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Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association
Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9960595/ https://www.ncbi.nlm.nih.gov/pubmed/36840275 http://dx.doi.org/10.3390/plants12040927 |
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author | Wang, Wenjun Qiu, Xianjin Wang, Ziqi Xie, Tianyi Sun, Wenqiang Xu, Jianlong Zhang, Fan Yu, Sibin |
author_facet | Wang, Wenjun Qiu, Xianjin Wang, Ziqi Xie, Tianyi Sun, Wenqiang Xu, Jianlong Zhang, Fan Yu, Sibin |
author_sort | Wang, Wenjun |
collection | PubMed |
description | Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color attributes of whole grain or brown rice are usually undesirable and need to be improved. To decipher the genetic basis of color variation in the whole grain rice, we conducted a genome-wide association analysis of three parameters of grain colors (brightness, redness, and yellowness) in a panel of 682 rice accessions. Twenty-six loci were identified for the color parameters, implying that grain color is under polygenic control. Among them, some major-effect loci were co-localized with the previously identified genes such as Rc and Rd. To eliminate the possible mask of Rc on other loci influencing grain color, we performed the association analysis in a subset of the panel that excluded the pigmented (red and black) rice. Eighteen loci or SNPs were detected to be associated with grain color in the subpopulation, many of which were not reported before. Two significant peak SNP regions on chromosomes 1 and 9 were validated using near-isogenic lines. Based on differential expression analysis of annotated genes within the SNP regions and metabolic analysis of pooled extreme samples, we found at least three annotated genes as potential candidates involved in the flavonoid metabolic pathway related to pericarp color. These results provide insights into the genetic basis of rice grain color and facilitate genomic breeding to improve appearance and commercial quality of whole grain rice. |
format | Online Article Text |
id | pubmed-9960595 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-99605952023-02-26 Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association Wang, Wenjun Qiu, Xianjin Wang, Ziqi Xie, Tianyi Sun, Wenqiang Xu, Jianlong Zhang, Fan Yu, Sibin Plants (Basel) Article Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color attributes of whole grain or brown rice are usually undesirable and need to be improved. To decipher the genetic basis of color variation in the whole grain rice, we conducted a genome-wide association analysis of three parameters of grain colors (brightness, redness, and yellowness) in a panel of 682 rice accessions. Twenty-six loci were identified for the color parameters, implying that grain color is under polygenic control. Among them, some major-effect loci were co-localized with the previously identified genes such as Rc and Rd. To eliminate the possible mask of Rc on other loci influencing grain color, we performed the association analysis in a subset of the panel that excluded the pigmented (red and black) rice. Eighteen loci or SNPs were detected to be associated with grain color in the subpopulation, many of which were not reported before. Two significant peak SNP regions on chromosomes 1 and 9 were validated using near-isogenic lines. Based on differential expression analysis of annotated genes within the SNP regions and metabolic analysis of pooled extreme samples, we found at least three annotated genes as potential candidates involved in the flavonoid metabolic pathway related to pericarp color. These results provide insights into the genetic basis of rice grain color and facilitate genomic breeding to improve appearance and commercial quality of whole grain rice. MDPI 2023-02-17 /pmc/articles/PMC9960595/ /pubmed/36840275 http://dx.doi.org/10.3390/plants12040927 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wang, Wenjun Qiu, Xianjin Wang, Ziqi Xie, Tianyi Sun, Wenqiang Xu, Jianlong Zhang, Fan Yu, Sibin Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title | Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title_full | Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title_fullStr | Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title_full_unstemmed | Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title_short | Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association |
title_sort | deciphering the genetic architecture of color variation in whole grain rice by genome-wide association |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9960595/ https://www.ncbi.nlm.nih.gov/pubmed/36840275 http://dx.doi.org/10.3390/plants12040927 |
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