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Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study

Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the...

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Autores principales: Minamikawa, Mai F., Kunihisa, Miyuki, Noshita, Koji, Moriya, Shigeki, Abe, Kazuyuki, Hayashi, Takeshi, Katayose, Yuichi, Matsumoto, Toshimi, Nishitani, Chikako, Terakami, Shingo, Yamamoto, Toshiya, Iwata, Hiroyoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917097/
https://www.ncbi.nlm.nih.gov/pubmed/33642580
http://dx.doi.org/10.1038/s41438-021-00485-3
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author Minamikawa, Mai F.
Kunihisa, Miyuki
Noshita, Koji
Moriya, Shigeki
Abe, Kazuyuki
Hayashi, Takeshi
Katayose, Yuichi
Matsumoto, Toshimi
Nishitani, Chikako
Terakami, Shingo
Yamamoto, Toshiya
Iwata, Hiroyoshi
author_facet Minamikawa, Mai F.
Kunihisa, Miyuki
Noshita, Koji
Moriya, Shigeki
Abe, Kazuyuki
Hayashi, Takeshi
Katayose, Yuichi
Matsumoto, Toshimi
Nishitani, Chikako
Terakami, Shingo
Yamamoto, Toshiya
Iwata, Hiroyoshi
author_sort Minamikawa, Mai F.
collection PubMed
description Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F(1) individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.
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spelling pubmed-79170972021-03-04 Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study Minamikawa, Mai F. Kunihisa, Miyuki Noshita, Koji Moriya, Shigeki Abe, Kazuyuki Hayashi, Takeshi Katayose, Yuichi Matsumoto, Toshimi Nishitani, Chikako Terakami, Shingo Yamamoto, Toshiya Iwata, Hiroyoshi Hortic Res Article Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F(1) individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties. Nature Publishing Group UK 2021-03-01 /pmc/articles/PMC7917097/ /pubmed/33642580 http://dx.doi.org/10.1038/s41438-021-00485-3 Text en © The Author(s) 2021 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/.
spellingShingle Article
Minamikawa, Mai F.
Kunihisa, Miyuki
Noshita, Koji
Moriya, Shigeki
Abe, Kazuyuki
Hayashi, Takeshi
Katayose, Yuichi
Matsumoto, Toshimi
Nishitani, Chikako
Terakami, Shingo
Yamamoto, Toshiya
Iwata, Hiroyoshi
Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title_full Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title_fullStr Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title_full_unstemmed Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title_short Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study
title_sort tracing founder haplotypes of japanese apple varieties: application in genomic prediction and genome-wide association study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917097/
https://www.ncbi.nlm.nih.gov/pubmed/33642580
http://dx.doi.org/10.1038/s41438-021-00485-3
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