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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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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. |
format | Online Article Text |
id | pubmed-7731653 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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