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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2014
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.
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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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