{"title":"基于 SNP 标记评估遗传多样性和构建大菱鲆种群核心种质","authors":"Qian Qin, Yanjing Dong, Jiaqi He, Jialong Chen, Danyang Wu, Shouwen Zhang","doi":"10.1016/j.jarmap.2024.100605","DOIUrl":null,"url":null,"abstract":"<div><div><em>Acorus tatarinowii</em> is a natural medicinal plant integral to traditional aromatic therapies. It is commonly employed in the treatment of depression, epilepsy, and Alzheimer's disease due to its significant medicinal and aromatic properties. However, the genetic diversity of wild <em>A. tatarinowii</em> resources has declined due to over-exploitation and habitat destruction. This study aims to assess the genetic diversity of the natural populations of <em>A. tatarinowii</em>, establish a core germplasm bank, explore its genetic richness and uniqueness, prevent genetic erosion, and identify beneficial genes. In this study, for the first time, 429A. tatarinowii samples from 40 populations were analyzed for genetic diversity and population structure using Hyper-Seq technology. A total of 4772,850 high-quality Single Nucleotide Polymorphisms (SNPs) and 1563,000 Insertions and Deletions (InDels) variant loci were identified, with C/T as the predominant variant type and a Ts/Tv ratio of 1.079. Annotation of these loci indicated that the majority of variants occurring in intergenic regions, accounting for 50.59 % of the total. Moreover, the heterozygosity, nucleotide diversity, and FST of <em>A. tatarinowii</em> suggested low genetic diversity within this species within the populations. The analysis of molecular variance (AMOVA) revealed that the population variation of <em>A. tatarinowii</em> is mainly caused by the variation between populations (72.06 %), while the variation within populations only contributes a small part (27.94 %) Through NJ tree, PCA, and ADMIXTURE analyses, the 429<em>A. tatarinowii</em> samples were classified into five subgroups, with some genetic exchange observed. A total of 7163 high-quality polymorphic SNPs were identified, and a core germplasm consisting of 85 samples was established, achieving genotype retention rates similar to those of the original germplasm. This indicates that a smaller number of germplasm resources can effectively represent the majority of the genetic diversity. Additionally, PCA analysis further confirmed the representativeness and validity of the constructed core germplasm resources. Furthermore, the DNA fingerprints of the 429 accessions were established using the most effective combinations of 26 SNP markers, which served as specific markers to effectively distinguish all samples. In conclusion, these findings offer valuable insights into the genetic structure of <em>A. tatarinowii</em>, facilitating the identification of high-quality genes and providing a scientific foundation for the development of breeding programs and conservation strategies for <em>A. tatarinowii</em>.</div></div>","PeriodicalId":15136,"journal":{"name":"Journal of Applied Research on Medicinal and Aromatic Plants","volume":"44 ","pages":"Article 100605"},"PeriodicalIF":3.8000,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Assessment of genetic diversity and construction of core germplasm in populations of Acorus tatarinowii based on SNP markers\",\"authors\":\"Qian Qin, Yanjing Dong, Jiaqi He, Jialong Chen, Danyang Wu, Shouwen Zhang\",\"doi\":\"10.1016/j.jarmap.2024.100605\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div><em>Acorus tatarinowii</em> is a natural medicinal plant integral to traditional aromatic therapies. It is commonly employed in the treatment of depression, epilepsy, and Alzheimer's disease due to its significant medicinal and aromatic properties. However, the genetic diversity of wild <em>A. tatarinowii</em> resources has declined due to over-exploitation and habitat destruction. This study aims to assess the genetic diversity of the natural populations of <em>A. tatarinowii</em>, establish a core germplasm bank, explore its genetic richness and uniqueness, prevent genetic erosion, and identify beneficial genes. In this study, for the first time, 429A. tatarinowii samples from 40 populations were analyzed for genetic diversity and population structure using Hyper-Seq technology. A total of 4772,850 high-quality Single Nucleotide Polymorphisms (SNPs) and 1563,000 Insertions and Deletions (InDels) variant loci were identified, with C/T as the predominant variant type and a Ts/Tv ratio of 1.079. Annotation of these loci indicated that the majority of variants occurring in intergenic regions, accounting for 50.59 % of the total. Moreover, the heterozygosity, nucleotide diversity, and FST of <em>A. tatarinowii</em> suggested low genetic diversity within this species within the populations. The analysis of molecular variance (AMOVA) revealed that the population variation of <em>A. tatarinowii</em> is mainly caused by the variation between populations (72.06 %), while the variation within populations only contributes a small part (27.94 %) Through NJ tree, PCA, and ADMIXTURE analyses, the 429<em>A. tatarinowii</em> samples were classified into five subgroups, with some genetic exchange observed. A total of 7163 high-quality polymorphic SNPs were identified, and a core germplasm consisting of 85 samples was established, achieving genotype retention rates similar to those of the original germplasm. This indicates that a smaller number of germplasm resources can effectively represent the majority of the genetic diversity. Additionally, PCA analysis further confirmed the representativeness and validity of the constructed core germplasm resources. Furthermore, the DNA fingerprints of the 429 accessions were established using the most effective combinations of 26 SNP markers, which served as specific markers to effectively distinguish all samples. In conclusion, these findings offer valuable insights into the genetic structure of <em>A. tatarinowii</em>, facilitating the identification of high-quality genes and providing a scientific foundation for the development of breeding programs and conservation strategies for <em>A. tatarinowii</em>.</div></div>\",\"PeriodicalId\":15136,\"journal\":{\"name\":\"Journal of Applied Research on Medicinal and Aromatic Plants\",\"volume\":\"44 \",\"pages\":\"Article 100605\"},\"PeriodicalIF\":3.8000,\"publicationDate\":\"2024-11-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Applied Research on Medicinal and Aromatic Plants\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2214786124000780\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Applied Research on Medicinal and Aromatic Plants","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2214786124000780","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
摘要
唐菖蒲是传统芳香疗法中不可或缺的天然药用植物。由于其显著的药用和芳香特性,它通常被用于治疗抑郁症、癫痫和老年痴呆症。然而,由于过度开发和栖息地破坏,野生 A. tatarinowii 资源的遗传多样性已经下降。本研究旨在评估 A. tatarinowii 自然种群的遗传多样性,建立核心种质库,探索其遗传丰富性和独特性,防止遗传侵蚀,并鉴定有益基因。本研究首次利用 Hyper-Seq 技术分析了来自 40 个种群的 429 个 A. tatarinowii 样本的遗传多样性和种群结构。共鉴定出 4772850 个高质量单核苷酸多态性(SNPs)和 1563000 个插入和缺失(InDels)变异位点,其中 C/T 为主要变异类型,Ts/Tv 比为 1.079。对这些位点的注释表明,大多数变异发生在基因间区域,占总数的 50.59%。此外,A. tatarinowii 的杂合度、核苷酸多样性和 FST 表明该物种在种群内的遗传多样性较低。分子方差分析(AMOVA)显示,A. tatarinowii的种群变异主要由种群间的变异引起(72.06%),而种群内的变异只占一小部分(27.94%)。通过NJ树、PCA和ADMIXTURE分析,429个A. tatarinowii样本被分为5个亚群,并观察到一些遗传交换。共鉴定出 7163 个高质量多态 SNPs,并建立了由 85 个样本组成的核心种质,其基因型保留率与原始种质相似。这表明,数量较少的种质资源也能有效代表大部分遗传多样性。此外,PCA 分析进一步证实了所构建的核心种质资源的代表性和有效性。此外,利用 26 个 SNP 标记的最有效组合,建立了 429 个样本的 DNA 指纹,这些标记作为特异性标记可有效区分所有样本。总之,这些研究结果为了解 A. tatarinowii 的遗传结构提供了宝贵的信息,有助于鉴定优质基因,并为制定 A. tatarinowii 的育种计划和保护策略提供了科学依据。
Assessment of genetic diversity and construction of core germplasm in populations of Acorus tatarinowii based on SNP markers
Acorus tatarinowii is a natural medicinal plant integral to traditional aromatic therapies. It is commonly employed in the treatment of depression, epilepsy, and Alzheimer's disease due to its significant medicinal and aromatic properties. However, the genetic diversity of wild A. tatarinowii resources has declined due to over-exploitation and habitat destruction. This study aims to assess the genetic diversity of the natural populations of A. tatarinowii, establish a core germplasm bank, explore its genetic richness and uniqueness, prevent genetic erosion, and identify beneficial genes. In this study, for the first time, 429A. tatarinowii samples from 40 populations were analyzed for genetic diversity and population structure using Hyper-Seq technology. A total of 4772,850 high-quality Single Nucleotide Polymorphisms (SNPs) and 1563,000 Insertions and Deletions (InDels) variant loci were identified, with C/T as the predominant variant type and a Ts/Tv ratio of 1.079. Annotation of these loci indicated that the majority of variants occurring in intergenic regions, accounting for 50.59 % of the total. Moreover, the heterozygosity, nucleotide diversity, and FST of A. tatarinowii suggested low genetic diversity within this species within the populations. The analysis of molecular variance (AMOVA) revealed that the population variation of A. tatarinowii is mainly caused by the variation between populations (72.06 %), while the variation within populations only contributes a small part (27.94 %) Through NJ tree, PCA, and ADMIXTURE analyses, the 429A. tatarinowii samples were classified into five subgroups, with some genetic exchange observed. A total of 7163 high-quality polymorphic SNPs were identified, and a core germplasm consisting of 85 samples was established, achieving genotype retention rates similar to those of the original germplasm. This indicates that a smaller number of germplasm resources can effectively represent the majority of the genetic diversity. Additionally, PCA analysis further confirmed the representativeness and validity of the constructed core germplasm resources. Furthermore, the DNA fingerprints of the 429 accessions were established using the most effective combinations of 26 SNP markers, which served as specific markers to effectively distinguish all samples. In conclusion, these findings offer valuable insights into the genetic structure of A. tatarinowii, facilitating the identification of high-quality genes and providing a scientific foundation for the development of breeding programs and conservation strategies for A. tatarinowii.
期刊介绍:
JARMAP is a peer reviewed and multidisciplinary communication platform, covering all aspects of the raw material supply chain of medicinal and aromatic plants. JARMAP aims to improve production of tailor made commodities by addressing the various requirements of manufacturers of herbal medicines, herbal teas, seasoning herbs, food and feed supplements and cosmetics. JARMAP covers research on genetic resources, breeding, wild-collection, domestication, propagation, cultivation, phytopathology and plant protection, mechanization, conservation, processing, quality assurance, analytics and economics. JARMAP publishes reviews, original research articles and short communications related to research.