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Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand

Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) minin...

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Autores principales: Riangwong, Kanamon, Wanchana, Samart, Aesomnuk, Wanchana, Saensuk, Chatree, Nubankoh, Phakchana, Ruanjaichon, Vinitchan, Kraithong, Tippaya, Toojinda, Theerayut, Vanavichit, Apichart, Arikit, Siwaret
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527488/
https://www.ncbi.nlm.nih.gov/pubmed/33082963
http://dx.doi.org/10.1038/s41438-020-00374-1
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author Riangwong, Kanamon
Wanchana, Samart
Aesomnuk, Wanchana
Saensuk, Chatree
Nubankoh, Phakchana
Ruanjaichon, Vinitchan
Kraithong, Tippaya
Toojinda, Theerayut
Vanavichit, Apichart
Arikit, Siwaret
author_facet Riangwong, Kanamon
Wanchana, Samart
Aesomnuk, Wanchana
Saensuk, Chatree
Nubankoh, Phakchana
Ruanjaichon, Vinitchan
Kraithong, Tippaya
Toojinda, Theerayut
Vanavichit, Apichart
Arikit, Siwaret
author_sort Riangwong, Kanamon
collection PubMed
description Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome.
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spelling pubmed-75274882020-10-19 Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand Riangwong, Kanamon Wanchana, Samart Aesomnuk, Wanchana Saensuk, Chatree Nubankoh, Phakchana Ruanjaichon, Vinitchan Kraithong, Tippaya Toojinda, Theerayut Vanavichit, Apichart Arikit, Siwaret Hortic Res Article Coconut (Cocos nucifera L.) is an important economic crop in tropical countries. However, the lack of a complete reference genome and the limitations of usable DNA markers hinder genomic studies and the molecular breeding of coconut. Here, we present the results of simple sequence repeat (SSR) mining from a high-throughput genotyping-by-sequencing (GBS) study of a collection of 38 coconut accessions. A total of 22,748 SSRs with di-, tri-, tetra-, penta- and hexanucleotide repeats of five or more were identified, 2451 of which were defined as polymorphic loci based on locus clustering in 38 coconut accessions, and 315 loci were suitable for the development of SSR markers. One hundred loci were selected, and primer pairs for each SSR locus were designed and validated in 40 coconut accessions. The analysis of 74 polymorphic markers identified between 2 and 9 alleles per locus, with an average of 3.01 alleles. The assessment of the genetic diversity and genetic relationships among the 40 coconut varieties based on the analysis of population structure, principal coordinate analysis (PCoA), and phylogenetic tree analysis using the 74 polymorphic SSR markers revealed three main groups of coconuts in Thailand. The identified SSR loci and SSR markers developed in this study will be useful for the study of coconut diversity and molecular breeding. The SSR mining approach used in this study could be applied to other plant species with a complex genome regardless of the availability of reference genome. Nature Publishing Group UK 2020-10-01 /pmc/articles/PMC7527488/ /pubmed/33082963 http://dx.doi.org/10.1038/s41438-020-00374-1 Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Riangwong, Kanamon
Wanchana, Samart
Aesomnuk, Wanchana
Saensuk, Chatree
Nubankoh, Phakchana
Ruanjaichon, Vinitchan
Kraithong, Tippaya
Toojinda, Theerayut
Vanavichit, Apichart
Arikit, Siwaret
Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title_full Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title_fullStr Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title_full_unstemmed Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title_short Mining and validation of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for the estimation of the genetic diversity and population structure of coconuts (Cocos nucifera L.) in Thailand
title_sort mining and validation of novel genotyping-by-sequencing (gbs)-based simple sequence repeats (ssrs) and their application for the estimation of the genetic diversity and population structure of coconuts (cocos nucifera l.) in thailand
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7527488/
https://www.ncbi.nlm.nih.gov/pubmed/33082963
http://dx.doi.org/10.1038/s41438-020-00374-1
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