Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing
Abstract
:Highlights
- -
- A diversity panel (SDP) of 308 common bean lines was established for GWAS
- -
- SDP gathered a wide genetic common bean diversity
- -
- The main Spanish local diversity is represented in the SDP
- -
- SDP is appropriate for the study of pod traits related to snap consumption
1. Introduction
2. Material and Methods
2.1. Plant Material
2.2. DNA Isolation
2.3. Genotyping by Sequencing
2.4. Linkage Disequilibrium
2.5. Data Analysis
2.6. Genome-Wide Association Study for Determinacy
3. Results
3.1. Genotyping
3.2. Population Structure
3.3. Linkage Disequilibrium
3.4. Unweighted Pair Group Method with Arithmetic Mean Clustering
- (i)
- Lines derived from commercial elite cultivars for snap bean consumption: ‘Perfeccion Negra Polo’ and ‘Emilia’, ‘Manteca de los Mercados’, and ‘Rocdor’;
- (ii)
- lines derived from accessions included in the SCC: BG026222-BGE004813, BGE026158-BGE002207, BGE040514-BGE002152, BGE003550-BGE003274, and BGE029629-BGE004489-BGE027085, BGE022494-V208;
- (iii)
- lines derived from commercial elite cultivars for snap bean consumption were included in the SCC, ‘Garrafal enana’-BGE026151, ‘Garrafal Oro’-BGE025180-BGE013964-BGE022837, and ‘Buenos Aires Roja’-BGE028940-BGE025142-BGV008281.
3.5. Principal Component Analysis
3.6. Utility of the Spanish Diversity Panel for Genome-Wide Association Study
4. Discussion
4.1. Genetic Diversity and Origin
4.2. Population Structure
4.3. Linkage Disequilibrium
4.4. Genome-Wide Association Study
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
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Group | n | No Polymorphic SNPs | Pairwase LD | ||
---|---|---|---|---|---|
Average r2 | %LD | %Significant LD | |||
Total Panel | 308 | 3099 | 0.18 | 10.11 | 100 |
Andean | 148 | 2152 | 0.03 | 0.95 | 92.61 |
Mesoamerican | 78 | 2596 | 0.05 | 0.92 | 90.2 |
Recombinants | 82 | 2994 | 0.06 | 1.08 | 89.2 |
Chr Pv01 | Chr Pv02 | Chr Pv03 | Chr Pv04 | Chr Pv05 | Chr Pv06 | Chr Pv07 | Chr Pv08 | Chr Pv09 | Chr Pv10 | Chr Pv11 | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Chr Pv01 | r2 | 0.3 | ||||||||||
%LD | 29.4% | |||||||||||
Chr Pv02 | r2 | 0.15 | 0.18 | |||||||||
%LD | 4% | 9.30% | ||||||||||
Chr Pv03 | r2 | 0.23 | 0.15 | 0.24 | ||||||||
%LD | 18.7% | 3.3% | 20.3% | |||||||||
Chr Pv04 | r2 | 0.15 | 0.13 | 0.15 | 0.16 | |||||||
%LD | 6.4% | 3.3% | 5.7% | 10% | ||||||||
Chr Pv05 | r2 | 0.19 | 0.13 | 0.17 | 0.13 | 0.19 | ||||||
%LD | 12.3% | 2.7% | 8.2 | 3.1% | 11.7% | |||||||
Chr Pv06 | r2 | 0.21 | 0.14 | 0.19 | 0.13 | 0.17 | 0.24 | |||||
%LD | 13.3% | 2% | 10.9% | 3.4% | 6.2% | 16.4% | ||||||
Chr Pv07 | r2 | 0.2 | 0.14 | 0.19 | 0.14 | 0.15 | 0.18 | 0.21 | ||||
%LD | 15.5% | 3.1% | 13.4% | 4.5% | 6.7% | 10.3 | 16% | |||||
Chr Pv08 | r2 | 0.18 | 0.14 | 0.18 | 0.14 | 0.15 | 0.17 | 0.17 | 0.19 | |||
%LD | 11.7% | 4.10% | 10.1% | 6.4% | 6.5% | 7.50% | 8.7% | 13.1% | ||||
Chr Pv09 | r2 | 0.26 | 0.18 | 0.24 | 0.17 | 0.19 | 0.22 | 0.24 | 0.21 | 0.35 | ||
%LD | 24.7% | 6.4% | 21.6% | 6.7% | 10.4% | 16.4% | 21.2% | 14% | 35.4% | |||
Chr Pv10 | r2 | 0.13 | 0.10 | 0.14 | 0.09 | 0.11 | 0.13 | 0.13 | 0.11 | 0.17 | 0.14 | |
%LD | 5.5% | 0.9% | 5.9% | 0.01% | 0.02% | 3.5% | 4.8% | 2.2% | 8.4% | 7% | ||
Chr Pv11 | r2 | 0.22 | 0.15 | 0.20 | 0.15 | 0.17 | 0.18 | 0.19 | 0.18 | 0.24 | 0.13 | 0.25 |
%LD | 19.4% | 3.8% | 15.1% | 6.2% | 9.5% | 10.6% | 13.7% | 11.7% | 22.1% | 4.2% | 21.4% |
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Campa, A.; Murube, E.; Ferreira, J.J. Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing. Genes 2018, 9, 518. https://doi.org/10.3390/genes9110518
Campa A, Murube E, Ferreira JJ. Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing. Genes. 2018; 9(11):518. https://doi.org/10.3390/genes9110518
Chicago/Turabian StyleCampa, Ana, Ester Murube, and Juan José Ferreira. 2018. "Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing" Genes 9, no. 11: 518. https://doi.org/10.3390/genes9110518
APA StyleCampa, A., Murube, E., & Ferreira, J. J. (2018). Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing. Genes, 9(11), 518. https://doi.org/10.3390/genes9110518