Rajendra K. Meena, Priyanka Kashyap, Ajay Sojitra, Payal Dhyani, Maneesh S. Bhandari, Shailesh Pandey, Santan Barthwal, Harish S. Ginwal
{"title":"Genome-wide SSR marker discovery and population genetic analysis in Rhododendron campanulatum: a Himalayan tree line species","authors":"Rajendra K. Meena, Priyanka Kashyap, Ajay Sojitra, Payal Dhyani, Maneesh S. Bhandari, Shailesh Pandey, Santan Barthwal, Harish S. Ginwal","doi":"10.1007/s00468-025-02651-9","DOIUrl":null,"url":null,"abstract":"<div><h3>Key message</h3><p>GSS is a rapid and cost-effective technique for identifying de novo SSRs in non-model plant species for their genetic analysis.</p><h3>Abstract</h3><p><i>Rhododendron campanulatum</i> is a tree line tree species occurring in the greater Himalayas at an altitude of 3000‒3600 m. The present study aims to generate novel genomic simple sequence repeats (SSRs) markers through a genome survey sequencing approach and investigate population-level genetic processes. A total of 91.18 million reads were generated through the Illumina protocol, and high-quality reads were assembled into 257,413 contigs with 39.60% GC content and contig N50 value 3596 bp. After scanning of genomic assembly, a total of 223,850 perfect SSRs, 10,026 cSSRs, 963,958 iSSRs and 67,332 VNTRs were identified. In perfect SSRs, di-nucleotide repeats were most abundant (43.80%), followed by mono-, tri-, tetra-, penta-, and hexa-nucleotide repeats, respectively. Afterwards, 30,715 primer pairs were designed, and a subset of 50 primers was tested for their amplification through polymerase chain reaction. As a result, 35 SSR loci were successfully amplified and 13 showed polymorphism, which were further utilized to characterize the seven natural populations of <i>R. campanulatum</i> of Uttarakhand Himalayas. Under this study, low genetic diversity (expected heterozygosity, He = 0.28; Allelic richness, Ar = 1.91) was recorded in the analysed populations, which primarily dominated by heterozygotic individuals (F<sub>IS</sub> = −0.268). Further, AMOVA revealed 83% variation within the populations and the remaining 17% between the populations, indicating a great genetic differentiation (F<sub>ST</sub> = 0.173). Due to high genetic divergence, STRUCTURE and cluster analysis revealed two prominent groups. The marker genetic information generated herein is novel and important for understanding the genetic processes and guiding its conservation programme. </p></div>","PeriodicalId":805,"journal":{"name":"Trees","volume":"39 4","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Trees","FirstCategoryId":"2","ListUrlMain":"https://link.springer.com/article/10.1007/s00468-025-02651-9","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"FORESTRY","Score":null,"Total":0}
引用次数: 0
Key message
GSS is a rapid and cost-effective technique for identifying de novo SSRs in non-model plant species for their genetic analysis.
Abstract
Rhododendron campanulatum is a tree line tree species occurring in the greater Himalayas at an altitude of 3000‒3600 m. The present study aims to generate novel genomic simple sequence repeats (SSRs) markers through a genome survey sequencing approach and investigate population-level genetic processes. A total of 91.18 million reads were generated through the Illumina protocol, and high-quality reads were assembled into 257,413 contigs with 39.60% GC content and contig N50 value 3596 bp. After scanning of genomic assembly, a total of 223,850 perfect SSRs, 10,026 cSSRs, 963,958 iSSRs and 67,332 VNTRs were identified. In perfect SSRs, di-nucleotide repeats were most abundant (43.80%), followed by mono-, tri-, tetra-, penta-, and hexa-nucleotide repeats, respectively. Afterwards, 30,715 primer pairs were designed, and a subset of 50 primers was tested for their amplification through polymerase chain reaction. As a result, 35 SSR loci were successfully amplified and 13 showed polymorphism, which were further utilized to characterize the seven natural populations of R. campanulatum of Uttarakhand Himalayas. Under this study, low genetic diversity (expected heterozygosity, He = 0.28; Allelic richness, Ar = 1.91) was recorded in the analysed populations, which primarily dominated by heterozygotic individuals (FIS = −0.268). Further, AMOVA revealed 83% variation within the populations and the remaining 17% between the populations, indicating a great genetic differentiation (FST = 0.173). Due to high genetic divergence, STRUCTURE and cluster analysis revealed two prominent groups. The marker genetic information generated herein is novel and important for understanding the genetic processes and guiding its conservation programme.
期刊介绍：
Trees - Structure and Function publishes original articles on the physiology, biochemistry, functional anatomy, structure and ecology of trees and other woody plants. Also presented are articles concerned with pathology and technological problems, when they contribute to the basic understanding of structure and function of trees. In addition to original articles and short communications, the journal publishes reviews on selected topics concerning the structure and function of trees.
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