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Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures

Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide assoc...

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Autores principales: Yang, Wu, Chen, Luo, Zhao, Junliang, Wang, Jian, Li, Wenhui, Yang, Tifeng, Dong, Jingfang, Ma, Yamei, Zhou, Lian, Chen, Jiansong, Wu, Wei, Zhang, Shaohong, Liu, Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8959774/
https://www.ncbi.nlm.nih.gov/pubmed/35356125
http://dx.doi.org/10.3389/fpls.2022.841191
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author Yang, Wu
Chen, Luo
Zhao, Junliang
Wang, Jian
Li, Wenhui
Yang, Tifeng
Dong, Jingfang
Ma, Yamei
Zhou, Lian
Chen, Jiansong
Wu, Wei
Zhang, Shaohong
Liu, Bin
author_facet Yang, Wu
Chen, Luo
Zhao, Junliang
Wang, Jian
Li, Wenhui
Yang, Tifeng
Dong, Jingfang
Ma, Yamei
Zhou, Lian
Chen, Jiansong
Wu, Wei
Zhang, Shaohong
Liu, Bin
author_sort Yang, Wu
collection PubMed
description Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.
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spelling pubmed-89597742022-03-29 Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures Yang, Wu Chen, Luo Zhao, Junliang Wang, Jian Li, Wenhui Yang, Tifeng Dong, Jingfang Ma, Yamei Zhou, Lian Chen, Jiansong Wu, Wei Zhang, Shaohong Liu, Bin Front Plant Sci Plant Science Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding. Frontiers Media S.A. 2022-03-09 /pmc/articles/PMC8959774/ /pubmed/35356125 http://dx.doi.org/10.3389/fpls.2022.841191 Text en Copyright © 2022 Yang, Chen, Zhao, Wang, Li, Yang, Dong, Ma, Zhou, Chen, Wu, Zhang and Liu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Yang, Wu
Chen, Luo
Zhao, Junliang
Wang, Jian
Li, Wenhui
Yang, Tifeng
Dong, Jingfang
Ma, Yamei
Zhou, Lian
Chen, Jiansong
Wu, Wei
Zhang, Shaohong
Liu, Bin
Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title_full Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title_fullStr Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title_full_unstemmed Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title_short Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
title_sort genome-wide association study of pericarp color in rice using different germplasm and phenotyping methods reveals different genetic architectures
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8959774/
https://www.ncbi.nlm.nih.gov/pubmed/35356125
http://dx.doi.org/10.3389/fpls.2022.841191
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