Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. RAD Sequencing and SNP Statistics
2.3. Genetic Map Construction and Quality Evaluation
2.4. QTL Mapping and Screening of Candidate Genes
3. Results
3.1. RAD Sequencing Data Analysis
3.2. Genetic Map Construction
3.3. Quality Evaluation of the Genetic Map
3.4. QTL Mapping and Candidate Gene Identification
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
RAD-seq | restriction site-associated DNA sequencing |
SNP | single-nucleotide polymorphism |
QTL | quantitative trait locus |
LOD | logarithm of the odds |
PVE | phenotypic variation explained |
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Linkage Group | SNP Number | Total Distance (cm) | Average Distance (cm) | Max Gap (cm) | Gaps < 5 cm (%) |
---|---|---|---|---|---|
LG1 | 465 | 79.45 | 0.17 | 3.35 | 100 |
LG2 | 389 | 142.71 | 0.37 | 18.23 | 98.97 |
LG3 | 384 | 77.04 | 0.2 | 2.87 | 100 |
LG4 | 333 | 92.18 | 0.28 | 24.22 | 99.7 |
LG5 | 305 | 79.2 | 0.26 | 2.39 | 100 |
LG6 | 265 | 90.52 | 0.34 | 20.17 | 99.62 |
LG7 | 197 | 57.01 | 0.29 | 12.71 | 98.98 |
LG8 | 153 | 54.6 | 0.36 | 5.28 | 98.68 |
Total | 2491 | 672.71 | - | - | - |
Average | 311.38 | 84.09 | 0.27 | 11.15 | 99.49 |
Year | Linkage Group | QTL | Confidence Interval (cm) | Mark Number | LOD | PVE (%) |
---|---|---|---|---|---|---|
2021 | LG2 | 21TA-1 | 69.433–69.912 | 6 | 3.87 | 12.03 |
LG2 | 21TA-2 | 74.218–77.568 | 16 | 3.86 | 12.01 | |
LG2 | 21TA-3 | 84.51–85.467 | 4 | 3.33 | 10.45 | |
LG2 | 21TA-4 | 86.663–87.381 | 6 | 3.25 | 10.19 | |
LG2 | 21TA-5 | 89.056–90.97 | 13 | 3.41 | 10.69 | |
LG2 | 21TA-6 | 91.209–92.405 | 10 | 3.68 | 11.45 | |
LG2 | 21TA-7 | 94.08–94.319 | 3 | 3.91 | 12.13 | |
LG5 | 21TA-8 | 42.349–42.588 | 3 | 3.47 | 10.83 | |
LG5 | 21TA-9 | 45.7–45.94 | 3 | 3.56 | 11.13 | |
LG5 | 21TA-10 | 48.093–48.811 | 8 | 5.43 | 16.44 | |
LG5 | 21TA-11 | 50.007–59.338 | 35 | 6.29 | 18.71 | |
LG5 | 21TA-12 | 60.056–61.971 | 10 | 11.28 | 31.13 | |
LG5 | 21TA-13 | 63.407–79.197 | 55 | 8.36 | 24.06 | |
2022 | LG1 | 22TA-1 | 29.432 | 3 | 3.86 | 8.7 |
LG2 | 22TA-2 | 60.336 | 1 | 3.81 | 8.6 | |
LG3 | 22TA-3 | 48.332 | 1 | 3.14 | 7.1 | |
LG5 | 22TA-4 | 34.693 | 1 | 3.23 | 7.3 | |
LG6 | 22TA-5 | 1.436 | 1 | 3.45 | 7.8 |
Correlation coefficient | Phosphatidate phosphatase gene (FPKM) |
Titratable acid content | 0.93 ** |
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Guo, C.; Hu, F.; Li, Y. Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map. Genes 2025, 16, 1157. https://doi.org/10.3390/genes16101157
Guo C, Hu F, Li Y. Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map. Genes. 2025; 16(10):1157. https://doi.org/10.3390/genes16101157
Chicago/Turabian StyleGuo, Caizhen, Fenglan Hu, and Yuqi Li. 2025. "Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map" Genes 16, no. 10: 1157. https://doi.org/10.3390/genes16101157
APA StyleGuo, C., Hu, F., & Li, Y. (2025). Quantitative Trait Locus Mapping and Candidate Gene Identification for Fruit Acidity in Chinese Dwarf Cherry (Cerasus humilis) Using a High-Density Genetic Map. Genes, 16(10), 1157. https://doi.org/10.3390/genes16101157