Unraveling New Genetic Elements Associated with the Morphological Changes and Relative Silicon Content in Rice Using Genome-Wide Association Studies (GWAS)
2024
Tran, G.S. | Nguyen, Q.H. | Nguyen, L.T.T. | Mai, H. | Phan, Q.Y. | Nguyen, M.N. | Tong, S.S. | Do, P.T. | To, H.T.M.
Rice (Oryza sativa L.) is a typical silicon-accumulating plant that positively benefits from silicon nutrition. Silicon (Si) has been demonstrated to have various advantages for plant growth, development, and stress responses. In this study, a genomewide association analysis (GWAS) was performed for a large-scale study using genetic information from 180 Vietnamese rice landrace in the control condition and saturated supplementation of Si to elucidate related quantitative trait loci (QTL) and potential novel genes associated to Si content and morphological changes in rice under the two conditions. The obtained results indicate a wide range of physiological traits and Si accumulation of rice varieties in response to Si supplementation. Most Vietnamese rice accessions in this panel enhanced their height, biomass, and Si content under Si supplementation. After conducting the association, 133 single nucleotide polymorphisms (SNP) were found, and most significant markers were located on chromosomes 1, 2, 3, and 12. Five significant QTLs were identified after analyzing the Linkage Disequilibrium and the haplotype. Interestingly, qSi1.3 represents the most promising QTL since it possesses three nitrate transporters and three ABC transporters inside its confident interval. Other transporters were also detected such as OsPT2 in qSi3.1, PHT4;6 in qSi12.1. Besides, several proteins such as Cinnamoyl CoA Reductase CCRs in qSi2.3 and OsCYPs in qSi1.3, ONACs in qSi2.3 might also relate to the transport of heavy metals, Si, nutrients, and plant development. These results provide new insight into new genes associated with Si transportation and serve as a premise for further in-depth investigation.
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