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Article

Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines

by
Lulu Chen
1,†,
Yujia Leng
1,†,
Caiyun Zhang
1,
Xixu Li
1,
Zhihui Ye
1,
Yan Lu
1,
Lichun Huang
2,
Qing Liu
2,3,
Jiping Gao
2,
Changquan Zhang
1,* and
Qiaoquan Liu
2,*
1
Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College, Yangzhou University, Yangzhou 225009, China
2
Key Laboratory of Plant Functional Genomics of the Ministry of Education/Zhongshan Biological Breeding Laboratory, Yangzhou University, Yangzhou 225009, China
3
Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2024, 13(24), 3588; https://doi.org/10.3390/plants13243588
Submission received: 11 November 2024 / Revised: 20 December 2024 / Accepted: 21 December 2024 / Published: 23 December 2024
(This article belongs to the Special Issue Crop Genetic Mechanisms and Breeding Improvement)
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Abstract

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC4F2 segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC4F2 population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement.
Keywords: rice; whiteness; quantitative trait loci; chromosomal segment substitution lines rice; whiteness; quantitative trait loci; chromosomal segment substitution lines

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MDPI and ACS Style

Chen, L.; Leng, Y.; Zhang, C.; Li, X.; Ye, Z.; Lu, Y.; Huang, L.; Liu, Q.; Gao, J.; Zhang, C.; et al. Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines. Plants 2024, 13, 3588. https://doi.org/10.3390/plants13243588

AMA Style

Chen L, Leng Y, Zhang C, Li X, Ye Z, Lu Y, Huang L, Liu Q, Gao J, Zhang C, et al. Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines. Plants. 2024; 13(24):3588. https://doi.org/10.3390/plants13243588

Chicago/Turabian Style

Chen, Lulu, Yujia Leng, Caiyun Zhang, Xixu Li, Zhihui Ye, Yan Lu, Lichun Huang, Qing Liu, Jiping Gao, Changquan Zhang, and et al. 2024. "Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines" Plants 13, no. 24: 3588. https://doi.org/10.3390/plants13243588

APA Style

Chen, L., Leng, Y., Zhang, C., Li, X., Ye, Z., Lu, Y., Huang, L., Liu, Q., Gao, J., Zhang, C., & Liu, Q. (2024). Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines. Plants, 13(24), 3588. https://doi.org/10.3390/plants13243588

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