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An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers

Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from eac...

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Autores principales: Wang, Rang Jian, Gao, Xiang Feng, Kong, Xiang Rui, Yang, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958088/
https://www.ncbi.nlm.nih.gov/pubmed/27504250
http://dx.doi.org/10.1186/s40064-016-2835-8
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author Wang, Rang Jian
Gao, Xiang Feng
Kong, Xiang Rui
Yang, Jun
author_facet Wang, Rang Jian
Gao, Xiang Feng
Kong, Xiang Rui
Yang, Jun
author_sort Wang, Rang Jian
collection PubMed
description Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait ‘cultivar processing-property’. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(−5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.
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spelling pubmed-49580882016-08-08 An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers Wang, Rang Jian Gao, Xiang Feng Kong, Xiang Rui Yang, Jun Springerplus Research Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait ‘cultivar processing-property’. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(−5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property. Springer International Publishing 2016-07-22 /pmc/articles/PMC4958088/ /pubmed/27504250 http://dx.doi.org/10.1186/s40064-016-2835-8 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Research
Wang, Rang Jian
Gao, Xiang Feng
Kong, Xiang Rui
Yang, Jun
An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title_full An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title_fullStr An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title_full_unstemmed An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title_short An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers
title_sort efficient identification strategy of clonal tea cultivars using long-core motif ssr markers
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958088/
https://www.ncbi.nlm.nih.gov/pubmed/27504250
http://dx.doi.org/10.1186/s40064-016-2835-8
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