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Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing...

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Autores principales: Wang, Zhixin, Sun, Yalin, Huang, Xinfang, Li, Feng, Liu, Yuping, Zhu, Honglian, Liu, Zhengwei, Ke, Weidong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731653/
https://www.ncbi.nlm.nih.gov/pubmed/33354429
http://dx.doi.org/10.7717/peerj.10485
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author Wang, Zhixin
Sun, Yalin
Huang, Xinfang
Li, Feng
Liu, Yuping
Zhu, Honglian
Liu, Zhengwei
Ke, Weidong
author_facet Wang, Zhixin
Sun, Yalin
Huang, Xinfang
Li, Feng
Liu, Yuping
Zhu, Honglian
Liu, Zhengwei
Ke, Weidong
author_sort Wang, Zhixin
collection PubMed
description Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
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spelling pubmed-77316532020-12-21 Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers Wang, Zhixin Sun, Yalin Huang, Xinfang Li, Feng Liu, Yuping Zhu, Honglian Liu, Zhengwei Ke, Weidong PeerJ Biodiversity Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro. PeerJ Inc. 2020-12-08 /pmc/articles/PMC7731653/ /pubmed/33354429 http://dx.doi.org/10.7717/peerj.10485 Text en ©2020 Wang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biodiversity
Wang, Zhixin
Sun, Yalin
Huang, Xinfang
Li, Feng
Liu, Yuping
Zhu, Honglian
Liu, Zhengwei
Ke, Weidong
Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title_full Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title_fullStr Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title_full_unstemmed Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title_short Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
title_sort genetic diversity and population structure of eddoe taro in china using genome-wide snp markers
topic Biodiversity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731653/
https://www.ncbi.nlm.nih.gov/pubmed/33354429
http://dx.doi.org/10.7717/peerj.10485
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