RESUMEN
In the current study, morphological traits and molecular markers were used to assess the genetic diversity of 29 cultivated tomatoes, 14 wild tomatoes and seven introgression lines. The three components of the principal component analysis (PCA) explained 78.54% of the total morphological variation in the 50 tomato genotypes assessed. Based on these morphological traits, a three-dimensional PCA plot separated the 50 genotypes into distinct groups, and a dendrogram divided them into six clusters. Fifteen polymorphic genomic simple- sequence repeat (genomic-SSR) and 13 polymorphic expressed sequence tag-derived SSR (EST-SSR) markers amplified 1115 and 780 clear fragments, respectively. Genomic-SSRs detected a total of 64 alleles, with a mean of 4 alleles per primer, while EST-SSRs detected 52 alleles, with a mean of 4 alleles per primer. The polymorphism information content was slightly higher in genomic-SSRs (0.49) than in EST-SSRs (0.45). The mean similarity coefficient among the wild tomatoes was lower than the mean similarity coefficient among the cultivated tomatoes. The dendrogram based on genetic distance divided the 50 tomato genotypes into eight clusters. The Mantel test between genomic-SSR and EST-SSR matrices revealed a good correlation, whereas the morphological matrices and the molecular matrices were weakly correlated. We confirm the applicability of EST-SSRs in analyzing genetic diversity among cultivated and wild tomatoes. High variability of the 50 tomato genotypes was observed at the morphological and molecular level, indicating valuable tomato germplasm, especially in the wild tomatoes, which could be used for further genetic studies.
Asunto(s)
Variación Genética , Repeticiones de Microsatélite , Fenotipo , Carácter Cuantitativo Heredable , Solanum lycopersicum/genética , Alelos , Análisis por Conglomerados , Etiquetas de Secuencia Expresada , Marcadores Genéticos , Genómica/métodos , Genotipo , Solanum lycopersicum/clasificación , FilogeniaRESUMEN
In order to study genetic variability and develop better strategies for the utilization of 48 tomato cultivars from America, China, the Netherlands, and Portugal, genomic simple sequence repeat (gSSR) and EST-derived SSR (EST-SSR) markers were applied. In all, 15 of 82 gSSR and 18 of 115 EST-SSR markers showed polymorphic loci. There were 995 and 2072 clear fragments amplified by polymorphic gSSR and EST-SSR markers, respectively. The total and average number of alleles detected by EST-SSRs (75, 4.2) was more than gSSRs (54, 3.6) as a result of some multi-locus EST-SSRs. A lower polymorphism information content value was found in gSSRs (0.529) compared to EST-SSRs (0.620). Similarity coefficient matrixes of the 48 tomato cultivars were established based on the gSSRs and EST-SSRs, and UPGMA dendrograms were constructed from the gSSRs and EST-SSRs similarity coefficient matrixes. A high similarity was observed between the gSSRs and EST-SSRs dendrograms. Genetic variability of four tomato populations from different countries showed that the observed number of alleles and Nei's genetic diversity were highest in the American population, and the effective number of alleles was highest in the Dutch population. The estimated genetic structure showed some tomato cultivars from different countries shared a common genetic background, which might be related to gene flow. It was inferred that both gSSR and EST-SSR markers were effective to assess genetic variability of tomato cultivars, and the combination of both markers could be more effective for genetic diversity analysis in tomato.
Asunto(s)
Etiquetas de Secuencia Expresada , Variación Genética , Repeticiones de Microsatélite , Solanum lycopersicum/genética , Alelos , Marcadores Genéticos , Solanum lycopersicum/clasificación , Filogenia , Polimorfismo GenéticoRESUMEN
In addition to the host immune response, genetic and environmental factors play crucial roles in the manifestation of hepatitis B virus (HBV) infection. The macrophage migration inhibitory factor (MIF) -173G/C polymorphism (rs755622), located in the promoter region of MIF, may play integral roles in diverse processes, including the immune response. Thus, the MIF -173G/C polymorphism may influence the immune response to HBV during natural infection. We investigated whether the MIF -173G/C polymorphism was associated with susceptibility to HBV infection in a Chinese Han population. A total of 596 HBV infection cases and 612 age-matched controls were recruited for the study. Genotyping of the MIF -173G/C polymorphism was performed using the allele-specific polymerase chain reaction method. The frequencies of the alleles and genotypes in patients and controls were compared using the χ(2) test. Carriers of the variant C allele in MIF -173 G/C were at significantly higher risk of HBV infection than carriers of the wild-type allele (P = 0.032, odds ratio = 0.799, 95% confidence interval = 0.651-0.981). However, there was no significant difference in the distribution of MIF -173G/C genotypes between case and control groups in either population (P = 0.096, degrees of freedom = 2). Our findings indicate that the G to C base change in MIF -173 G/C confers an increased risk of development of HBV infection by altering the expression of MIF in our Chinese Han population.
Asunto(s)
Hepatitis B Crónica/genética , Oxidorreductasas Intramoleculares/genética , Factores Inhibidores de la Migración de Macrófagos/genética , Adulto , Anciano , Pueblo Asiatico/genética , Estudios de Casos y Controles , China , Femenino , Frecuencia de los Genes , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Virus de la Hepatitis B/aislamiento & purificación , Hepatitis B Crónica/enzimología , Humanos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Reacción en Cadena de la Polimerasa , Polimorfismo de Nucleótido Simple , Regiones Promotoras GenéticasRESUMEN
Cultivar identification diagrams (CIDs) provide a rapid and efficient approach for identifying cultivars based on random amplified polymorphic DNA (RAPD) markers. In this paper, 64 tomato cultivars were identified using a CID. Using RAPD profiles, clustering analysis was performed to analyze genetic diversity. The results showed that 8 RAPD primers could completely separate the 64 cultivars according to the obtained polymorphic bands; a CID of the 64 tomato cultivars was then constructed. As verification of the CID validity, 8 randomly selected cultivars were investigated and proven to be well distinguished. In addition, 33 DNA bands were obtained, 20 (60.6%) of which were polymorphic. Genetic distances were calculated with a range of 0.032 to 1.402. Clustering analysis showed that the 64 tomato cultivars were divided into 4 groups with a similarity coefficient of 0.40. Using this novel strategy, with the same RAPD data, both CID and clustering analysis can simultaneously determine tomato cultivars and their genetic diversity.