RESUMO
A combination of phenotypic characterization and molecular markers may provide reliable information on new plant varieties and elucidate the conservation status of rare species. Five newly developed Magnolia wufengensis cultivars, an endangered plant species endemic to Hubei Province, China, possess more distinctive phenotypes than common Magnolia cultivars. With reference to a wild species population of M. wufengensis and a population of Magnolia denudata, morphological traits of flower organs, simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers were used. In the morphological study, six traits of floral organs were investigated and their relationships were analyzed between cultivars. In the genetic study, 9 SSR primer pairs and 10 SRAP primer combinations were screened. The five cultivars maintained a high level of genetic diversity. Genetic diversity of each M. wufengensis cultivar was much lower than that of the wild population, but was slightly higher than that of the M. denudata population. Analysis of molecular variance (AMOVA) revealed that genetic variation among populations was 20% (SRAP) and 30% (SSR), which showed a high degree of genetic differentiation among populations of the five cultivars. The dendrograms illustrated a clear separation between M. wufengensis populations and outer species, and identified two major groups among cultivars. Correlation analysis indicated a good fit between the two marker systems, but a relatively low fit between morphological and genetic traits (SRAP: r = 0.60, SSR: r = 0.52). These findings provide reliable references for the application of these molecular markers in the breeding and conservation of M. wufengensis.
Assuntos
Conservação dos Recursos Naturais/métodos , Marcadores Genéticos/genética , Variação Genética , Magnolia/genética , Repetições de Microssatélites/genética , Melhoramento Vegetal/métodos , Análise de Variância , Antocianinas/análise , Antocianinas/metabolismo , China , Cromatografia Líquida de Alta Pressão , Análise por Conglomerados , Cor , Espécies em Perigo de Extinção , Flores/genética , Flores/metabolismo , Magnolia/classificação , Magnolia/metabolismo , Fenótipo , Filogenia , Pigmentação/genética , Especificidade da EspécieRESUMO
Two rice doubled haploid (DH) populations derived from the crosses of ZYQ8/JX17 and CJ06/TN1 were used to detect quantitative trait loci (QTLs) for flag leaf length (FLL), width (FLW), and angle (FLA) under long-day conditions in Hangzhou (subtropical zone) and short-day conditions in Hainan (tropical zone), China. The four parents differed significantly in all 3 traits. FLL was found to be positively correlated with FLW in the 2 populations. A total of 30 QTLs were identified for flag leaf traits, with a contribution to the phenotypic variation of each QTL from 4.49 to 26.30%. Among these, qFLL-4b, qFLW-12, and qFLA-2a showed larger additive effects on the phenotype and explained more variations compared to the other QTLs. qFLL-1a and qFLL-8 were detected in both environments, while qFLL-2, qFLL-3, qFLL-10, qFLL-12, qFLW11, qFLW2, and qFLA8 were novel QTLs, which may be beneficial to rice ideal-type breeding.
Assuntos
Genoma de Planta , Haploidia , Oryza/genética , Folhas de Planta/genética , Locos de Características Quantitativas , Cruzamento , China , Mapeamento Cromossômico , Cruzamentos Genéticos , Genótipo , Oryza/anatomia & histologia , Fenótipo , Fotoperíodo , Folhas de Planta/anatomia & histologia , Clima TropicalRESUMO
Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism.
Assuntos
Vírus da Febre Suína Clássica/classificação , Vírus da Febre Suína Clássica/genética , RNA Viral/genética , Sequências Reguladoras de Ácido Ribonucleico , Animais , Vírus da Febre Suína Clássica/fisiologia , Códon de Iniciação , Evolução Molecular , Variação Genética , Filogenia , Biossíntese de Proteínas , RNA de Transferência/genética , Análise de Sequência de RNARESUMO
Adaptation in the overall codon usage pattern of West Nile virus (WNV) to that of two hosts was estimated based on the synonymous codon usage value (RSCU). Synonymous codon usage biases for the beginning coding sequence of this virus were also analyzed by calculating the usage fluctuation for each synonymous codon along the target region (the first 270 codon sites of the whole coding sequence of WNV). Adaptation of WNV to Anopheles gambiae regarding the overall codon usage revealed a mixture of synonymous codon usage patterns between this virus and its vector. Regarding the adaptation of WNV to its dead-end host and codon usage, although a mixture of overall codon usage patterns exists, the number of codons with reversed tendency codon usage is lower than that between the virus and its vector. In addition, some codons with low RSCU values for this virus are highly selected in the beginning translation region of WNV, while codons with low RSCU values in this region tend to pair with tRNAs present in low abundance in the host, suggesting that highly selected codons in a specific region in the beginning region of WNV are, to some degree, influenced by the corresponding low tRNA abundance of hosts to regulate the translation speed of the WNV polyprotein.
Assuntos
Códon , Fases de Leitura Aberta , RNA Viral , Vírus do Nilo Ocidental/genética , Interações Hospedeiro-Patógeno , RNA de TransferênciaRESUMO
In this study, a total of 1047 insertion-deletion (InDel) primer pairs distributed across the rice genome were developed and experimentally validated. The primer pairs were designed based on the InDel length polymorphisms between 93-11 (Oryza sativa ssp indica cv.) and Nipponbare (Oryza sativa ssp japonica cv.), aiming for utilization between indica and japonica rice, or between other inter-subspecific rice cultivars. The 1047 primer pairs were dispersed across all 12 of the rice chromosomes, with one InDel marker found every 371.3 kb on average. The InDel length of the markers varied from 3 to 39 bp: 88.2% of the markers contained 6 to 25 bp, only 6.2% of markers were ≤ 5 bp, and 5.6% were ≥ 26 bp. Six hundred and twenty-three (59.5%) of the 1047 InDel markers were shown to amplify well and were polymorphic between Taichung65 and IR8, and 476 (45.5%) markers were polymorphic between Lemont and Yangdao4, while 398 (38.0%) were polymorphic in both combinations. These results demonstrated that the polymerase chain reaction-based InDel markers developed in this study could be of immediate use for rice genetic studies and breeding programs.