利用多样性阵列的单核苷酸多态性分析非洲南部青蒿的多样性

IF 3.8 2区 农林科学 Q1 PLANT SCIENCES
Moosa Mahmood Sedibe , Matumelo A. Rafiri , Goitsemang Mahlomola Hendry Dikane , Matthew Chilaka Achilonu , S’busiso Mfan’vele Nkosi , Xolile Veronica Ngubane , Rian Pierneef
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引用次数: 0

摘要

非洲蒿是一种芳香灌木,在非洲南部用作草药治疗各种疾病,包括咳嗽、感冒、流感,最重要的是用于预防和治疗恶性疟原虫感染。现代高通量测序基因分型结合了下一代测序和多样性阵列技术(DArTseq)复杂性降低方法,可以在没有任何先前可能妨碍多样性分析的生物遗传信息的情况下生成高质量的全基因组图谱。本研究探讨了将dartseq衍生的单核苷酸多态性(snp)和生物活性化合物纳入地理信息系统,以预测非洲南部地区afra基因多样性空间分布的可行性。对在莱索托的Roma和Mohale’s Hoek以及南非的Wepener和Hobhouse收集的总共80个基因型进行DNA提取、测序和SNP调用矿物分析(使用R Studio)。带算术平均值的非加权对群法(UPGMA)和邻联树形图揭示了基因型间的3个变异簇;然而,地理分布对非洲古猿的遗传多样性没有影响。基因型间平均杂合度为7.7%。在Roma和Mohale’s Hoek收集的基因型显示出高水平的遗传多样性。非洲南方古猿的遗传多样性相对较低,表明每个地方的亚种具有一致性。基因型间的多样性表明,afra单核苷酸多态性可能与地理位置无关。鉴于遗传多样性可以提高作物的生产性能,我们的研究结果可以用于种质资源管理、生产非洲侧翼草副产品的工业和植物育种计划。为了南非药用植物的长期保护,需要大量的采样和区域数据。除了评估植物化学物质的定性和定量评估外,还需要评估从研究地点收集的标本的叶面矿物组成以及农艺和形态特征。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Diversity analysis of southern African Artemisia afra using a single nucleotide polymorphism derived from diversity arrays

Artemisia afra is an aromatic shrub used as a herbal remedy in southern Africa for various disorders, including coughs, colds, influenza, and, most notably, for the prophylaxis and treatment of Plasmodium falciparum infections. Modern high-throughput genotyping by sequencing, which combines next generation sequencing and diversity array technology (DArTseq) complexity reduction methods, allows for the generation of high-quality whole-genome profiles without any previous organismal genetic information that may hamper the diversity analyses. This study investigated the feasibility of incorporating DArTseq-derived single-nucleotide polymorphisms (SNPs) and bioactive compounds into a geographic information system to predict the spatial distribution of A. afra gene diversity in selected southern African environs. DNA extraction, sequencing, and SNP calling mineral analyses (using R Studio) were performed on a total of 80 genotypes collected around Roma and Mohale’s Hoek, Lesotho, and Wepener and Hobhouse, South Africa. The unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining dendrograms revealed three clusters of variation among genotypes; however, geographic distribution did not influence A. afra genetic diversity. The mean heterozygosity among genotypes was 7.7%. Genotypes collected in Roma and Mohale’s Hoek exhibited high levels of genetic diversity. Local A. afra genetic diversity was relatively low, indicating uniformity of subspecies per locality. The diversity among genotypes indicated that A. afra SNPs may occur despite the location. Given that genetic diversity enhances crop performance, our findings can be useful in germplasm management, industries producing by-products of A. afra, and plant breeding programs. For the long-term conservation of medicinal plants in South Africa, significant sampling and regional data are required. In addition to evaluating qualitative and quantitative assessments of phytochemicals, it is necessary to evaluate foliar mineral composition, as well as the agronomic and morphological characteristics of collected specimens from studied locations.

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来源期刊
Journal of Applied Research on Medicinal and Aromatic Plants
Journal of Applied Research on Medicinal and Aromatic Plants Pharmacology, Toxicology and Pharmaceutics-Drug Discovery
CiteScore
6.40
自引率
7.70%
发文量
80
审稿时长
41 days
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.
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