Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. DNA Extraction and Genotyping-By-Sequencing (GBS) Procedures
2.3. Data Analysis
2.3.1. SNP Discovery
2.3.2. SNP Marker Properties
2.3.3. Population Molecular Characterization
3. Results
3.1. Characterization and Distribution of the GBS-Generated SNPs in the Olive Genomes
3.2. Characterization of the SNP Markers
3.3. Characterization of the Population and the Genetic Relationships
3.3.1. Structure Analysis and the Genetic Relationships
3.3.2. Cluster Analysis
3.3.3. Analysis of Molecular Variance (AMOVA)
3.4. Marker Characteristics across the Populations
4. Discussion
4.1. GBS Analysis of the Olive Genomes
4.2. Features of the SNP Markers
4.3. Features of the US Repository Olive Population
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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Origin | No. of Genotypes | |
---|---|---|
Climatic zone | Country | |
Continental | Russia | 2 |
Dry | Algeria | 1 |
Argentina | 1 | |
Chile | 1 | |
Egypt | 3 | |
Israel | 1 | |
Morocco | 1 | |
Pakistan | 1 | |
Palestine | 1 | |
Syria | 1 | |
Tunisia | 5 | |
Temperate | Albania | 2 |
Cyprus | 3 | |
France | 5 | |
Greece | 5 | |
Italy | 22 | |
Japan | 1 | |
Spain | 14 | |
US | 17 | |
Tropical | Colombia | 1 |
Peru | 2 | |
Unknown | 6 |
Transitions | Transversions | |||||
---|---|---|---|---|---|---|
Type of SNP | A/G | C/T | A/C | A/T | G/T | C/G |
Number of sites | 15,875 | 16,010 | 5513 | 7476 | 5288 | 3913 |
Frequencies | 29.36% | 29.61% | 10.20% | 13.83% | 9.78% | 7.24% |
Total | 31,885 (59.96%) | 22,190 (41.04%) |
Source of Variation | df | SS | MS | Variation | p-Value |
---|---|---|---|---|---|
Between the population | 7 | 630,346.08 | 90,049.44 | 32.94 | 0.001 |
Within the population | 88 | 1,277,390.84 | 14,515.80 | 67.06 | 0.001 |
Total | 95 | 1,907,736.91 | 20,081.44 | 100.00 |
Source of Variation | df | SS | MS | Variation | p-Value |
---|---|---|---|---|---|
Between the population | 7 | 310,271.04 | 44,324.43 | 4.29 | 0.04 |
Between the climatic zones within the population | 13 | 493,233.74 | 37,941.06 | 25.82 | 0.001 |
Within the population | 75 | 1,104,232.13 | 14,723.10 | 69.89 | 0.001 |
Total | 95 | 1,907,736.91 | 20,081.44 | 100.00 |
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Islam, A.S.M.F.; Sanders, D.; Mishra, A.K.; Joshi, V. Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS). Genes 2021, 12, 2007. https://doi.org/10.3390/genes12122007
Islam ASMF, Sanders D, Mishra AK, Joshi V. Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS). Genes. 2021; 12(12):2007. https://doi.org/10.3390/genes12122007
Chicago/Turabian StyleIslam, A. S. M. Faridul, Dean Sanders, Amit Kumar Mishra, and Vijay Joshi. 2021. "Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)" Genes 12, no. 12: 2007. https://doi.org/10.3390/genes12122007