Genome-wide identification of SSR markers for Curcuma alismatifolia Gagnep., and their potential for wider application in this genus

IF 3.8 2区 农林科学 Q1 PLANT SCIENCES Journal of Applied Research on Medicinal and Aromatic Plants Pub Date : 2024-08-10 DOI:10.1016/j.jarmap.2024.100572
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Abstract

The genus Curcuma, containing over 120 species, have considerable ornamental, edible and medicinal value. Due to the persistent lack of efficient genomic SSR markers, the conservation and identification of Curcuma genetic resources have faced substantial challenges in practical applications. To date, there are few systematic researches on whole-genome mining of SSR locus in the genus Curcuma. Herein, we performed the first deep identification of genome-wide SSR markers based on the whole-genome data of C. alismatifolia. A total of 257,032 SSR loci were identified with an average density of 216.1–367.3 SSRs/Mb within each chromosome. Mononucleotide repeat loci were most abundant, accounting for 55.1 % of all SSRs, with dinucleotide and trinucleotide repeats accounting for 22.6 % and 20.3 %, respectively. Moreover, 38 polymorphic genomic SSRs (g-SSR) were screened from the synthesized 280 primer pairs, with an average allele number (Na) and polymorphic information content (PIC) of 15.342 and 0.775 per locus, respectively. These markers had excellent cross-species transferability with an overall efficiency of 97.5 % in 21 Curcuma species. According to the cluster and structure analyses, the 178 Curcuma accessions were devided into three major clades correspongding to their origins, hybrid affinities and use values. Finally, a total of 66 Curcuma core collections were preserved, with no significant difference in genetic diversity between the core and entire collections by the t-test. A combination of numbers and letters was employed to establish DNA barcodes for 66 core collections. This study provides valuable molecular markers for wild-collection and conservation, genetic diversity analysis and marker-assisted selection breeding of Curcuma.

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莪术 SSR 标记的全基因组鉴定及其在该属植物中的广泛应用潜力
莪术属包含 120 多个物种,具有相当高的观赏、食用和药用价值。由于长期缺乏高效的基因组 SSR 标记,莪术遗传资源的保护和鉴定在实际应用中面临巨大挑战。迄今为止,关于莪术属 SSR 位点全基因组挖掘的系统研究还很少。在此,我们首次基于 C. alismatifolia 的全基因组数据对全基因组 SSR 标记进行了深度鉴定。共鉴定出 257,032 个 SSR 位点,每个染色体内 SSR 的平均密度为 216.1-367.3 SSRs/Mb。单核苷酸重复位点最多,占所有 SSR 的 55.1%,二核苷酸和三核苷酸重复位点分别占 22.6% 和 20.3%。此外,从合成的 280 对引物中筛选出 38 个多态基因组 SSR(g-SSR),每个位点的平均等位基因数(Na)和多态信息含量(PIC)分别为 15.342 和 0.775。这些标记具有良好的跨物种转移性,在 21 个莪术物种中的总体效率为 97.5%。根据聚类和结构分析,178 个莪术品种被划分为三个主要支系,分别对应于它们的起源、杂交亲缘关系和使用价值。最后,共保留了 66 个莪术核心品系,经 t 检验,核心品系与整个品系的遗传多样性无显著差异。通过数字和字母的组合,为 66 个核心藏品建立了 DNA 条形码。这项研究为莪术的野生采集与保护、遗传多样性分析和标记辅助选育提供了宝贵的分子标记。
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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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