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Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica

Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially importan...

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Autores principales: Uchiyama, Kentaro, Iwata, Hiroyoshi, Moriguchi, Yoshinari, Ujino-Ihara, Tokuko, Ueno, Saneyoshi, Taguchi, Yuriko, Tsubomura, Miyoko, Mishima, Kentaro, Iki, Taiichi, Watanabe, Atsushi, Futamura, Norihiro, Shinohara, Kenji, Tsumura, Yoshihiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833940/
https://www.ncbi.nlm.nih.gov/pubmed/24260312
http://dx.doi.org/10.1371/journal.pone.0079866
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author Uchiyama, Kentaro
Iwata, Hiroyoshi
Moriguchi, Yoshinari
Ujino-Ihara, Tokuko
Ueno, Saneyoshi
Taguchi, Yuriko
Tsubomura, Miyoko
Mishima, Kentaro
Iki, Taiichi
Watanabe, Atsushi
Futamura, Norihiro
Shinohara, Kenji
Tsumura, Yoshihiko
author_facet Uchiyama, Kentaro
Iwata, Hiroyoshi
Moriguchi, Yoshinari
Ujino-Ihara, Tokuko
Ueno, Saneyoshi
Taguchi, Yuriko
Tsubomura, Miyoko
Mishima, Kentaro
Iki, Taiichi
Watanabe, Atsushi
Futamura, Norihiro
Shinohara, Kenji
Tsumura, Yoshihiko
author_sort Uchiyama, Kentaro
collection PubMed
description Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica.
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spelling pubmed-38339402013-11-20 Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica Uchiyama, Kentaro Iwata, Hiroyoshi Moriguchi, Yoshinari Ujino-Ihara, Tokuko Ueno, Saneyoshi Taguchi, Yuriko Tsubomura, Miyoko Mishima, Kentaro Iki, Taiichi Watanabe, Atsushi Futamura, Norihiro Shinohara, Kenji Tsumura, Yoshihiko PLoS One Research Article Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica, based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica. Public Library of Science 2013-11-19 /pmc/articles/PMC3833940/ /pubmed/24260312 http://dx.doi.org/10.1371/journal.pone.0079866 Text en © 2013 Uchiyama et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Uchiyama, Kentaro
Iwata, Hiroyoshi
Moriguchi, Yoshinari
Ujino-Ihara, Tokuko
Ueno, Saneyoshi
Taguchi, Yuriko
Tsubomura, Miyoko
Mishima, Kentaro
Iki, Taiichi
Watanabe, Atsushi
Futamura, Norihiro
Shinohara, Kenji
Tsumura, Yoshihiko
Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title_full Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title_fullStr Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title_full_unstemmed Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title_short Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
title_sort demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in cryptomeria japonica
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833940/
https://www.ncbi.nlm.nih.gov/pubmed/24260312
http://dx.doi.org/10.1371/journal.pone.0079866
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