIP-derived SSRs were identified in a set 370 bZIP genes and shown high polymorphism and cross-species transferability in wheat. The findings provide resources for future utilization in genetic resource conservation, trait introgression, breeding and varietal development.


Asunto(s)
Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Repeticiones de Microsatélite , Proteínas de Plantas/genética , Triticum/genética , Marcadores Genéticos , Filogenia , Triticum/clasificación
15.
Gene ; 754: 144890, 2020 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-32534057

RESUMEN

PURPOSE: Stargardt disease (STGD) is the most frequent cause of hereditary macular dystrophy in childhood. Variants in the ABCA4, ELOVL4, PROM1, BEST1, and PRPH2 genes have been detected in patients with autosomal recessive or dominant STGD. This study was aimed at identifying the novel disease-associated variants in Chinese patients with STGD. METHODS: Ten Chinese families and two sporadic cases with STGD (n = 32) were enrolled in the study. All subjects underwent genetic analysis with next-generation sequencing (NGS), which was based on a specially customized capture panel targeting exons and untranslated regions (UTRs) of 792 genes related to common hereditary ophthalmopathy. Variants were analyzed to assess possible pathogenicity. RESULTS: Fourteen disease-associated variants of ABCA4 were detected in 9 Chinese families with autosomal recessive STGD, including 11 pathogenic variants and 3 likely pathogenic variants. Variant c.4253 + 4C > T in ABCA4 was identified as one de novo variant. Of the 14 distinct variants in ABCA4, 7 novel variants were found. In addition, one known variant of PROM1, c.1117C > T (p.Arg373Cys), was detected in one family and one sporadic case with autosomal dominant STGD, respectively. One novel missense variant of ELOVL4, c.59A > G (p.Asn20Ser), was found in one sporadic case with autosomal dominant STGD. The potential deleterious effects of these novel variants were confirmed through intensive analysis. CONCLUSION: By panel-based NGS, 8 novel disease-associated variants are identified in two genes responsible for STGD, including ABCA4 and ELOVL4. Our results further extend the mutation spectrum of these two genes in Chinese patients with STGD. One ABCA4 c.4253 + 4C > T variant is identified as a de novo splicing variant.


Asunto(s)
Grupo de Ascendencia Continental Asiática/genética , Marcadores Genéticos , Variación Genética , Mutación , Enfermedad de Stargardt/genética , Transportadoras de Casetes de Unión a ATP/genética , Adulto , Niño , Proteínas del Ojo/genética , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Proteínas de la Membrana/genética , Linaje , Adulto Joven
16.
Arch Virol ; 165(8): 1803-1813, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32474688

RESUMEN

In recent years, the availability of reverse genetics systems for porcine reproductive and respiratory syndrome virus (PRRSV) has created new perspectives for the use of recombinant viruses as expression vectors. Most of these recombinant PRRSV vectors express foreign genes through either an independent transcription unit inserted in ORF1b and ORF2, or in ORF7 and the 3' UTR. The aim of this study was to find an alternative site for foreign gene insertion into the PRRSV genome. Here, we constructed an infectious cDNA clone for a cell-adapted PRRSV strain, GXNN1396-P96. This cDNA-clone-derived recombinant virus (rGXAM) was comparable in its growth kinetics in MARC-145 cells to the parental virus, GX1396-P96. Using the infectious cDNA-clone, we inserted an independent transcription unit in ORF4 and ORF5a to generate a novel PRRSV-based recombinant virus expressing the green fluorescent protein (GFP) gene. Biological characterization of the recombinant virus, rGX45BSTRS-GFP, showed that it maintained similar growth characteristics but produced fewer infectious virions than the parental PRRSV. These data demonstrate that the ORF4 and ORF5a site is able to tolerate the insertion of foreign genes.


Asunto(s)
Marcadores Genéticos/genética , Sistemas de Lectura Abierta/genética , Síndrome Respiratorio y de la Reproducción Porcina/virología , Virus del Síndrome Respiratorio y Reproductivo Porcino/genética , Animales , Línea Celular , Proteínas Fluorescentes Verdes/genética , Porcinos , Replicación Viral/genética
17.
Fa Yi Xue Za Zhi ; 36(2): 256-262, 2020 Apr.
Artículo en Inglés, Chino | MEDLINE | ID: mdl-32530177

RESUMEN

Abstract: Recently, researches on copy number variation (CNV) have extended to every field, such as etiological exploration and precise treatment of complex diseases, as well as genetic breeding and evolution. The unique genetic characteristics of CNV have made people gradually believe that it could be used as a biological genetic marker to solve related problems. With the development of detection technology, application of CNV in forensic medicine will increase gradually. In this paper, the concept and development of CNV, as well as its application in forensic medicine are summarized, to provide new ideas for the practical application of CNV in the future.


Asunto(s)
Variaciones en el Número de Copia de ADN , Medicina Legal , Marcadores Genéticos
18.
Sci Total Environ ; 739: 139928, 2020 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-32540662

RESUMEN

The development of microbial source tracking methods has resulted in an array of genetic faecal markers for assessing human health risks posed from surface water pollution. However, their use as performance metrics at wastewater treatment plants (WWTPs) has not been explored extensively. Here we compared three Bacteroides (HF183, HumM2, AllBac) and two E. coli (H8, RodA) genetic markers for summer and winter performance monitoring at twelve small rural (<250 PE) and three larger WWTPs in NE England. Small WWTPs are of interest because they are poorly understood and their impact on surface water quality may be underestimated. Overall, genetic marker data showed significant differences in treatment performance at smaller versus larger WWTPs. For example, effluent abundances of HF183 and HumM2 were significantly higher in smaller systems (p = 0.003 for HumM2; p = 0.02 for HF183). Genetic markers also showed significant differences in performance between seasons (p < 0.01, n = 120), with human-specific markers (i.e., HF183, HumM2, H8) being generally better for summer WWTP monitoring. In contrast, Bacteroides markers were much more suitable for winter monitoring, possibly because the E. coli markers are less sensitive to differences in temperature and sunlight conditions. Overall, Bacteroides markers best described WWTP treatment performance across all samples, although seasonal differences suggest caution is needed when markers are used for performance monitoring. Genetic markers definitely provide rapid and new information about WWTP performance, but more spatially diverse studies are needed to refine their use for routine WWTP monitoring.


Asunto(s)
Aguas Residuales , Microbiología del Agua , Inglaterra , Monitoreo del Ambiente , Escherichia coli , Heces , Marcadores Genéticos , Humanos , Estaciones del Año
19.
Mol Biol Rep ; 47(6): 4827-4833, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: covidwho-277073

RESUMEN

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.


Asunto(s)
Betacoronavirus/patogenicidad , Infecciones por Coronavirus/transmisión , Euterios/genética , Repeticiones de Microsatélite , Pandemias , Neumonía Viral/transmisión , Zoonosis/transmisión , Alelos , Animales , Camerún/epidemiología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/prevención & control , Infecciones por Coronavirus/virología , Reservorios de Enfermedades/virología , Euterios/virología , Femenino , Sitios Genéticos , Marcadores Genéticos , Genotipo , Humanos , Desequilibrio de Ligamiento , Masculino , Pandemias/prevención & control , Neumonía Viral/epidemiología , Neumonía Viral/prevención & control , Neumonía Viral/virología , Zoonosis/epidemiología , Zoonosis/prevención & control , Zoonosis/virología
20.
Environ Sci Pollut Res Int ; 27(24): 30615-30624, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32472511

RESUMEN

A dog-associated 16S rDNA genetic marker (ED-1) was designed to detect dog fecal contamination in water through a comparative bioinformatics analysis of Faecalibacterium sequences. For the dog fecal samples, ED-1 had 100% specificity, a high positive rate (89% in dog feces and 92.3% in dog fecal-contaminated water samples), and a low detection limit (107 copies/100 mL) in dog-contaminated water samples. Detection of water samples from seven provinces or cities of China showed that ED-1 was stable enough to be applied in practice. Furthermore, the abundance and diversity of dog gut microbiota from two private house pets (PHP) and Third Military Medical University (TMMU) dogs were estimated by using operational taxonomic units, and the significant differences of dog feces were found, as the PHP dogs have a more diverse diet and closer contact with human than dogs in TMMU. However, ED-1 could detect the feces from the two regions, indicating that ED-1 has good reliability.


Asunto(s)
Animales , China , ADN Ribosómico , Perros , Faecalibacterium/genética , Heces , Marcadores Genéticos , Humanos , ARN Ribosómico 16S , Reproducibilidad de los Resultados
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