M. Alp Furan, Gulistan Genli, Mehtap Yıldız, Hyeon-Jin Sun
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The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon’s approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on <i>Medicago sativa</i> that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties.</p>","PeriodicalId":20216,"journal":{"name":"Plant Biotechnology Reports","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Exploring secondary structures within the nuclear ribosomal DNA internal transcribed spacers (nr DNA ITS) for enhanced phylogenetic insights in Medicago sativa (alfalfa)\",\"authors\":\"M. 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引用次数: 0
摘要
ITS 区段位于核糖体 DNA 操作子内部,具有高度的多样性和缓慢的进化速度,因此对植物系统发育研究非常重要。这项工作的目的是利用 18 个紫花苜蓿(Medicago sativa)基因型/品种的内部转录间隔区(ITS)来确定它们之间的遗传关系,并验证用于品种识别和分类的可能遗传标记。为此,我们验证了 ITS 区域的二级结构,并观察了最低能量状态、可能的二级结构发夹总数和(GC)含量之间关系的影响。结果表明,ITS 序列的长度在 426 和 629 个核苷酸之间变化,ITS 区域的 G + C 含量在 46.6 和 50% 之间变化。本研究采用分子方差分析(AMOVA)验证了配置分析的有效性,结果表明,数据的波动占观察到的总方差的很大一部分。此外,所分析的基因型中有 94% 表现出显著的多样性。这表明,观测到的变异有很大一部分可能归因于遗传变异。由 Bilensoy80、Emily、Quin、Vendor 和 Felicia 组成的种群四的杂合度最高,为 68.8%,而由 Gozlu1、Prosementi、Nimet 和 Local(Van)组成的种群二的杂合度最低,为 37.5%。作为种群遗传学研究中使用的无偏估计方法,最初的香农方法验证了紫花苜蓿基因型之间的差异与本研究的 AMOVA 分析结果一致。发现个体差异为 59%,而群体差异为 41%。已经有一些关于麦冬属植物的 ITS 研究利用 ITS 作为系统发育标记来估算联系和定义新的分类类别(如部落)。然而,我们的研究还包括对这些序列的二级结构进行分析,研究结果表明,ITS 序列和二级结构数据可用于了解不同紫花苜蓿品种的种内遗传组成。
Exploring secondary structures within the nuclear ribosomal DNA internal transcribed spacers (nr DNA ITS) for enhanced phylogenetic insights in Medicago sativa (alfalfa)
ITS sections, which are situated inside the ribosomal DNA operon, are recognized for their high levels of diversity and slow rate of evolution, which makes them important for plant phylogenetic studies. The objective of this work is to use the internal transcribed spacer (ITS) regions of 18 alfalfa (Medicago sativa) genotypes/varieties to determine their genetic relationships and to verify possible genetic markers for variety identification and classification. This has been done by validating the secondary structures of the ITS regions and observing the effects of the relationships among the lowest energy state, the total number of possible secondary structure hairpins, and (GC) content. The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon’s approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on Medicago sativa that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties.
期刊介绍:
Plant Biotechnology Reports publishes original, peer-reviewed articles dealing with all aspects of fundamental and applied research in the field of plant biotechnology, which includes molecular biology, genetics, biochemistry, cell and tissue culture, production of secondary metabolites, metabolic engineering, genomics, proteomics, and metabolomics. Plant Biotechnology Reports emphasizes studies on plants indigenous to the Asia-Pacific region and studies related to commercialization of plant biotechnology. Plant Biotechnology Reports does not exclude studies on lower plants including algae and cyanobacteria if studies are carried out within the aspects described above.