Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

Abstract Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total o...

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Autores principales:	Feifei Wu, Shangxiong Zhang, Qiu Gao, Fang Liu, Jianli Wang, Xianguo Wang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Vicia amoena SSR development genetic variation population structure Botany QK1-989
Acceso en línea:	https://doaj.org/article/1b35b44bea35438396cbe587328b1b40
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spelling	oai:doaj.org-article:1b35b44bea35438396cbe587328b1b402021-11-21T12:05:42ZGenetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers10.1186/s12870-021-03330-w1471-2229https://doaj.org/article/1b35b44bea35438396cbe587328b1b402021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03330-whttps://doaj.org/toc/1471-2229Abstract Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.Feifei WuShangxiong ZhangQiu GaoFang LiuJianli WangXianguo WangBMCarticleVicia amoenaSSR developmentgenetic variationpopulation structureBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Vicia amoena SSR development genetic variation population structure Botany QK1-989
spellingShingle	Vicia amoena SSR development genetic variation population structure Botany QK1-989 Feifei Wu Shangxiong Zhang Qiu Gao Fang Liu Jianli Wang Xianguo Wang Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
description	Abstract Vicia amoena is a high-nutritional quality forage similar to alfalfa. However, studies on the genetic background of V. amoena are scarce. In the present study, the genetic variation of 24 V. amoena populations was assessed with newly developed simple sequence repeat (SSR) markers. A total of 8799 SSRs were identified in the V. amoena genomic-enriched sequences, and the most abundant repeat number was four. A total of 569 sampled individuals were assayed to evaluate the genetic diversity of the V. amoena populations based on 21 polymorphic SSR primers. The polymorphism information content (PIC) ranged from 0.896 to 0.968, with an average of 0.931, which indicated that the markers were highly informative. Based on analysis of molecular variance, 88% of the variance occurred within populations, and the remaining 12% of the variance occurred among populations. The high degree of gene flow (Nm= 4.958) also showed slight differentiation among the V. amoena populations. The V. amoena populations were mainly clustered by steppe and mountain habitats based on principal coordinate analysis (PCoA) and STRUCTURE analysis. This indicated that the elevation and special habitat of geographical origins may be important factors affecting the clustered pattern of V. amoena populations. Neighbour-joining (NJ) analysis did not separate the populations well by geographical origin, which indicated that the genetic structure of V. amoena was complex and needs further study. Overall, our results showed that the newly developed SSR markers could benefit the V. amoena research community by providing genetic background information to help establish a foundation for breeding improvement and germplasm resource conservation.
format	article
author	Feifei Wu Shangxiong Zhang Qiu Gao Fang Liu Jianli Wang Xianguo Wang
author_facet	Feifei Wu Shangxiong Zhang Qiu Gao Fang Liu Jianli Wang Xianguo Wang
author_sort	Feifei Wu
title	Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
title_short	Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
title_full	Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
title_fullStr	Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
title_full_unstemmed	Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers
title_sort	genetic diversity and population structure analysis in a large collection of vicia amoena in china with newly developed ssr markers
publisher	BMC
publishDate	2021
url	https://doaj.org/article/1b35b44bea35438396cbe587328b1b40
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Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

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