Origins and Genetic Characteristics of Egyptian Peach
Abstract
:1. Introduction
2. Results
2.1. Geographical Distribution and Morphological Characteristics of Egyptian Peaches
2.2. Sequencing and Mapping of Egyptian Peach Cultivars
2.3. Genome-Wide Nucleotide Variants
2.4. Annotation of Nucleotide Variants
2.5. Phylogenetic Analysis and Origin of Egyptian Peach Cultivars
2.6. Population Structure
2.7. Principal Component Analysis (PCA)
2.8. Identity-by-Descent (IBD) Analysis
3. Discussion
4. Materials and Methods
4.1. Sample Collection of Egyptian Peach Cultivars
4.2. Extraction and Purification of Genomic DNA
4.3. Library Construction and Sequencing
4.4. Read Mapping and Variants Calling
4.5. Functional Annotation of Genetic Variants
4.6. Phylogenetics, Population Structure, and Principal Component Analysis (PCA)
4.7. Identification of Identity-by-Descent (IBD) Segments
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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Cultivar | Governorate | Chilling Hours | Ripening Time | Latitude (N) | Longitude (E) |
---|---|---|---|---|---|
Florida prince | Alexandria | 100–150 | First week of April | 30°33′36.7″ | 30°15′18.0″ |
Early swelling | Alexandria | 150–250 | Third week of April | 30°33′33.8″ | 30°15′32.4″ |
Early grand | North Sinai | 150–250 | Late April | 31°11′26.1″ | 34°04′42.5″ |
Desert red | Alexandria | 200–250 | Mid-May | 30°33′47.7″ | 30°15′28.8″ |
Swelling | Alexandria | 200–250 | First week of June | 30°32′53.2″ | 30°15′16.2″ |
Met ghamr | Al-Qalyubia | 450 | Mid-June | 30°22′37.4″ | 31°07′25.0″ |
Nemaguard | Alexandria | - | - | 30°33′47.7″ | 30°15′28.8″ |
Bitter almond | North Sinai | - | - | 31°12′12.7″ | 34°02′14.1″ |
Cultivar | Clean Reads | Clean Bases | Q30 (%) | GC (%) | Mapped (%) | Sequencing Coverage (×) | Coverage Rate (1×) |
---|---|---|---|---|---|---|---|
Met ghamr | 22,723,292 | 6,735,864,568 | 93.4 | 40.12 | 93.37 | 26.07 | 92.14 |
Florida prince | 22,765,569 | 6,757,607,956 | 93.44 | 39.32 | 94.61 | 30.12 | 98.04 |
Early swelling | 22,359,252 | 6,650,374,896 | 93.60 | 38.53 | 96.22 | 29.43 | 98.23 |
Early grand | 21,192,361 | 6,296,956,610 | 92.78 | 37.61 | 93.15 | 29.21 | 92.88 |
Desert red | 21,002,961 | 6,249,157,770 | 96.32 | 37.65 | 95.38 | 28.56 | 96.97 |
Swelling | 21,488,706 | 6,380,695,324 | 92.57 | 38.33 | 95.69 | 28.56 | 97.12 |
Nemaguard | 19,692,875 | 5,851,569,914 | 92.69 | 39.00 | 93.08 | 26.58 | 93.09 |
Bitter almond | 19,833,337 | 5,885,734,930 | 92.40 | 38.08 | 92.48 | 28.44 | 91.32 |
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Ezzat, M.; Zhang, W.; Amar, M.; Nishawy, E.; Zhao, L.; Belal, M.; Han, Y.; Liao, L. Origins and Genetic Characteristics of Egyptian Peach. Int. J. Mol. Sci. 2024, 25, 8497. https://doi.org/10.3390/ijms25158497
Ezzat M, Zhang W, Amar M, Nishawy E, Zhao L, Belal M, Han Y, Liao L. Origins and Genetic Characteristics of Egyptian Peach. International Journal of Molecular Sciences. 2024; 25(15):8497. https://doi.org/10.3390/ijms25158497
Chicago/Turabian StyleEzzat, Mohamed, Weihan Zhang, Mohamed Amar, Elsayed Nishawy, Lei Zhao, Mohammad Belal, Yuepeng Han, and Liao Liao. 2024. "Origins and Genetic Characteristics of Egyptian Peach" International Journal of Molecular Sciences 25, no. 15: 8497. https://doi.org/10.3390/ijms25158497