DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis
Abstract
:1. Introduction
2. Results
2.1. Characteristics of SNPs in Training Data
2.2. Fingerprint of 1135 Arabidopsis Varieties Established by DT-PICS
2.3. Fingerprint of the Identification Power of Same-Named and Different-Named Varieties in Test Datasets
2.4. Generation of QR Codes
3. Discussion
4. Materials and Methods
4.1. Genotype Dataset of Materials
4.2. Marker Polymorphism Analysis
4.3. Selecting SNPs from the Training Dataset to Construct a Fingerprint Map
4.4. Variety Identification in the Training Set Using the DT-PICS Method
4.5. Independent Testing of Variety Identification
4.6. Generation of QR Codes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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SNP Combination | Distinguishing Accuracy (%) | Mean Accuracy (%) | |||
---|---|---|---|---|---|
Raw SNP | Modify 5% SNP | Modify 10% SNP | Modify 15% SNP | ||
59 DT-PICS SNPs | 100 | 96.74 | 92.78 | 84.64 | 93.54 |
39 DT-PICS + 20 hPIC | 94.19 | 91.28 | 88.65 | 85.21 | 89.83 |
20 DT-PICS + 39 hPIC | 91.28 | 85.94 | 84.68 | 82.67 | 86.14 |
59 hPICS SNPs | 87.14 | 82.32 | 81.71 | 80.51 | 82.92 |
59 random SNPs | 86.70 | 80.42 | 77.90 | 68.26 | 78.32 |
SNP Combination | Distinguishing Accuracy (%) | Mean Accuracy (%) | |||
---|---|---|---|---|---|
Raw SNP | Modify 5% SNP | Modify 10% SNP | Modify 15% SNP | ||
109 DT-PIC SNPs | 100 | 99.44 | 97.94 | 95.64 | 98.26 |
73 DT-PIC + 36 hPIC | 99.56 | 97.28 | 94.82 | 92.56 | 96.06 |
36 DT-PIC + 73 hPIC | 95.51 | 92.02 | 90.19 | 88.58 | 91.58 |
109 hPIC SNPs | 87.93 | 83.86 | 83.57 | 83.14 | 84.63 |
109 random SNPs | 87.58 | 83.10 | 82.57 | 81.59 | 83.71 |
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Xiong, L.; Li, Z.; Li, W.; Li, L. DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis. Int. J. Mol. Sci. 2023, 24, 8742. https://doi.org/10.3390/ijms24108742
Xiong L, Li Z, Li W, Li L. DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis. International Journal of Molecular Sciences. 2023; 24(10):8742. https://doi.org/10.3390/ijms24108742
Chicago/Turabian StyleXiong, Liwen, Zirong Li, Weihua Li, and Lanzhi Li. 2023. "DT-PICS: An Efficient and Cost-Effective SNP Selection Method for the Germplasm Identification of Arabidopsis" International Journal of Molecular Sciences 24, no. 10: 8742. https://doi.org/10.3390/ijms24108742