Frontiers in Plant Science (Mar 2022)
Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures
- Wu Yang,
- Wu Yang,
- Wu Yang,
- Luo Chen,
- Luo Chen,
- Luo Chen,
- Junliang Zhao,
- Junliang Zhao,
- Junliang Zhao,
- Jian Wang,
- Jian Wang,
- Jian Wang,
- Wenhui Li,
- Wenhui Li,
- Wenhui Li,
- Tifeng Yang,
- Tifeng Yang,
- Tifeng Yang,
- Jingfang Dong,
- Jingfang Dong,
- Jingfang Dong,
- Yamei Ma,
- Yamei Ma,
- Yamei Ma,
- Lian Zhou,
- Lian Zhou,
- Lian Zhou,
- Jiansong Chen,
- Jiansong Chen,
- Jiansong Chen,
- Wei Wu,
- Wei Wu,
- Wei Wu,
- Shaohong Zhang,
- Shaohong Zhang,
- Shaohong Zhang,
- Bin Liu,
- Bin Liu,
- Bin Liu
Affiliations
- Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Wu Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Wu Yang
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Luo Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Luo Chen
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Junliang Zhao
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Junliang Zhao
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Jian Wang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Jian Wang
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Wenhui Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Wenhui Li
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Wenhui Li
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Tifeng Yang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Tifeng Yang
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Jingfang Dong
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Jingfang Dong
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Yamei Ma
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Yamei Ma
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Lian Zhou
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Lian Zhou
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Jiansong Chen
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Jiansong Chen
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Wei Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Wei Wu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Wei Wu
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Shaohong Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Shaohong Zhang
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Bin Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Bin Liu
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- DOI
- https://doi.org/10.3389/fpls.2022.841191
- Journal volume & issue
-
Vol. 13
Abstract
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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