Genetic Diversity and Population Structure of a Large USDA Sesame Collection
Abstract
:1. Introduction
2. Results and Discussion
2.1. Single-Nucleotide Polymorphism Markers Coverage and Polymorphism Analyses
2.2. Analysis of Population Structure
2.3. Analysis of Molecular Variance (AMOVA) and Genetic Diversity Indices
2.4. Linkage Disequilibrium
2.5. Applications of High-Throughput Genotyping of Sesame Accessions
3. Materials and Methods
3.1. Plant Materials
3.2. DNA Extraction and Genotyping-by-Sequencing (GBS)
3.3. GBS Sequencing and Genotyping Pipeline Analyses
3.4. Population Genetic Analyses
3.4.1. Marker Polymorphism Analyses
3.4.2. Analysis of Population Structure
3.5. Analysis of Molecular Variance (AMOVA) and Genetic Diversity Indices
3.6. Linkage Disequilibrium (LD)
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Chromosomes * | Length (Mbp) * | No. of SNP | Maker Density ** | |
---|---|---|---|---|
Kbp | SNP/Mbp | |||
LG01 | 23.75 | 2389 | 9.94 | 100.60 |
LG02 | 23.37 | 1240 | 18.85 | 53.05 |
LG03 | 31.44 | 3118 | 10.08 | 99.18 |
LG04 | 21.23 | 1466 | 14.48 | 69.07 |
LG05 | 20.96 | 1434 | 14.62 | 68.40 |
LG06 | 27.99 | 2467 | 11.35 | 88.13 |
LG07 | 16.12 | 1259 | 12.80 | 78.11 |
LG08 | 31.99 | 2342 | 13.66 | 73.22 |
LG09 | 26.74 | 2336 | 11.45 | 87.36 |
LG10 | 22.21 | 1705 | 13.03 | 76.76 |
LG11 | 17.33 | 1716 | 10.10 | 99.01 |
LG12 | 19.10 | 2065 | 9.25 | 108.11 |
LG13 | 19.50 | 1198 | 16.28 | 61.44 |
Total | 301.73 | 24,735 | - | - |
Average | - | 1903 | 12.76 | 81.73 |
SNP Type | Transitions | Transversions | ||||
---|---|---|---|---|---|---|
A/G | C/T | A/T | A/C | G/T | G/C | |
Number of SNPs | 7145 | 7292 | 2609 | 2555 | 2529 | 2605 |
Allele frequency | 0.289 | 0.295 | 0.105 | 0.103 | 0.102 | 0.105 |
Total (percentage) | 0.584 | 0.416 |
Source | df | Sum of Squares | Variance Components | Variation % |
---|---|---|---|---|
Among subpopulations | 1 | 155,958.45 | 308.77 | 29.50 |
Among accessions within subpopulations | 499 | 667,180.45 | 599.25 | 57.26 |
Within accessions | 501 | 69,405.00 | 138.53 | 13.24 |
Total | 892,543.90 | 1046.56 |
Chromosome | LD |
---|---|
LG01 | 148.77 |
LG02 | 132.90 |
LG03 | 148.88 |
LG04 | 131.75 |
LG05 | 123.26 |
LG06 | 151.14 |
LG07 | 149.29 |
LG08 | 161.50 |
LG09 | 167.65 |
LG10 | 133.18 |
LG11 | 146.04 |
LG12 | 159.01 |
LG13 | 148.82 |
Whole population | 160.69 |
Subpopulation 1 | 166.45 |
Subpopulation 2 | 143.78 |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Seay, D.; Szczepanek, A.; De La Fuente, G.N.; Votava, E.; Abdel-Haleem, H. Genetic Diversity and Population Structure of a Large USDA Sesame Collection. Plants 2024, 13, 1765. https://doi.org/10.3390/plants13131765
Seay D, Szczepanek A, De La Fuente GN, Votava E, Abdel-Haleem H. Genetic Diversity and Population Structure of a Large USDA Sesame Collection. Plants. 2024; 13(13):1765. https://doi.org/10.3390/plants13131765
Chicago/Turabian StyleSeay, Damien, Aaron Szczepanek, Gerald N. De La Fuente, Eric Votava, and Hussein Abdel-Haleem. 2024. "Genetic Diversity and Population Structure of a Large USDA Sesame Collection" Plants 13, no. 13: 1765. https://doi.org/10.3390/plants13131765
APA StyleSeay, D., Szczepanek, A., De La Fuente, G. N., Votava, E., & Abdel-Haleem, H. (2024). Genetic Diversity and Population Structure of a Large USDA Sesame Collection. Plants, 13(13), 1765. https://doi.org/10.3390/plants13131765