Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.

The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic tr...

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Autores principales:	Qun Ji, Honglian Zhu, Xinfang Huang, Kai Zhou, Zhengwei Liu, Yalin Sun, Zhixin Wang, Weidong Ke
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/893d4523287347eba75ebc54382ed7b4
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spelling	oai:doaj.org-article:893d4523287347eba75ebc54382ed7b42021-12-02T20:05:12ZUncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.1932-620310.1371/journal.pone.0249825https://doaj.org/article/893d4523287347eba75ebc54382ed7b42021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0249825https://doaj.org/toc/1932-6203The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.Qun JiHonglian ZhuXinfang HuangKai ZhouZhengwei LiuYalin SunZhixin WangWeidong KePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0249825 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qun Ji Honglian Zhu Xinfang Huang Kai Zhou Zhengwei Liu Yalin Sun Zhixin Wang Weidong Ke Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
description	The water dropworts Oenanthe linearis Wall. ex DC. and O. javanica (Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed that Oenanthe linearis was readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering. Oenanthe javanica was classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination between O. linearis and O. javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that the O. linearis accessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that the O. javanica accessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity for O. linearis (π = 0.1902) was slightly lower than that which was estimated for O. javanica (π = 0.2174). There was a low level of genetic differentiation between O. linearis and O. javanica (Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.
format	article
author	Qun Ji Honglian Zhu Xinfang Huang Kai Zhou Zhengwei Liu Yalin Sun Zhixin Wang Weidong Ke
author_facet	Qun Ji Honglian Zhu Xinfang Huang Kai Zhou Zhengwei Liu Yalin Sun Zhixin Wang Weidong Ke
author_sort	Qun Ji
title	Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
title_short	Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
title_full	Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
title_fullStr	Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
title_full_unstemmed	Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.
title_sort	uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and snp markers.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/893d4523287347eba75ebc54382ed7b4
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Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers.

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