Table 1.
Details of peak regions associated with different traits identified via a genome wide association study (GWAS) in pepper.
| 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 | - | - | - | - | - | |
Note: Pt, plant type; Bh, branching habit; Msc, main stem color; Msp, main stem pubescence; Ls, leaf shape; Lc, leaf color; Lm, leaf margin; Lp, leaf pubescence; Lsc, leaf surface characteristics; Cc, corolla color; Sc, style color; Ac, anther color; Ffn, first flower node; Nfpa, number of flowers per axil; Fpgs, flower pedicel growing state; Ms, Male-sterility; Aif, anthocyanin on immature fruit; Fsf, fruit surface furrow; Fg, fruit glossy; Fsc, fruit surface characteristics; Fss, fruit shoulder shape; Fas, fruit apex shape; Ab, appendage at blossom-end; Mfc, mature fruit color; St, spicy type; Fpl, fruit pedicel length; Pw, placenta width; Pl, placenta length; Psi, placenta size index; Fw, Fruit width; Fl, fruit length; Fsi, fruit shape index; Wpf, weight per fruit; Dmc, dry matter content; Tf, thickness of flesh; Nol, Number of locules (full text identical). Bold font represents the 13 quantitative traits classified by data type. ‘-’, which indicated that there were no significant peaks.