Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers
Abstract
:1. Introduction
2. Results
2.1. SNP Analysis
2.2. Population Structure in the Global Cowpea Germplasm
2.3. Population Structure in the Korean Cowpea Accessions
2.4. Analysis of Genetic Diversity
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Phenotypic Evaluation
4.2. DNA Isolation and SNP Genotyping
4.3. Filtering SNP Data
4.4. Population Structure Analysis
4.5. Principal Component Analysis (PCA) and Phylogeny Tree Analysis
4.6. Genetic Diversity Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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MAF | PIC | Ho | He | Fis | |
---|---|---|---|---|---|
Global Accessions | |||||
Min | 0.044 | 0.080 | 0.000 | 0.045 | –0.091 |
Median | 0.278 | 0.321 | 0.000 | 0.257 | 1.000 |
Max | 0.500 | 0.375 | 0.113 | 0.502 | 1.000 |
Mean | 0.269 | 0.287 | 0.002 | 0.254 | 0.993 |
KoreanAccessions | |||||
Min | 0.000 | 0.000 | 0.000 | 0.000 | –0.045 |
Median | 0.263 | 0.313 | 0.000 | 0.246 | 1.000 |
Max | 0.500 | 0.375 | 0.138 | 0.521 | 1.000 |
Mean | 0.254 | 0.265 | 0.003 | 0.234 | 0.988 |
Category | Ho | He | Fis | MAF | PIC |
---|---|---|---|---|---|
Groups Based on Global Accessions | |||||
1 | 0.0016 | 0.2504 | 0.9889 | 0.1797 | 0.2027 |
2 | 0.0005 | 0.1421 | 0.9920 | 0.0904 | 0.1183 |
3 | 0.0018 | 0.3278 | 0.9928 | 0.2443 | 0.2580 |
4 | 0.0005 | 0.1895 | 0.9951 | 0.1328 | 0.1523 |
Groups Based on Korean Accessions | |||||
1 | 0.0006 | 0.1888 | 0.9945 | 0.1355 | 0.1570 |
2 | 0.0017 | 0.2395 | 0.9887 | 0.1837 | 0.1939 |
3 | 0.0005 | 0.1903 | 0.9951 | 0.1460 | 0.1527 |
Df | SS | MS | Sigma † | Var. % | Phi ‡ | p-Value | |
---|---|---|---|---|---|---|---|
Global Accessions | |||||||
19Between pop | 3 | 1,435,162 | 478,387.3 | 5965.9055 | 41.5 | 0.4159 | <0.001 |
Between samples | 335 | 2,806,352 | 8377.171 | 8377.1712 | 58.5 | ||
Total | 338 | 4,241,514 | 12,548.86 | 14,343.0768 | 100.0 | ||
Korean Accessions | |||||||
Between pop | 2 | 955,123.1 | 477,561.535 | 6761.786 | 47.5 | 0.4747 | <0.001 |
Between samples | 218 | 1,630,585.8 | 7479.751 | 7479.751 | 52.5 | ||
Total | 220 | 2,585,708.9 | 11,753.222 | 14,241.537 | 100.0 |
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Seo, E.; Kim, K.; Jun, T.-H.; Choi, J.; Kim, S.-H.; Muñoz-Amatriaín, M.; Sun, H.; Ha, B.-K. Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. Plants 2020, 9, 1190. https://doi.org/10.3390/plants9091190
Seo E, Kim K, Jun T-H, Choi J, Kim S-H, Muñoz-Amatriaín M, Sun H, Ha B-K. Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. Plants. 2020; 9(9):1190. https://doi.org/10.3390/plants9091190
Chicago/Turabian StyleSeo, Eunju, Kipoong Kim, Tae-Hwan Jun, Jinsil Choi, Seong-Hoon Kim, María Muñoz-Amatriaín, Hokeun Sun, and Bo-Keun Ha. 2020. "Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers" Plants 9, no. 9: 1190. https://doi.org/10.3390/plants9091190