Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Cinnamomum camphora (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of C. camphora trees have...

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Autores principales:	Xue Gong, Aihong Yang, Zhaoxiang Wu, Caihui Chen, Huihu Li, Qiaoli Liu, Faxin Yu, Yongda Zhong
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	<i>Cinnamomum camphora</i> genotyping by sequencing (GBS) genetic diversity population structure single nucleotide polymorphism (SNP) Plant ecology QK900-989
Acceso en línea:	https://doaj.org/article/5db2aa5bd74d45dd98d255f50b24bffc
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spelling	oai:doaj.org-article:5db2aa5bd74d45dd98d255f50b24bffc2021-11-25T17:38:07ZEmploying Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing10.3390/f121115111999-4907https://doaj.org/article/5db2aa5bd74d45dd98d255f50b24bffc2021-11-01T00:00:00Zhttps://www.mdpi.com/1999-4907/12/11/1511https://doaj.org/toc/1999-4907<i>Cinnamomum camphora</i> (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of <i>C. camphora</i> trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 <i>C. camphora</i> trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the <i>C. camphora</i> populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise <i>F</i><sub>ST</sub> was 0.099, and gene flow <i>N</i>m was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 <i>C. camphora</i> populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of <i>C. camphora</i> in East Asia and provides genetic tools for developing strategies of <i>C. camphora</i> germplasm utilization.Xue GongAihong YangZhaoxiang WuCaihui ChenHuihu LiQiaoli LiuFaxin YuYongda ZhongMDPI AGarticle<i>Cinnamomum camphora</i>genotyping by sequencing (GBS)genetic diversitypopulation structuresingle nucleotide polymorphism (SNP)Plant ecologyQK900-989ENForests, Vol 12, Iss 1511, p 1511 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	<i>Cinnamomum camphora</i> genotyping by sequencing (GBS) genetic diversity population structure single nucleotide polymorphism (SNP) Plant ecology QK900-989
spellingShingle	<i>Cinnamomum camphora</i> genotyping by sequencing (GBS) genetic diversity population structure single nucleotide polymorphism (SNP) Plant ecology QK900-989 Xue Gong Aihong Yang Zhaoxiang Wu Caihui Chen Huihu Li Qiaoli Liu Faxin Yu Yongda Zhong Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
description	<i>Cinnamomum camphora</i> (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of <i>C. camphora</i> trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 <i>C. camphora</i> trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the <i>C. camphora</i> populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise <i>F</i><sub>ST</sub> was 0.099, and gene flow <i>N</i>m was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 <i>C. camphora</i> populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of <i>C. camphora</i> in East Asia and provides genetic tools for developing strategies of <i>C. camphora</i> germplasm utilization.
format	article
author	Xue Gong Aihong Yang Zhaoxiang Wu Caihui Chen Huihu Li Qiaoli Liu Faxin Yu Yongda Zhong
author_facet	Xue Gong Aihong Yang Zhaoxiang Wu Caihui Chen Huihu Li Qiaoli Liu Faxin Yu Yongda Zhong
author_sort	Xue Gong
title	Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
title_short	Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
title_full	Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
title_fullStr	Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
title_full_unstemmed	Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing
title_sort	employing genome-wide snp discovery to characterize the genetic diversity in <i>cinnamomum camphora</i> using genotyping by sequencing
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5db2aa5bd74d45dd98d255f50b24bffc
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Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in <i>Cinnamomum camphora</i> Using Genotyping by Sequencing

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