Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification and Characterization of OsRS Genes
2.2. Collinearity Analysis of RS Genes
2.3. Ka/Ks Ratio Analysis of OsRS Homologous Genes
2.4. Expression Profile of OsRS Genes in Different Tissues and under Abiotic Stress
2.5. Real-Time Fluorescence Quantitative PCR Analysis of OsRS Genes
2.6. Genetic Diversity and Allelic Diversity of OsRS Loci in Rice Population
2.7. Effects of Modern Breeding on gcHap Diversity of OsRS Genes
2.8. Comparison of Trait Values between the Favorable and Unfavorable gcHaps of OsRS Genes in Rice
2.9. Correlation Analysis of Major gcHaps of OsRS Genes and Important Agronomic Traits
2.10. Mining of Favorable Alleles at OsRS Loci for Yield Improvement
3. Discussion
4. Materials and Methods
4.1. Identification of the OsRS Gene Family Members
4.2. Phylogenetic Analysis of OsRS Genes
4.3. Analysis of Cis-Acting Elements, Conserved Motifs, Conserved Domains, and Promoter Regions of OsRS Family Proteins
4.4. Collinear Analysis of OsRS Genes
4.5. Gene Expression Profile Based on RNA-seq
4.6. Material Handling
4.7. Real-Time Fluorescence Quantitative PCR Analysis
4.8. OsRS Gene gcHaps and gcHap Diversity in Modern and Local Varieties
4.9. Extraction of Major gcHap Phenotypes for OsRS Genes
4.10. Construction of CDS Haplotype (gcHap) Network of OsRS Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene 1 | Gene 2 | Ka | Ks | Ka/Ks |
---|---|---|---|---|
OsRS2 | OsRS54 | 0.137 | 0.283 | 0.484 |
Gene Name | Xian (Indica) | |||||||
---|---|---|---|---|---|---|---|---|
LANs | MVs | MVs—LANs | Statistical | Artificial Selection Effect | ||||
EH | gcHapN | EH | gcHapN | EH | gcHapN | |||
OsRS1 | 0.127 | 26 | 0.229 | 28 | 0.102 | 2 | ** | up |
OsRS2 | 0.090 | 6 | 0.103 | 7 | 0.013 | 1 | ns | up |
OsRS3 | 0.326 | 49 | 0.413 | 46 | 0.087 | −3 | ** | up |
OsRS4 | 0.263 | 62 | 0.344 | 44 | 0.081 | −18 | ** | up |
OsRS5 | 0.312 | 63 | 0.438 | 51 | 0.126 | −12 | ** | up |
OsRS6 | 0.214 | 19 | 0.229 | 11 | 0.016 | −8 | ns | up |
Mean | 0.250 | 42.4 | 0.329 | 35.1 | 0.079 |
Gene Name | Geng (Japonica) | |||||||
---|---|---|---|---|---|---|---|---|
LANs | MVs | MVs—LANs | Statistical | Artificial Selection Effect | ||||
EH | gcHapN | EH | gcHapN | EH | gcHapN | |||
OsRS1 | 0.192 | 19 | 0.211 | 13 | 0.019 | −6 | ns | up |
OsRS2 | 0.028 | 6 | 0.045 | 3 | 0.016 | −3 | ns | up |
OsRS3 | 0.163 | 20 | 0.204 | 13 | 0.041 | −7 | ns | up |
OsRS4 | 0.244 | 29 | 0.214 | 12 | −0.029 | −17 | ns | down |
OsRS5 | 0.257 | 27 | 0.300 | 18 | 0.043 | −9 | ns | up |
OsRS6 | 0.129 | 8 | 0.205 | 8 | 0.076 | 0 | * | up |
Mean | 0.171 | 18 | 0.210 | 12 |
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Zhang, J.; Meng, D.; Li, J.; Bao, Y.; Yu, P.; Dou, G.; Guo, J.; Tang, C.; Lv, J.; Wang, X.; et al. Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity. Int. J. Mol. Sci. 2024, 25, 9815. https://doi.org/10.3390/ijms25189815
Zhang J, Meng D, Li J, Bao Y, Yu P, Dou G, Guo J, Tang C, Lv J, Wang X, et al. Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity. International Journal of Molecular Sciences. 2024; 25(18):9815. https://doi.org/10.3390/ijms25189815
Chicago/Turabian StyleZhang, Jinguo, Dezhuang Meng, Jianfeng Li, Yaling Bao, Peng Yu, Guohui Dou, Jinmeng Guo, Chenghang Tang, Jiaqi Lv, Xinchen Wang, and et al. 2024. "Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity" International Journal of Molecular Sciences 25, no. 18: 9815. https://doi.org/10.3390/ijms25189815