RESUMO
Cytosine DNA methylation is a significant form of DNA modification closely associated with gene expression in eukaryotes, fungi, animals, and plants. Although the reference genomes of cotton (Gossypium hirsutum L.) have been publically available, the salinity-stress-induced DNA methylome alterations in cotton are not well understood. Here, we constructed a map of genome-wide DNA methylation characteristics of cotton leaves under salt stress using the methylated DNA immunoprecipitation sequencing method. The results showed that the methylation reads on chromosome 9 were most comparable with those on the other chromosomes, but the greatest changes occurred on chromosome 8 under salt stress. The DNA methylation pattern analysis indicated that a relatively higher methylation density was found in the upstream2k and downstream2k elements of the CDS region and CG-islands. Almost 94% of the reads belonged to LTR-gspsy and LTR-copia, and the number of methylation reads in LTR-gypsy was four times greater than that in LTR-copia in both control and stressed samples. The analysis of differentially methylated regions (DMRs) showed that the gene elements upstream2k, intron, and downstream2k were hypomethylated, but the CDS regions were hypermethylated. The GO (Gene Ontology) analysis suggested that the methylated genes were most enriched in cellular processes, metabolic processes, cell parts and catalytic activities, which might be closely correlated with response to NaCl stress. In this study, we completed a genomic DNA methylation profile and conducted a DMR analysis under salt stress, which provided valuable information for the better understanding of epigenetics in response to salt stress in cotton.
Assuntos
Metilação de DNA , Genoma de Planta , Gossypium/genética , Salinidade , Estresse Fisiológico , Cromossomos de Plantas/genética , Estudo de Associação Genômica AmplaRESUMO
Calcineurin B-like protein-interacting protein kinase (CIPK) plays a key regulatory role in the growth, development, and stress resistance of plants by combining with phosphatase B subunit-like protein. In the present study, CIPK genes were identified in the whole genomes of diploid cottons and their sequences were subjected to bioinformatic analyses. The results demonstrated that the CIPK gene family was unevenly distributed in two diploid cotton genomes. Forty-one CIPKs were identified in the D genome, mainly located on chromosomes 9 and 10, whereas thirty-nine CIPKs were identified in the A genome, mainly located on chromosomes 8 and 11. Based on the gene structures, CIPKs in cotton could be classified into two types: one that is intron-rich and the other that has few introns. Phylogenetic analysis revealed that the CIPK gene family members in cotton had close evolutionary relationships with those of the dicotyledonous plants, such as Arabidopsis thaliana and poplar. The analysis of transcriptome sequence data demonstrated that there were differences in gene expression in different tissues, indicating that the expression of the CIPKs in cotton had spatio-temporal specificity. The expression analysis of CIPKs under abiotic stresses (drought, salt, and low temperature) in different tissues at trefoil stage demonstrated that these stresses induced the expression of CIPKs.
Assuntos
Diploide , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Gossypium/genética , Proteínas de Plantas/genética , Cromossomos de Plantas/genética , Análise por Conglomerados , Éxons/genética , Perfilação da Expressão Gênica , Íntrons/genética , Família Multigênica , Filogenia , Folhas de Planta/genética , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Domínios Proteicos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sequência de RNA , Especificidade da Espécie , Estresse Fisiológico/genética , Transcriptoma/genéticaRESUMO
The identification of simple sequence repeat (SSR) markers associated with salt tolerance in cotton contributes to molecular assisted selection (MAS), which can improve the efficiency of traditional breeding. In this study, 134 samples of upland cotton cultivars were selected. The seedling emergence rates were tested under 0.3% NaCl stress. A total of 74 SSR markers were used to scan the genomes of these samples. To identify SSR markers associated with salt tolerance, an association analysis was performed between salt tolerance and SSR markers using TASSEL 2.1, based on the analysis of genetic structure using Structure 2.3.4. The results showed that the seedling emergence rates of 134 cultivars were significantly different, and 27 salt-sensitive and 10 salt-tolerant cultivars were identified. A total of 148 loci were found in 74 SSR markers involving 246 allelic variations, which ranged from 2 to 7 with an average of 3.32 per SSR marker. The gene diversity ranged from 0.0295 to 0.4959, with the average being 0.2897. The polymorphic information content ranged from0.0290 to 0.3729, with the average being 0.2381. This natural population was classified into two subgroups by Structure 2.3.4, containing 89 and 45 samples, respectively. Finally, eight SSR sites associated with salt tolerance ware found through an association analysis, with the rate of explanation ranging from 2.91 to 7.82% and an average of 4.32%. These results provide reference data for the use MAS for salt tolerance in cotton.
Assuntos
Gossypium/genética , Repetições de Microssatélites/genética , Tolerância ao Sal/genética , Alelos , Cruzamento , Mapeamento Cromossômico , Estudos de Associação Genética , Variação Genética , Gossypium/crescimento & desenvolvimento , Fenótipo , Locos de Características Quantitativas/genéticaRESUMO
Germline mutations in identified breast cancer susceptibility genes account for less than 20% of Chinese familial breast cancers. Dicer is an essential component of the microRNA-producing machinery; germline mutations of DICER1 have been confirmed in familial pleuropulmonary blastoma, ovarian sex cord-stromal tumors, and other cancers. Low expression of DICER1 is frequently detected in breast cancer. However, whether germline mutations of DICER1 occur in familial breast cancers remain unknown. Sixty-five breast cancer probands from BRCA1/BRCA2-negative Chinese breast cancer families were screened for germline mutations in DICER1. In addition, 100 unrelated healthy females were enrolled as controls. A polymerase chain reaction sequencing assay was used to screen for mutations in coding regions and at the exon-intron boundaries of DICER1. All variants in introns were evaluated using the NNSplice software to determine the potential splicing effect. A total of 12 germline variants were found, including 11 variants in introns and 1 variant in the 3'-non-coding region. Four variants (IVS8-205 C>T, IVS11+131 delGAAA, IVS16+42 delTA, and IVS19+160 T>C) were novel. Three variants (IVS11+105 C>T, IVS16+42 delTA, and 6095 T>A) may affect splice sites. None of the observed variants appeared to be disease-related, suggesting that germline mutations in DICER1 are rare or absent in familial breast cancer patients.
Assuntos
RNA Helicases DEAD-box/genética , Mutação em Linhagem Germinativa , Neoplasias Ovarianas/genética , Blastoma Pulmonar/genética , Ribonuclease III/genética , Tumores do Estroma Gonadal e dos Cordões Sexuais/genética , Adulto , Idoso , Proteína BRCA1/metabolismo , Proteína BRCA2/metabolismo , Neoplasias da Mama/genética , Neoplasias da Mama/metabolismo , China , Simulação por Computador , RNA Helicases DEAD-box/metabolismo , Feminino , Humanos , Pessoa de Meia-Idade , Neoplasias Ovarianas/metabolismo , Isoformas de Proteínas/metabolismo , Blastoma Pulmonar/metabolismo , Ribonuclease III/metabolismo , Tumores do Estroma Gonadal e dos Cordões Sexuais/metabolismo , Adulto JovemRESUMO
The human X-ray repair cross-complementing protein 1 (XRCC1) gene is a potentially gene determining hepatocellular carcinoma (HCC) susceptibility. The purpose of this study was to evaluate the association between XRCC1 and susceptibility to HCC. The association of XRCC1 polymorphisms with HCC susceptibility was investigated in 460 HCC patients and 463 controls using the created restriction site-polymerase chain reaction method. Our results indicate that the c.1471G>A variant could be detected and that the allele and genotype frequencies were statistically different between cases and controls. The AA genotype was strongly associated with increased HCC susceptibility as compared with the GG wild genotype (OR = 2.214, 95%CI = 1.493-3.283, χ(2) = 15.97, P < 0.0001). In addition, significantly increased HCC susceptibility was also found in a dominant and recessive model (P < 0.01). The allele A could contribute to HCC susceptibility compared with the G allele (OR = 1.480, 95%CI = 1.224-1.789, χ(2) = 16.44, P = 0.0001). Results from this study indicate that the XRCC1 c.1471G>A polymorphism is associated with HCC susceptibility in the Chinese Han population. Future studies on larger populations are essential to confirm this association.