RESUMO
This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding.
Assuntos
Repetições de Microssatélites , Piper nigrum/genética , Polimorfismo Genético , Etiquetas de Sequências Expressas , Especiação Genética , Sementes/genéticaRESUMO
Black pepper is a perennial climbing vine. It is widely cultivated because its berries can be utilized not only as a spice in food but also for medicinal use. This study aimed to construct a standardized, high-quality cDNA library to facilitated identification of new Piper hainanense transcripts. For this, 262 unigenes were used to generate raw reads. The average length of these 262 unigenes was 774.8 bp. Of these, 94 genes (35.9%) were newly identified, according to the NCBI protein database. Thus, identification of new genes may broaden the molecular knowledge of P. hainanense on the basis of Clusters of Orthologous Groups and Gene Ontology categories. In addition, certain basic genes linked to physiological processes, which can contribute to disease resistance and thereby to the breeding of black pepper. A total of 26 unigenes were found to be SSR markers. Dinucleotide SSR was the main repeat motif, accounting for 61.54%, followed by trinucleotide SSR (23.07%). Eight primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among twenty-one piper germplasm. These results present a novel sequence information of P. hainanense, which can serve as the foundation for further genetic research on this species.
Assuntos
Etiquetas de Sequências Expressas , Piper/genética , DNA de Plantas/genética , Regulação da Expressão Gênica de Plantas , Biblioteca Gênica , Genoma de Planta/genética , Polimorfismo Genético/genéticaRESUMO
The A-20C polymorphism in the angiotensinogen (AGT) gene has been associated with increased risk of essential hypertension in several studies; however, these studies gave inconsistent results. In this study, we performed a meta-analysis to assess the association between AGT A-20C polymorphism and essential hypertension. Published literature was retrieved from PubMed. Pooled odd's ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effect models. A total of 10 case-control studies containing 3653 cases and 3457 controls were enrolled to this meta-analysis. In a combined analysis, the results showed a significant association between the AGT A-20C polymorphism and risk of essential hypertension (AA vs CC: OR = 0.62, 95%CI = 0.46-0.84; recessive model: OR = 0.66, 95%CI = 0.49-0.88). In the subgroup analysis stratified by race, significant associations were found between the AGT A-20C polymorphism and essential hypertension risk in Asians (AA vs CC: OR = 0.59, 95%CI = 0.43-0.80; recessive model: OR = 0.63, 95%CI = 0.46-0.85). In conclusion, the results of this meta-analysis suggested that the AGT A-20C polymorphism was associated with risk of essential hypertension in Asians.
Assuntos
Angiotensinogênio/genética , Hipertensão/genética , Polimorfismo de Nucleotídeo Único/genética , Povo Asiático , Hipertensão Essencial , Predisposição Genética para Doença/genética , Humanos , Razão de ChancesRESUMO
Ulcerative colitis (UC) is an immune-related disease with genetic predisposition. The aim of this study was to investigate the association of three polymorphisms in the receptor for advanced glycation end-products (RAGE) gene with UC risk in a Chinese population. This case-control study involved 72 UC patients and 479 age- and gender-matched healthy controls. Genotyping was performed using the polymerase chain reaction-ligase detection reaction method. Data were analyzed using the Haplo.stats program. There were no significant differences between patients and controls in the allele/genotype distributions of rs1800624 (P(allele)= 0.11; Pgenotype = 0.20), rs1800625 (P(allele) = 0.16; Pgenotype = 0.11), or rs2070600 (P(allele) = 0.37; Pgenotype = 0.65). In addition, no positive haplotypes were identified. To the best of our knowledge, the current study describes polymorphisms of RAGE in Chinese UC for the first time. We found no association between RAGE polymorphisms and the development of UC in the Chinese population.
Assuntos
Colite Ulcerativa/genética , Polimorfismo Genético , Receptor para Produtos Finais de Glicação Avançada/genética , Adulto , Alelos , Povo Asiático , Estudos de Casos e Controles , Colite Ulcerativa/diagnóstico , Colite Ulcerativa/etnologia , Colite Ulcerativa/patologia , Suscetibilidade a Doenças , Feminino , Expressão Gênica , Frequência do Gene , Haplótipos , Humanos , Masculino , Pessoa de Meia-IdadeRESUMO
Ulcerative colitis (UC) is a chronic inflammation of the large intestine. The aim of this study was to investigate the association of two polymorphisms in STAT3 with the risk of UC development in the Chinese Han population. This is a hospital-based case-control study involving 56 UC patients and 274 controls. Genotyping was performed using the polymerase chain reaction with sequence-specific primers (PCR-SSP) method. Statistical analyses were conducted using logistic regression and genotype risk score. Overall, there was a significant difference between patients and controls in the genotype distribution of rs2293152 (P = 0.044). The risk for UC associated with the rs2293152-G mutant allele was increased (odds ratio = 2.76; 95% confidence interval = 1.06- 7.24) under the dominant model. However, we failed to find any obvious differences in the rs4796793 genotype or allele distributions between the UC patients and controls, and did not detect any significant association of the rs4796793 polymorphism with UC across different genetic models of inheritance. Our study implies that the STAT3 rs2293152 polymorphism may be associated with the occurrence of UC and might be used as a predictive factor for UC in the Chinese Han population.
Assuntos
Colite Ulcerativa/genética , Estudos de Associação Genética , Predisposição Genética para Doença , Fator de Transcrição STAT3/genética , Adolescente , Adulto , Idoso , Alelos , Estudos de Casos e Controles , Criança , Pré-Escolar , Colite Ulcerativa/patologia , Feminino , Genótipo , Haplótipos , Humanos , Masculino , Pessoa de Meia-Idade , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The gene encoding vitamin D receptor (VDR) is recognized as a promising candidate for indicating the development of inflammatory bowel disease (IBD). Four genetic polymorphisms (ApaI, BsmI, FokI, TaqI) in VDR have been widely evaluated to determine their association with IBD, and the results of these evaluations are often inconsistent. Therefore, we conducted a meta-analysis to shed some light on this issue and explored the sources of the heterogeneity between studies. We identified six articles for ApaI (cases/controls: 1902/1468), eight for TaqI (3053/2145), and five each for BsmI (1512/1616) and FokI (2315/1676). Data were analyzed under the random-effects model, and heterogeneity was explored by subgroup analyses. Overall, except for TaqI in allelic comparison [odds ratio (OR) = 0.90, 95% confidence interval (CI): 0.83-0.98], ApaI, BsmI, and FokI polymorphisms showed no significant associations with IBD across different genetic models of inheritance. However, subgroup analyses indicated significance for the association of ApaI with Crohn's disease (CD) risk (AA versus aa: OR = 1.40; 95%CI = 1.05-1.88), for BsmI in East Asians (BB plus Bb versus bb: OR = 1.77, 95%CI = 1.14-2.74), for TaqI in Caucasians (TT plus Tt versus tt: OR = 0.79, 95%CI = 0.63- 1.00), and with ulcerative colitis (UC) risk (T versus t: OR = 0.89, 95%CI = 0.80-0.99). There was a low probability of publication bias for all studied polymorphisms. Pooling previous individual studies on IBD, our findings demonstrated that the ApaI polymorphism may increase the risk of CD, whereas the TaqI polymorphism may decrease the risk of UC, especially in Caucasians. Moreover, this study leaves open the question of divergent genetic profiles across different ethnic groups.