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Article

New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS

by
Liqiang He
1,*,†,
Yao Sui
1,†,
Yanru Che
1,
Lihua Liu
1,
Shuo Liu
1,
Xiaobing Wang
2 and
Guangping Cao
3,*
1
School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
2
Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
3
Hainan Key Laboratory of Crop Genetics and Breeding, Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou 571100, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(9), 4667; https://doi.org/10.3390/ijms25094667
Submission received: 7 April 2024 / Revised: 21 April 2024 / Accepted: 22 April 2024 / Published: 25 April 2024
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 4.0)
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Abstract

Lysine is an essential amino acid that cannot be synthesized in humans. Rice is a global staple food for humans but has a rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying lysine content is crucial to increase lysine accumulation. In this study, five grain and three leaf lysine content datasets and 4,630,367 single nucleotide polymorphisms (SNPs) of 387 rice accessions were used to perform a genome-wide association study (GWAS) by ten statistical models. A total of 248 and 71 common QTNs associated with grain/leaf lysine content were identified. The accuracy of genomic selection/prediction RR-BLUP models was up to 0.85, and the significant correlation between the number of favorable alleles per accession and lysine content was up to 0.71, which validated the reliability and additive effects of these QTNs. Several key genes were uncovered for fine-tuning lysine accumulation. Additionally, 20 and 30 QTN-by-environment interactions (QEIs) were detected in grains/leaves. The QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted for gene-by-environment interaction was identified in grains. These findings suggested the application of multi-model GWAS facilitates a better understanding of lysine accumulation in rice. The identified QTNs and genes hold the potential for lysine-rich rice with a normal phenotype.
Keywords: rice; free lysine content; genome-wide association study; quantitative trait nucleotide; gene; QTN-by-environment interaction; genomic selection/prediction rice; free lysine content; genome-wide association study; quantitative trait nucleotide; gene; QTN-by-environment interaction; genomic selection/prediction

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MDPI and ACS Style

He, L.; Sui, Y.; Che, Y.; Liu, L.; Liu, S.; Wang, X.; Cao, G. New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS. Int. J. Mol. Sci. 2024, 25, 4667. https://doi.org/10.3390/ijms25094667

AMA Style

He L, Sui Y, Che Y, Liu L, Liu S, Wang X, Cao G. New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS. International Journal of Molecular Sciences. 2024; 25(9):4667. https://doi.org/10.3390/ijms25094667

Chicago/Turabian Style

He, Liqiang, Yao Sui, Yanru Che, Lihua Liu, Shuo Liu, Xiaobing Wang, and Guangping Cao. 2024. "New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS" International Journal of Molecular Sciences 25, no. 9: 4667. https://doi.org/10.3390/ijms25094667

APA Style

He, L., Sui, Y., Che, Y., Liu, L., Liu, S., Wang, X., & Cao, G. (2024). New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS. International Journal of Molecular Sciences, 25(9), 4667. https://doi.org/10.3390/ijms25094667

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