Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Wenjun, Qiu, Xianjin, Wang, Ziqi, Xie, Tianyi, Sun, Wenqiang, Xu, Jianlong, Zhang, Fan, Yu, Sibin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
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
_version_ 1784895550572724224
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
work_keys_str_mv AT wangwenjun decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT qiuxianjin decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT wangziqi decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT xietianyi decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT sunwenqiang decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT xujianlong decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT zhangfan decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation
AT yusibin decipheringthegeneticarchitectureofcolorvariationinwholegrainricebygenomewideassociation