선택한 단어 수는 입니다.
최소 단어 이상 선택하여야 합니다.
최소 단어 이상 선택하여야 합니다.
선택한 단어 수는 30입니다.
최대 10 단어까지만 선택 가능합니다.
최대 10 단어까지만 선택 가능합니다.
문제 정의
- tricuspidata ecotypes using markers derived from plastid and nuclear DNA sequences and demonstrated that marker polymorphisms can be efficiently detected by ARMS-PCR and HRM analysis. This is the first report of the development and characterization of Korean-specific C. tricuspidata ecotypes using SNP markers derived from plastid and nuclear DNA sequences. Our data from DNA barcoding analysis using chloroplast and nuclear genomic sequence regions (MatK and ITS) reveal inter- and intraspecific variation among C.
제안 방법
- A primer set was designed based on the intergenic sequences of the MatK and ITS regions to develop a plastid sequence HRM assay for identifying specific plant ecotypes. HRM analysis was performed to detect polymorphisms in this marker sequence.
- Since short amplicons usually result in better resolution in HRM analysis, primers were designed to amplify a short region of the intergenic sequence. Specific primer sets were designed for HRM analysis to discriminate between each of the three plant species based on specific SNPs (Table 2C). HRM analysis was conducted using the Mx3005P QPCR System (Agilent Technologies, CA, USA).
- Based on the results of nucleotide sequence alignment of each C. tricuspidata ecotype, we designed a primer set to amplify a short fragment of each sequence (MatK, 197 bp and ITS, 205 bp) and to locate the SNP site in the middle of each amplicon for HRM curve analysis (Fig. 5A). When we performed HRM analysis of the MatK plastid sequences and the ITS nuclear sequences using DNA from each plant sample, two different melting curve patterns were detected (Fig.
- 3 and 4). HRM curve analysis of specific markers in the plastid MatK region and the nuclear ITS region using DNA samples from C. tricuspidata ecotypes originating from Korea and China resulted in melting curve patterns consistent with the nucleotide differences determined by sequence analysis (Fig. 5). As expected, the melting curve patterns differed between Korean- and Chinese-specific C.
- Therefore, in this study, we developed an effective method for identifying Korean-specific C. tricuspidata ecotypes using markers derived from plastid and nuclear DNA sequences and demonstrated that marker polymorphisms can be efficiently detected by ARMS-PCR and HRM analysis. This is the first report of the development and characterization of Korean-specific C.
대상 데이터
- Twelve Cudrania tricuspidata Bureau ecotypes from different regions were used in this study (Table 1 and Fig. 1). Sample identities were confirmed by comparing sequences from the chloroplast MatK and nuclear ITS regions in these samples with those in NCBI GenBank: MatK (accession number JF317421.
- 1). All plant materials were assigned identification numbers and preserved at the Gyeongnam National University of Science and Technology (Jinju, Korea)(Table 1).
데이터처리
- A dendrogram describing the genetic distances between the ecotypes based on their MatK and ITS sequences was constructed using the Mega 6.0 statistical program. Pairwise comparisons between species were performed by measuring genetic distances using the Tamura-Nei distance method.
이론/모형
- 0 statistical program. Pairwise comparisons between species were performed by measuring genetic distances using the Tamura-Nei distance method. A genetic distance matrix was used for cluster analysis via the neighbor-joining method (Tamura et al.
성능/효과
- tricuspidata ecotype originating from the same country, such as Korean and China, revealed a very high degree of sequence homology. Phylogenetic analysis using the MatK and ITS sequence regions demonstrated more similarity among ecotypes originating from Korea than among those from China, with 100% sequence homology detected between each Korean ecotype, such as 2014-30, 31, 33, 34, 36, 37, 38, 39, and 42 (Fig. 2). Among Chinese C.
- 3C). Thus, Korean C. tricuspidata could clearly be identified from among different C. tricuspidata ecotypes.
- 5A). When we performed HRM analysis of the MatK plastid sequences and the ITS nuclear sequences using DNA from each plant sample, two different melting curve patterns were detected (Fig. 5B): the melting curve patterns exactly corresponded with the classification of each ecotype of Korean and Chinese C. tricuspidata. When we subjected C.
- Sequence analysis of highly variable DNA is commonly used for species identification and phylogenetic analysis. In this study, we demonstrated that ARMS-PCR and HRM analysis could be used to detect polymorphic SNPs and to discriminate among ecotypes of C. tricuspidata collected from different locations in South Korea. The main advantage of ARMS is that the amplification and authentication steps are combined, in that the presence of an amplified product indicates the presence of a particular allele and vice versa.
- 5). As expected, the melting curve patterns differed between Korean- and Chinese-specific C. tricuspidata ecotypes based on MatK and ITS markers. Therefore, the results demonstrate that, even though the ecotypes investigated in this study are related and share morphological characteristics, ARMS-PCR and HRM curve analysis using the plastid marker MatK and nuclear marker ITS are sufficient for providing an ecotype-specific DNA barcode to distinguish between ecotypes with different countries of origin.
- tricuspidata ecotypes based on MatK and ITS markers. Therefore, the results demonstrate that, even though the ecotypes investigated in this study are related and share morphological characteristics, ARMS-PCR and HRM curve analysis using the plastid marker MatK and nuclear marker ITS are sufficient for providing an ecotype-specific DNA barcode to distinguish between ecotypes with different countries of origin.
- In conclusion, we performed molecular genetic identification of C. tricuspidata ecotypes collected from different locations using SNP-based ARMS-PCR and HRM analysis with specific primers. The results suggest that it is possible to identify plant materials using assays based on the chloroplast MatK and nuclear ITS region.
- Compared with other methods involving the use of molecular markers, our method is reliable, efficient, and scalable for testing large numbers of ecotypes collected from different locations. The results demonstrate that the plastid DNA region MatK and the nuclear DNA ITS can be used for intraspecific polymorphism studies and that they represent useful tools for markerassisted identification and selection of specific C. tricuspidata ecotypes or cultivars.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.