Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome se...

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Autores principales:	Hanjing Liu, Yuli Zhang, Zhen Wang, Yingjuan Su, Ting Wang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Cephalotaxus oliveri transcriptome EST-SSRs genetic diversity population structure transferability Genetics QH426-470
Acceso en línea:	https://doaj.org/article/8a54e11dde6d4b6cadf8315ca3ac54bc
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spelling	oai:doaj.org-article:8a54e11dde6d4b6cadf8315ca3ac54bc2021-11-17T06:03:58ZDevelopment and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences1664-802110.3389/fgene.2021.759557https://doaj.org/article/8a54e11dde6d4b6cadf8315ca3ac54bc2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.759557/fullhttps://doaj.org/toc/1664-8021Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.Hanjing LiuYuli ZhangZhen WangYingjuan SuYingjuan SuTing WangFrontiers Media S.A.articleCephalotaxus oliveritranscriptomeEST-SSRsgenetic diversitypopulation structuretransferabilityGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Cephalotaxus oliveri transcriptome EST-SSRs genetic diversity population structure transferability Genetics QH426-470
spellingShingle	Cephalotaxus oliveri transcriptome EST-SSRs genetic diversity population structure transferability Genetics QH426-470 Hanjing Liu Yuli Zhang Zhen Wang Yingjuan Su Yingjuan Su Ting Wang Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
description	Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
format	article
author	Hanjing Liu Yuli Zhang Zhen Wang Yingjuan Su Yingjuan Su Ting Wang
author_facet	Hanjing Liu Yuli Zhang Zhen Wang Yingjuan Su Yingjuan Su Ting Wang
author_sort	Hanjing Liu
title	Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
title_short	Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
title_full	Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
title_fullStr	Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
title_full_unstemmed	Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences
title_sort	development and application of est-ssr markers in cephalotaxus oliveri from transcriptome sequences
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/8a54e11dde6d4b6cadf8315ca3ac54bc
work_keys_str_mv	AT hanjingliu developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences AT yulizhang developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences AT zhenwang developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences AT yingjuansu developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences AT yingjuansu developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences AT tingwang developmentandapplicationofestssrmarkersincephalotaxusoliverifromtranscriptomesequences
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Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

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