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Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China
Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly rep...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271808/ https://www.ncbi.nlm.nih.gov/pubmed/25532848 http://dx.doi.org/10.3390/molecules191221541 |
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author | Guo, Zhi-Hui Fu, Kai-Xin Zhang, Xin-Quan Bai, Shi-Qie Fan, Yan Peng, Yan Huang, Lin-Kai Yan, Yan-Hong Liu, Wei Ma, Xiao |
author_facet | Guo, Zhi-Hui Fu, Kai-Xin Zhang, Xin-Quan Bai, Shi-Qie Fan, Yan Peng, Yan Huang, Lin-Kai Yan, Yan-Hong Liu, Wei Ma, Xiao |
author_sort | Guo, Zhi-Hui |
collection | PubMed |
description | Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21%) were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC) was 0.358, the Shannon diversity index (H) was 0.534, the marker index (MI) was 4.040, the resolving power (RP) was 6.108, and the genotype index (GI) was 0.782. Genetic similarity coefficients (GS) between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA) based on GS largely confirmed the results of principal coordinate analysis (PCoA). PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel’s test (r = 0.2268, p = 0.9999). In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA) and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species. |
format | Online Article Text |
id | pubmed-6271808 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-62718082018-12-28 Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China Guo, Zhi-Hui Fu, Kai-Xin Zhang, Xin-Quan Bai, Shi-Qie Fan, Yan Peng, Yan Huang, Lin-Kai Yan, Yan-Hong Liu, Wei Ma, Xiao Molecules Article Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21%) were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC) was 0.358, the Shannon diversity index (H) was 0.534, the marker index (MI) was 4.040, the resolving power (RP) was 6.108, and the genotype index (GI) was 0.782. Genetic similarity coefficients (GS) between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA) based on GS largely confirmed the results of principal coordinate analysis (PCoA). PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel’s test (r = 0.2268, p = 0.9999). In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA) and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species. MDPI 2014-12-22 /pmc/articles/PMC6271808/ /pubmed/25532848 http://dx.doi.org/10.3390/molecules191221541 Text en © 2014 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Guo, Zhi-Hui Fu, Kai-Xin Zhang, Xin-Quan Bai, Shi-Qie Fan, Yan Peng, Yan Huang, Lin-Kai Yan, Yan-Hong Liu, Wei Ma, Xiao Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title | Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title_full | Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title_fullStr | Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title_full_unstemmed | Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title_short | Molecular Insights into the Genetic Diversity of Hemarthria compressa Germplasm Collections Native to Southwest China |
title_sort | molecular insights into the genetic diversity of hemarthria compressa germplasm collections native to southwest china |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271808/ https://www.ncbi.nlm.nih.gov/pubmed/25532848 http://dx.doi.org/10.3390/molecules191221541 |
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