Genetic diversity analysis in finger millet through RAPD and ISSR marker

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics Pub Date : 2025-04-16 DOI:10.1016/j.egg.2025.100350

Kirankumar P. Suthar , Diwakar Singh , J.V. Patel , Rehana Niyaria , Komal G. Lakhani , A.K. Pandey

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引用次数: 0

Abstract

Finger millet (Eleusine coracana), also known as “Nutra-cereals” is a self-pollinated crop well versed in unfavorable environmental conditions. Despite its agronomic and nutritional importance, the genetic diversity within available germplasm resources remains underexplored. To bridge this gap, this study assessed genetic diversity among twenty-five finger millet genotypes using random amplified polymorphic deoxyribonucleic acid (RAPD) and inter-simple sequence repeat (ISSR) PCR genotyping methods. Analysis with fourteen RAPD primers produced 182 loci, 77 % of which were polymorphic, with a Polymorphic Information Content (PIC) of 0.29. ISSR analysis utilizing ten primers generated 83 bands with 74 % polymorphism. PopGene analysis revealed higher Nei's genetic diversity for ISSR than for RAPD. The RAPD primers exhibited a higher Shannon's Information Index than ISSR, indicating superior genotype differentiation. RAPD primers OPA-18, OPH-05, OPI-10, and ISSR primers UBC-841, UBC-857, and UBC-863 were determined to be the most effective in identifying genetic diversity in finger millet based on Polymorphic Information Content (PIC), Marker Index (MI), and Effective Multiplex Ratio (EMR) values. The Jaccard's similarity coefficient indicated moderate genetic diversity in finger millet based on combined RAPD and ISSR analysis, as the similarity coefficient values were arranged from 0.59 to 0.87. Combined RAPD and ISSR-based PCA and HCA grouped genotypes based on genetic relationships indicated through geographical origin, revealing the highest diversity between GN-4 and GPU-48 & GPU-28. Analysis of Molecular Variance (AMOVA) indicated that genotypes from different ecological regions explained higher variation, whereas within regions showed less variation. The genetic relationship among genotypes could be explored for breeding and genetic improvement of finger millet. The comprehensive data presented here highlight the potential for utilizing these genotypes in finger millet improvement programs, enhancing productivity and resilience.

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利用RAPD和ISSR标记分析手指粟的遗传多样性

谷子（Eleusine coracana），也被称为“营养谷物”，是一种适应不利环境条件的自花授粉作物。尽管具有重要的农艺和营养意义，但现有种质资源的遗传多样性仍未得到充分开发。为了弥补这一空白，本研究利用随机扩增多态性脱氧核糖核酸（RAPD）和简单序列重复间（ISSR） PCR基因分型方法评估了25种小米基因型的遗传多样性。用14条RAPD引物分析得到182个位点，其中77%为多态性位点，多态性信息含量（PIC）为0.29。利用10条引物进行ISSR分析，得到83条条带，多态性为74%。PopGene分析显示，ISSR组Nei的遗传多样性高于RAPD组。RAPD引物的Shannon’s Information Index高于ISSR引物，表明RAPD引物具有较好的基因型分化能力。RAPD引物OPA-18、opho -05、OPI-10和ISSR引物UBC-841、UBC-857和UBC-863基于多态性信息含量（PIC）、标记指数（MI）和有效多重倍率（EMR）值确定了对指谷遗传多样性鉴定最有效的引物。RAPD和ISSR联合分析的Jaccard相似系数为0.59 ~ 0.87，表明小谷子遗传多样性处于中等水平。基于RAPD和issr的PCA和HCA结合，根据地理来源的遗传关系对基因型进行分组，发现GN-4和GPU-48之间的多样性最高；GPU-28。分子方差分析（AMOVA）表明，不同生态区域的基因型差异较大，而区域内的差异较小。研究不同基因型间的遗传关系，可为谷子的选育和遗传改良提供理论依据。本文提供的综合数据强调了在谷子改良计划中利用这些基因型、提高生产力和恢复力的潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Ecological Genetics and Genomics Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics

CiteScore

1.80

自引率

0.00%

发文量

期刊介绍： Ecological Genetics and Genomics publishes ecological studies of broad interest that provide significant insight into ecological interactions or/ and species diversification. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are shared where appropriate. The journal also provides Reviews, and Perspectives articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context. Topics include: -metagenomics -population genetics/genomics -evolutionary ecology -conservation and molecular adaptation -speciation genetics -environmental and marine genomics -ecological simulation -genomic divergence of organisms