{"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}
引用次数: 0
Abstract
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.