Table 1.
Quantitative trait loci (QTL) for pod morphological characters and pod color detected in this association study (GWAS). The description of specific associations trait-SNP are reported in Tables S2, S3, S4 and S5. QTL in bold indicates associations detected by different types of analysis (SL-GWAS & ML-GWAS)
| QTL name | N SNP | Chr | Start | End | N associations | Associated traits |
|---|---|---|---|---|---|---|
| Number or seed per pod | ||||||
| NSPCol01_51 | 3 | Pv01 | 50,878,622 | 51,047,344 | 3 | NSP, b* |
| NSP02_48.7 | 1 | Pv02 | 48,762,536 | 1 | NSP | |
| NSP03_49.5 | 1 | Pv03 | 49,492,839 | 1 | NSP | |
| NSP04_46.0 | 1 | Pv04 | 45,971,702 | 1 | NSP | |
| NSPLS06_18.4 | 5 | Pv06 | 18,457,867 | 19,126,326 | 12 | NSP, PLA, PLC, PLW, PSH, PSH/PSW |
| NSPCol08_1.7 | 2 | Pv08 | 1,752,338 | 1,771,186 | 2 | NSP, a* |
| NSP08_56.1 | 1 | Pv08 | 56,050,073 | 1 | NSP | |
| NSP10_2.2 | 1 | Pv10 | 2,237,697 | 1 | NSP | |
| NSP10_44.2 | 1 | Pv10 | 44,171,947 | 1 | NSP | |
| Pod Color | ||||||
| PodCol02_0.2 | 1 | Pv02 | 174,425 | 1 | PCOL | |
| PodCol02_0.8 | 4 | Pv02 | 884,794 | 959,169 | 6 | a*, L*, PCOL |
| PodCol02_2.4 | 2 | Pv02 | 2,394,009 | 2,438,673 | 2 | a*, L* |
| PodCol02_43.6 | 1 | Pv02 | 43,578,508 | 1 | PCOL | |
| PodCol03_52.3 | 1 | Pv03 | 52,336,057 | 1 | L* | |
| PodCol04_47.8 | 1 | Pv04 | 47,856,639 | 2 | a*, PCOL | |
| PodCol04_7.2 | 1 | Pv04 | 7,272,451 | 3 | L*, PCOL | |
| PodCol06_0.5 | 1 | Pv06 | 525,323 | 1 | PCOL | |
| PodCol07_32 | 11 | Pv07 | 32,026,373 | 32,413,401 | 12 | L*, b* |
| PodCol07_36.6 | 1 | Pv07 | 36,645,454 | 1 | PCOL | |
| PodCol08_6.2 | 1 | Pv08 | 6,230,633 | 1 | a* | |
| PodCol08_60.2 | 1 | Pv08 | 60,199,606 | 1 | L* | |
| PodCol08_61.0 | 1 | Pv08 | 60,982,396 | 1 | L* | |
| PodCol09_35.1 | 1 | Pv09 | 35,055,136 | 1 | a* | |
| PodCol10_5.8 | 1 | Pv10 | 5,805,361 | 1 | L* | |
| PodCol10_38.7 | 1 | Pv10 | 38,666,148 | 1 | a* | |
| PodCol10_43.4 | 2 | Pv10 | 43,424,753 | 43,472,349 | 2 | b*, PCOL |
| PodCol11_2.8 | 2 | Pv11 | 2,821,983 | 2,850,497 | 2 | b* |
| Pod length | ||||||
| PodL01_13.5 | 1 | Pv01 | 13,548,264 | 1 | PLC | |
| PodL01_38.1 | 1 | Pv01 | 38,143,057 | 1 | PLA | |
| PodL01_45.8 | 4 | Pv01 | 45,582,871 | 45,878,761 | 15 | PL, PLA, PLC, PLP |
| PodLCol01_48 | 4 | Pv01 | 48,090,873 | 48,454,962 | 18 | b*, PL, PLA, PLC, PLP |
| PodL01_49 | 1 | Pv01 | 49,004,631 | 3 | PL, PLC, PLP | |
| PodL02_01.7 | 1 | Pv02 | 1,719,474 | 1 | PLP | |
| PodL02_29.1 | 1 | Pv02 | 29,140,583 | 1 | PL | |
| PodL02_41.9 | 1 | Pv02 | 41,937,636 | 1 | PLC | |
| PodLCol02_47.6 | 3 | Pv02 | 47,302,543 | 47,669,811 | 13 | PCOL, PL, PLC, PLP |
| PodLCol02_49.4 | 1 | Pv02 | 49,430,892 | 2 | PCOL, PLW | |
| PodL03_37.3 | 1 | Pv03 | 37,253,089 | 1 | PLP | |
| PodL03_43.9 | 1 | Pv03 | 43,931,440 | 1 | PLC | |
| PodL04_3.8 | 1 | Pv04 | 3,787,273 | 1 | PLP | |
| PodL04_45.4 | 1 | Pv04 | 45,356,178 | 1 | PLA | |
| PodL05_31 | 1 | Pv05 | 31,050,333 | 3 | PLA, PLW | |
| PodL06_4.4 | 1 | Pv06 | 4,419,626 | 2 | PL/PLC | |
| PodL06_11.5 | 1 | Pv06 | 11,514,633 | 1 | PL/PLC | |
| PodL06_27.6 | 1 | Pv06 | 27,600,824 | 1 | PLP | |
| PodLCol08_2.7 | 3 | Pv08 | 2,442,492 | 2,753,777 | 3 | L*, PLW, PSA |
| PodL09_6.2 | 1 | Pv09 | 6,248,166 | 2 | PLC, PLP | |
| PodL09_35.6 | 1 | Pv09 | 35,616,441 | 1 | PLP | |
| PodL10_01.4 | 1 | Pv10 | 1,425,611 | 1 | PL | |
| PodL10_10.9 | 1 | Pv10 | 10,889,298 | 1 | PLC | |
| PodL10_19.2 | 1 | Pv10 | 19,251,851 | 5 | PL, PLA, PLC, PLP | |
| PodLS10_26.2 | 1 | Pv10 | 26,235,406 | 3 | PL, PLC, PLP | |
| PodL10_40.2 | 1 | Pv10 | 40,284,910 | 2 | PLA, PLP | |
| PodL11_4.6 | 1 | Pv11 | 4,616,391 | 1 | PLA | |
| Pod cross-section | ||||||
| PodS02_39.5 | 1 | Pv02 | 39,483,988 | 1 | PSH/PSW | |
| PodS04_44.1 | 1 | Pv04 | 44,087,509 | 1 | PSH | |
| PodLS04_44.5 | 1 | Pv04 | 44,563,602 | 2 | PLW, PSH/PSW | |
| PodS05_39.5 | 1 | Pv05 | 39,514,093 | 2 | PSH, PSP | |
| PodS08_57.2 | 1 | Pv08 | 57,231,193 | 1 | PSH | |
| PodS09_27.1 | 1 | Pv09 | 27,118,120 | 1 | PSP | |
| PodS09_34.5 | 1 | Pv09 | 34,496,801 | 1 | PSH/PSW | |
| PodLS10_36.1 | 1 | Pv10 | 36,133,101 | 2 | PLA, PSH | |