Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Rice Datasets
2.2. Dimensionality Reduction
2.3. Genome-Wide Association Study
2.4. Candidate Gene Identification and Enrichment Analysis
2.5. Tissue-Specific Expression Analysis
3. Results
3.1. Phenotypic Variation
3.2. Genetic Dissection of Epistatic Interactions
3.3. Functional Enrichment Analysis of the Candidate Genes
3.4. Expression Profile of the Candidate Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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NO. | QTN1 | QTN2 | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Chr | Pos | Gene ID | Gene | Chr | Pos | Gene ID | Gene | LOD | aa.Effect | ad.Effect | da.Effect | dd.Effect | Variance | PVE (%) | p-Value | |
QTN1 | 1 | 38111539 | 6.79 | 12.63 | −19.11 | 57.09 | 12.832 | 1.62 × 10−7 | ||||||||
QQI 1 | 1 | 723562 | 11 | 25849860 | 5.75 | 3.76 | 12.94 | 2.910 | 2.66 × 10−7 | |||||||
QQI 2 | 1 | 29384858 | 2 | 2233430 | LOC_Os02g04680 | LCRN1; OsSPL3 | 5.68 | 2.69 | 6.03 | 31.82 | 7.151 | 2.09 × 10−6 | ||||
QQI 3 | 1 | 29557152 | 12 | 15325876 | 6.87 | 5.75 | 24.38 | 5.480 | 1.85 × 10−8 | |||||||
QQI 4 | 1 | 30547272 | LOC_Os01g53160 | OFP3; OsOFP04 | 5 | 1015771 | 5.56 | −4.94 | 21.98 | 4.940 | 4.24 × 10−7 | |||||
QQI 5 | 1 | 31651011 | LOC_Os01g54810 LOC_Os01g54930 | THIS1 OsVOZ1 | 9 | 9425939 | 3.23 | −4.19 | 6.25 | 1.406 | 1.14 × 10−4 | |||||
QQI 6 | 1 | 39419765 | LOC_Os01g68000 | PLA2; LHD2 | 6 | 3636360 | 6.97 | 3.69 | 2.58 | 9.16 | 2.059 | 1.07 × 10−7 | ||||
QQI 7 | 3 | 13773095 | LOC_Os03g24220 | VLN2 | 9 | 11706989 | 5.72 | 4.36 | 8.18 | 1.839 | 2.89 × 10−7 | |||||
QQI 8 | 4 | 29851050 | 12 | 21716878 | 6.32 | −4.51 | 20.16 | 4.531 | 6.89 × 10−8 | |||||||
QQI 9 | 5 | 25953209 | LOC_Os05g44310 LOC_Os05g44760 | OsSec18 OsHXK5 | 6 | 1524748 | LOC_Os06g03710 LOC_Os06g03770 LOC_Os06g03810 LOC_Os06g04010 | DLT; SMOS2 OsATM3 ROD1 OsGBP1 | 4.65 | 3.20 | 8.66 | 1.946 | 3.69 × 10−6 | |||
QQI 10 | 5 | 27196868 | LOC_Os05g47446 | OsPDCD5 | 8 | 4731022 | LOC_Os08g08210 | SDG701 | 4.06 | 3.99 | 7.59 | 1.707 | 1.52 × 10−5 | |||
QQI 11 | 5 | 28309324 | 7 | 26640298 | 4.18 | −4.67 | −3.22 | 14.83 | 3.334 | 6.67 × 10−5 | ||||||
QQI 12 | 6 | 29357275 | LOC_Os06g48530 | Du13 | 7 | 6016810 | 5.88 | 2.54 | 5.07 | 1.139 | 1.95 × 10−7 | |||||
QQI 13 | 7 | 4724800 | 7 | 27550702 | LOC_Os07g46460 | Fd-GOGAT1 | 4.79 | 5.73 | −1.32 | 22.64 | 5.090 | 1.61 × 10−5 | ||||
QQI 14 | 8 | 51045 | 9 | 854638 | 8.16 | 4.86 | 15.52 | 3.488 | 8.76 × 10−10 |
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Li, L.; Wu, X.; Chen, J.; Wang, S.; Wan, Y.; Ji, H.; Wen, Y.; Zhang, J. Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model. Plants 2022, 11, 2504. https://doi.org/10.3390/plants11192504
Li L, Wu X, Chen J, Wang S, Wan Y, Ji H, Wen Y, Zhang J. Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model. Plants. 2022; 11(19):2504. https://doi.org/10.3390/plants11192504
Chicago/Turabian StyleLi, Ling, Xinyi Wu, Juncong Chen, Shengmeng Wang, Yuxuan Wan, Hanbing Ji, Yangjun Wen, and Jin Zhang. 2022. "Genetic Dissection of Epistatic Interactions Contributing Yield-Related Agronomic Traits in Rice Using the Compressed Mixed Model" Plants 11, no. 19: 2504. https://doi.org/10.3390/plants11192504