Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS
Abstract
:1. Introduction
2. Results
2.1. Genetic Diversity Analysis for the GWAS Population
2.2. Identification and Distribution Analysis for Labels
2.3. Population Structure Analysis for the GWAS Population
2.4. Large-Scale GWAS for 36 Agronomic Traits
2.4.1. The Three Stem-Related Traits
Plant Type
Branching Habit
Main Stem Pubescence
2.4.2. The Two Leaf-Related Traits
Leaf Margin
Leaf Pubescence
2.4.3. The Five Flower-Related Traits
Corolla Color
Style Color
Number of Flowers Per Axil
Flower Pedicel Growing State
Male Sterility
2.4.4. The Five Fruit-Related Traits
Anthocyanin on Immature Fruit
Mature Fruit Color
Spicy Type
Placenta Width
Fruit Width
2.5. Global Exploration of Correlations Among the 36 Agronomic Traits
2.6. Verification of GWAS Results Based on Fine Mapping of Male-Sterility (Rf) Gene
3. Discussion
4. Materials and Methods
4.1. Global Exploration of Correlations among the 36 Agronomic Traits
4.2. Analysis of Phenotypic Data
4.3. Extraction of Genomic DNA
4.4. Design of Enzyme Digestion Scheme
4.5. Construction of SLAF Libraries and High-Throughput Sequencing
4.6. Identification and Distribution Analysis of Labels (SLAF Tags and SNPs)
4.7. Population Structure Analysis
4.8. Genome-Wide Association Analyses of 36 Agronomic Traits
4.9. Molecular Mapping of the Nuclear Fertility-Restoring Gene (Rf) for Cytoplasmic Male Sterility
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Plant Organ | Trait | Model | Chromosome | Number of SNPs (p < 1.707 × 10−8) in Peak Region | Trait-Associated Peak Region | ||
---|---|---|---|---|---|---|---|
Start | End | Size (Mbp) | |||||
Stem | Pt | FaST-LMM | Chr01 | 9 | 278425275 | 280417460 | 1.992185 |
Chr04 | 2 | 23932585 | 23972683 | 0.040098 | |||
Chr05 | 5 | 17744799 | 19221034 | 1.476235 | |||
Chr06 | 10 | 5675663 | 5759294 | 0.083631 | |||
Chr09 | 10 | 12510495 | 19373800 | 6.863305 | |||
Chr09 | 14 | 118192571 | 119757960 | 1.565389 | |||
Chr09 | 10 | 171029237 | 173134444 | 2.105207 | |||
Chr11 | 3 | 37287718 | 40113909 | 2.826191 | |||
Chr11 | 17 | 107259335 | 107501665 | 0.24233 | |||
Bh | EMMAX | Chr01 | 59 | 275555035 | 277575138 | 2.020103 | |
Chr02 | 6 | 83643192 | 85422044 | 1.778852 | |||
Chr02 | 21 | 104238462 | 104524382 | 0.28592 | |||
Chr03 | 13 | 253213778 | 254639900 | 1.426122 | |||
Chr06 | 14 | 13971060 | 18672334 | 4.701274 | |||
Chr07 | 9 | 5373860 | 7707856 | 2.333996 | |||
Chr07 | 35 | 184612786 | 184825374 | 0.212588 | |||
Chr09 | 10 | 191839433 | 200002779 | 8.163346 | |||
Msc | FaST-LMM | Chr06 | 2 | 20231877 | 20231907 | 0.00003 | |
Chr08 | 6 | 114388151 | 114431559 | 0.043408 | |||
Chr09 | 2 | 214330476 | 214330504 | 0.000028 | |||
Msp | EMMAX | Chr11 | 28 | 27131483 | 28706358 | 1.574875 | |
Leaf | Ls | GLM | - | - | - | - | - |
Lc | GLM | - | - | - | - | - | |
Lm | GLM | Chr01 | 8 | 158420891 | 158729605 | 0.308714 | |
Chr04 | 7 | 58610574 | 59222198 | 0.611624 | |||
Chr06 | 7 | 212371837 | 212424874 | 0.053037 | |||
Chr08 | 7 | 131427437 | 134733324 | 3.305887 | |||
Chr12 | 4 | 12354265 | 19260025 | 6.90576 | |||
Lp | EMMAX | Chr10 | 9 | 162170912 | 162221229 | 0.050317 | |
Chr10 | 4 | 197927729 | 200867123 | 2.939394 | |||
Chr12 | 3 | 22681366 | 22692847 | 0.011481 | |||
Lsc | GLM | - | - | - | - | - | |
Flower | Cc | EMMAX | Chr02 | 4 | 68060203 | 68060282 | 0.000079 |
Chr04 | 6 | 189062369 | 192962061 | 3.899692 | |||
Chr06 | 8 | 41630661 | 41857768 | 0.227107 | |||
Chr07 | 2 | 214559213 | 214585881 | 0.026668 | |||
Chr07 | 6 | 220688885 | 220941545 | 0.25266 | |||
Chr08 | 8 | 135096972 | 135952487 | 0.855515 | |||
Chr09 | 5 | 201471658 | 202362543 | 0.890885 | |||
Chr11 | 5 | 28177723 | 28191389 | 0.013666 | |||
Chr11 | 6 | 214289893 | 216304968 | 2.015075 | |||
Sc | GLM | Chr01 | 3 | 211183454 | 211183884 | 0.00043 | |
Chr10 | 24 | 155035157 | 155097491 | 0.062334 | |||
Chr11 | 114 | 27555236 | 29305711 | 1.750475 | |||
Ac | FaST-LMM | Chr01 | 17 | 246812579 | 249477491 | 2.664912 | |
Chr07 | 2 | 130948617 | 130973590 | 0.024973 | |||
Ffn | FaST-LMM | - | - | - | - | - | |
Nfpa | EMMAX | Chr01 | 3 | 220458255 | 220462790 | 0.004535 | |
Chr01 | 7 | 280054497 | 280417460 | 0.362963 | |||
Chr04 | 3 | 57766474 | 58558409 | 0.791935 | |||
Chr05 | 2 | 206654389 | 206654579 | 0.00019 | |||
Chr06 | 10 | 13971060 | 19735646 | 5.764586 | |||
Chr06 | 39 | 219098248 | 219470017 | 0.371769 | |||
Chr07 | 3 | 185249295 | 185271463 | 0.022168 | |||
Chr09 | 22 | 10463866 | 12820022 | 2.356156 | |||
Chr09 | 12 | 118192571 | 119641888 | 1.449317 | |||
Chr10 | 7 | 29037048 | 33183732 | 4.146684 | |||
Chr11 | 5 | 209423789 | 210867712 | 1.443923 | |||
Chr12 | 20 | 192018036 | 193789860 | 1.771824 | |||
Fpgs | EMMAX | Chr12 | 23 | 32930746 | 38073141 | 5.142395 | |
Ms | FaST-LMM | Chr06 | 101 | 214443037 | 215536517 | 1.09348 | |
Fruit | Aif | EMMAX | Chr08 | 4 | 130745390 | 131501395 | 0.756005 |
Chr09 | 6 | 104816188 | 104816287 | 0.000099 | |||
Chr09 | 5 | 167226310 | 167226390 | 0.00008 | |||
Chr10 | 86 | 148782468 | 155625398 | 6.84293 | |||
Fsf | EMMAX | - | - | - | - | - | |
Fg | FaST-LMM | Chr07 | 8 | 6280167 | 6685034 | 0.404867 | |
Chr09 | 3 | 39263 | 1201526 | 1.162263 | |||
Chr12 | 8 | 180112718 | 186338088 | 6.22537 | |||
Fsc | EMMAX | - | - | - | - | - | |
Fss | FaST-LMM | Chr01 | 3 | 202642462 | 203121398 | 0.478936 | |
Chr04 | 2 | 15454448 | 15454730 | 0.000282 | |||
Chr09 | 4 | 94667918 | 94693832 | 0.025914 | |||
Chr09 | 8 | 126292337 | 127360615 | 1.068278 | |||
Chr11 | 9 | 30762829 | 49631336 | 18.868507 | |||
Fas | FaST-LMM | - | - | - | - | - | |
Ab | FaST-LMM | - | - | - | - | - | |
Mfc | EMMAX | Chr06 | 17 | 3758563 | 10060744 | 6.302181 | |
St | FaST-LMM | Chr04 | 2 | 3047655 | 3280037 | 0.232382 | |
Chr05 | 2 | 54372525 | 54372671 | 0.000146 | |||
Chr06 | 3 | 40301536 | 40301894 | 0.000358 | |||
Chr10 | 3 | 201908626 | 203356884 | 1.448258 | |||
Chr12 | 3 | 6307012 | 12354265 | 6.047253 | |||
Chr12 | 45 | 35222952 | 35714999 | 0.492047 | |||
Fpl | FaST-LMM | - | - | - | - | - | |
Pw | FaST-LMM | Chr08 | 4 | 133185108 | 133433188 | 0.24808 | |
Chr12 | 203552366 | 206591342 | 3.038976 | ||||
Pl | FaST-LMM | - | - | - | - | - | |
Psi | FaST-LMM | - | - | - | - | - | |
Fw | FaST-LMM | Chr01 | 4 | 103860245 | 105083614 | 1.223369 | |
Chr08 | 22 | 133045048 | 133584887 | 0.539839 | |||
Chr12 | 9 | 201671262 | 206591342 | 4.92008 | |||
Fl | FaST-LMM | - | - | - | - | - | |
Fsi | EMMAX | - | - | - | - | - | |
Wpf | FaST-LMM | Chr01 | 7 | 103860245 | 105083614 | 1.223369 | |
Chr05 | 2 | 168537584 | 168540175 | 0.002591 | |||
Chr08 | 4 | 133396929 | 133433188 | 0.036259 | |||
Chr12 | 14 | 200798023 | 211814051 | 11.016028 | |||
Dmc | FaST-LMM | Chr02 | 7 | 69956806 | 79414868 | 9.458062 | |
Chr11 | 5 | 85204434 | 85204791 | 0.000357 | |||
Tf | FaST-LMM | Chr01 | 3 | 103860245 | 105083388 | 1.223143 | |
Chr08 | 3 | 126042291 | 133396929 | 7.354638 | |||
Chr11 | 5 | 128979925 | 128979983 | 0.000058 | |||
Chr12 | 8 | 200798023 | 207472045 | 6.674022 | |||
Nol | FaST-LMM | - | - | - | - | - |
© 2019 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 (http://creativecommons.org/licenses/by/4.0/).
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Wu, L.; Wang, P.; Wang, Y.; Cheng, Q.; Lu, Q.; Liu, J.; Li, T.; Ai, Y.; Yang, W.; Sun, L.; et al. Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. Int. J. Mol. Sci. 2019, 20, 5675. https://doi.org/10.3390/ijms20225675
Wu L, Wang P, Wang Y, Cheng Q, Lu Q, Liu J, Li T, Ai Y, Yang W, Sun L, et al. Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. International Journal of Molecular Sciences. 2019; 20(22):5675. https://doi.org/10.3390/ijms20225675
Chicago/Turabian StyleWu, Lang, Peng Wang, Yihao Wang, Qing Cheng, Qiaohua Lu, Jinqiu Liu, Ting Li, Yixin Ai, Wencai Yang, Liang Sun, and et al. 2019. "Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS" International Journal of Molecular Sciences 20, no. 22: 5675. https://doi.org/10.3390/ijms20225675