Start Codon Targeted (SCoT) markers unveiled the genetic diversity of Nelumbo nucifera Gaertn. from Kerala, South India

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-05-18 DOI:10.1016/j.genrep.2025.102262

Divyashri, B. Vishnu, E.A. Siril

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引用次数: 0

Abstract

Start Codon Targeted (SCoT) DNA markers are dominant and commonly used for the evaluation of the genetic diversity of several horticultural crops. Nelumbo nucifera Gaertn. is an important perennial species chiefly valued in horticulture, ornamental, and medicinal uses. In the present study, SCoT markers were used to assess the genetic diversity of N. nucifera accessions from Kerala along with some collections hail from Tamil Nadu, and Andhra Pradesh of India. A total of 94.2 % SCoT alleles were found to be polymorphic amidst 31 accessions. Simultaneously, the polymorphism information content (PIC), heterozygosity, effective multiplex ratio, marker index, discriminating and resolving power values indicated the efficacy of selected primers. Further, midpoint values of diversity indices such as Shannon's information index (0.36), gene diversity (0.23), the effective number of alleles (1.38), and the observed number of alleles (1.94) revealed moderate genetic diversity among the accessions studied. This was also supported by a Dendrogram plotted based on the Unweighted neighbor joining method using Jaccard's similarity coefficient. The arrangement of accessions, regardless of their geographical location, was confirmed by the dendrogram and scatter plot based on the principal coordinate analysis. Relationships established by Andhra Pradesh and Tamil Nadu accessions with the individuals from three political zones of Kerala strengthen the chances of genetic mix-up via migrations. However, conservation strategies have been duly implemented for this species since it faces severe habitat destruction. The study is the first report on the genetic diversity analysis of N. nucifera using highly informative SCoT markers.

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启动密码子靶向（SCoT）标记揭示了莲属植物的遗传多样性。来自印度南部喀拉拉邦

起始密码子靶向（Start Codon targeting, SCoT） DNA标记是一种显性DNA标记，常用来评价几种园艺作物的遗传多样性。荷叶莲。是一种重要的多年生植物，主要用于园艺、观赏和药用。本研究利用SCoT标记对来自印度喀拉拉邦、泰米尔纳德邦和安得拉邦的白芨种质资源的遗传多样性进行了分析。在31份材料中，共发现94.2%的SCoT等位基因多态性。同时，通过多态性信息含量（PIC）、杂合度、有效多重倍率、标记指数、鉴别分辨能力值等指标来反映所选引物的有效性。Shannon’s信息指数（0.36）、基因多样性指数（0.23）、有效等位基因数（1.38）和观察等位基因数（1.94）的多样性指数中点值表明，所研究材料的遗传多样性处于中等水平。基于Jaccard相似系数的非加权邻居连接法绘制的树形图也支持了这一点。基于主坐标分析的树状图和散点图证实了不同地理位置植物的排列。安得拉邦和泰米尔纳德邦的加入与喀拉拉邦三个政治区域的个体建立了关系，通过迁徙增加了基因混淆的可能性。然而，由于该物种面临严重的栖息地破坏，保护策略已得到适当实施。该研究是首次利用高信息量SCoT标记分析核桃树遗传多样性的报道。

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

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.