Table 2.
QTLs detected in F2 and BC3F2 populations
| QTLs detected in F2 populationa |
QTLs detected in BC3F2 populationa |
||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Trait | QTL name | QTL positiona | Flanking marker 1 | Flanking marker 2 | Closest DNA marker | LOD | PVE (%) | Additive effect of Peking allele | s.d. | Dominance effect | s.d. | QTL positionb | Flanking marker 1 | Flanking marker 2 | Closest DNA marker | LOD | PVE (%) | Additive effect of Peking allele | s.d. | Dominance effect | s.d. | Confirmation of QTL with CSSLc | Confirmed QTLs between F2 and BC3 F2 population | Candidate genes or related QTLs | ID of related QTLs reported in Soybase | References | |
| DFF | qDFF_Gm19 | Gm19@118.9 | FT3-751 | C19-BARC- 018175-02533 | FT3-751 | 51.2** | 23.9 | 4.9 | 0.2 | 1.6 | 0.3 | Gm19@106.0 | Sat_286 | FT3-751 | FT3-751 | 174.8** | 29.5 | 3.3 | 0.1 | 0.5 | 0.2 | Confirmed | Confirmed | Dt1/E3 | Liu et al. 2009, Watanabe et al. 2009 | ||
| qDFF_Gm06 | Gm06@102.0 | sF3H | C06-BARC- 041345-07969 | C06-BARC- 041345-07969 | 57.5** | 29.6 | –5.5 | 0.2 | 2.6 | 0.4 | Gm06@106.4 | sF3H | FT1SSR9 | FT1SSR9 | 145.1** | 22.7 | –3.2 | 0.1 | 1.2 | 0.2 | Confirmed | Confirmed | E1 | Xia et al. 2012 | |||
| qDFF_Gm12 | Gm12@33.0 | C12-BARC- 015603-02006 | s024200450 | s024200450 | 36.3** | 13.6 | 3.7 | 0.2 | 0.3 | 0.4 | Gm12@49.0 | s024200450 | s023500372 | s024200450 | 74.5** | 9.8 | 2.0 | 0.1 | –0.1 | 0.2 | Confirmed | Confirmed | qDFF_Gm12 | First flower 25–2 | Kuroda et al. 2013 | ||
| qDFF_Gm10 | Gm10@116.0 | C10-BARC- 015003-01948 | C10-BARC- 015925-02017 | C10-BARC- 015925-02017 | 37.4** | 14.3 | 4.0 | 0.2 | 1.2 | 0.4 | Gm10@103.0 | Satt331 | FT2-300H01d | FT2-300H01d | 70.7** | 9.2 | 1.9 | 0.1 | 0.2 | 0.2 | Confirmed | Confirmed | E2 | Watanabe et al. 2011 | |||
| qDFF_Gm11 | Gm11@71.0 | s008000014-2 | T001111280m | T001111280m | 18.9** | 5.6 | –2.4 | 0.2 | 0.0 | 0.4 | Gm11@61.5 | GMES0766 | T001111280m | T001111280m | 38.7** | 4.7 | –1.2 | 0.1 | –0.2 | 0.2 | Confirmed(partially) | Confirmed | qDFF_Gm11 | First flower 8–4 | Yamanaka et al. 2001 | ||
| qDFF_Gm16 | Gm16@33.0 | C16-BARC- 020505-04644 | GMES0775 | GMES0775 | 10.3** | 2.7 | 1.7 | 0.2 | 0.8 | 0.4 | Gm16@68.5 | GMES4751 | s026800043 | GMES4751 | 16.9** | 1.9 | –0.9 | 0.1 | –0.2 | 0.2 | Confirmed | Confirmed | GmFT5a | Takeshima et al. 2016 | |||
| qDFF_Gm13 | Gm13@7.0 | s000702358-2 | s000701869-2 | s000701869-2 | 6.8* | 1.7 | –1.5 | 0.3 | –0.1 | 0.4 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Confirmed | - | qDFF_Gm13 | First flower 11–4 | Gai et al. 2007 | ||
| DFT | qDFT_Gm19_1d | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm19@102.0 | Sat_286 | FT3-751 | FT3-751 | 285.3** | 55.3 | 8.8 | 0.2 | 0.0 | 0.4 | Confirmed | NA | Dt1 | Liu et al. 2009 | ||
| qDFT_Gm19_2d | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm19@106.0 | Sat_286 | FT3-751 | FT3-751 | 193.8** | 37.9 | 4.8 | 0.2 | 2.8 | 0.3 | Confirmed | NA | E3 | Watanabe et al. 2009 | |||
| qDFT_Gm06 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm06@105.6 | Satt277 | sF3H | sF3H | 78.8** | 11.5 | –3.5 | 0.2 | 1.1 | 0.3 | Confirmed | NA | E1 | “ | |||
| qDFT_Gm10 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm10@103.0 | Satt331 | FT2-300H01d | FT2-300H01d | 74.5** | 10.7 | 3.1 | 0.2 | 0.1 | 0.3 | Confirmed | NA | E2 | “ | |||
| qDFT_Gm12 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm12@49.0 | s024200450 | s023500372 | s024200450 | 68.5** | 9.7 | 3.0 | 0.2 | –0.2 | 0.3 | Confirmed | NA | qDFF_Gm12 | “ | |||
| qDFT_Gm11 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm11@60.0 | GMES0766 | T001111280m | T001111280m | 35.3** | 4.6 | –2.1 | 0.2 | 0.4 | 0.3 | Confirmed | NA | qDFF_Gm11 | “ | |||
| FP | qFP_Gm19_1d | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm19@100.0 | Sat_286 | FT3-751 | FT3-751 | 242.4** | 67.4 | 5.4 | 0.1 | –0.2 | 0.3 | Confirmed(partially) | NA | Dt1 | “ | ||
| qFP_Gm19_2d | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm19@102.0 | Sat_286 | FT3-751 | FT3-751 | 131.9** | 45.8 | 2.7 | 0.2 | 2.6 | 0.3 | Confirmed(partially) | NA | E3 | “ | |||
| DH | qDH_Gm19 | Gm19@118.0 | Satt229 | FT3-751 | FT3-751 | 22.4** | 14.2 | 8.1 | 0.7 | 2.5 | 1.0 | Gm19@105.0 | Sat_286 | FT3-751 | FT3-751 | 39.7** | 12.1 | 6.1 | 0.5 | –0.6 | 0.9 | Confirmed | Confirmed | Dt1/E3 | “ | ||
| qDH_Gm06 | Gm06@102.0 | sF3H | C06-BARC- 041345-07969 | C06-BARC- 041345-07969 | 34.8** | 26.2 | –11.2 | 0.7 | 2.1 | 1.0 | Gm06@104.4 | Satt277 | sF3H | sF3H | 30.6** | 9.1 | –5.4 | 0.5 | 0.8 | 0.9 | Confirmed | Confirmed | E1 | “ | |||
| qDH_Gm11 | Gm11@71.0 | s008000014-2 | T001111280m | T001111280m | 29.9** | 21.1 | –10.0 | 0.7 | 0.0 | 1.0 | Gm11@41.0 | GMES0045 | Satt197 | Satt197 | 18.8** | 5.5 | –4.3 | 0.5 | 0.5 | 1.1 | Confirmed | Confirmed | qDFF_Gm11 | Reproductive stage length 8–1 | Komatsu et al. 2012 | ||
| qDH_Gm10 | Gm10@119.0 | FT2-300H01d | s005205820-2 | s005205820-2 | 17.6** | 10.5 | 7.3 | 0.8 | 1.9 | 1.0 | Gm10@103.0 | Satt331 | FT2-300H01d | FT2-300H01d | 13.3** | 3.8 | 3.4 | 0.5 | –0.4 | 0.9 | Confirmed | Confirmed | E2 | “ | |||
| qDH_Gm12 | Gm12@33.5 | s024200450 | s024200389 | s024200450 | 16.4** | 9.6 | 6.4 | 0.7 | 1.3 | 1.0 | Gm12@49.0 | s024200450 | s023500372 | s024200450 | 11.8** | 3.4 | 3.0 | 0.5 | 0.0 | 0.9 | Confirmed | Confirmed | qDFF_Gm12 | “ | |||
| qDH_Gm02 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm02@48.0 | Satt701 | Satt296 | Satt701 | 8.2** | 2.3 | 2.3 | 0.5 | 1.6 | 1.1 | –– | –– | qRP_Gm02 | Pod maturity 22–4 | Reinprecht et al. 2006 | ||
| qDH_Gm13 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm13@125.0 | Satt362 | s003004926-2 | Satt362 | 5.2** | 1.5 | –2.3 | 0.5 | 2.7 | 1.0 | Confirmed | –– | qRP_Gm13 | Novel | |||
| qDH_Gm17 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm17@46.0 | T001709449l | T001710954m | T001709449l | 5.0* | 1.4 | –2.5 | 0.6 | 1.3 | 1.0 | Confirmed | –– | qRP_Gm17 | Reproductive period 1–7 | Wang et al. 2015 (position is slightly different) | ||
| qDH_Gm01 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm01@43.8 | Satt221 | Satt370 | Satt221 | 4.6* | 1.3 | 2.2 | 0.5 | –2.2 | 0.9 | –– | –– | qRP_Gm01 | Pod maturity 1–2 | Keim et al. 1990B | ||
| RP | qRP_Gm11 | Gm11@70.0 | s008000014-2 | T001111280m | s008000014-2 | 16.4** | 27.4 | –7.0 | 0.7 | 0.1 | 1.1 | Gm11@38.0 | GMES0045 | Satt197 | GMES0045 | 12.3** | 4.6 | –3.4 | 0.5 | 0.2 | 1.1 | Confirmed | Confirmed | qDFF_Gm11 | Reproductive stage length 8–1 | Komatsu et al. 2012 | |
| qRP_Gm02 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm02@49.0 | Satt701 | Satt296 | Satt701 | 9.3** | 3.5 | 2.6 | 0.6 | 1.2 | 1.1 | –– | –– | qRP_Gm02 | “ | |||
| qRP_Gm13 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm13@124.0 | Satt362 | s003004926-2 | Satt362 | 7.5** | 2.8 | –2.6 | 0.5 | 2.8 | 1.0 | Confirmed | –– | qRP_Gm13 | Novel | |||
| qRP_Gm19 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm19@105.0 | Sat_286 | FT3-751 | FT3-751 | 7.2** | 2.7 | 2.7 | 0.5 | –1.1 | 0.9 | Confirmed | –– | Dt1/E3 | “ | |||
| qRP_Gm06 | Gm06@98.4 | Satt277 | C06-BARC- 014491-01562 | Satt277 | 10.9** | 16.9 | –5.4 | 0.7 | –0.9 | 1.1 | Gm06@104.4 | Satt277 | sF3H | sF3H | 6.3** | 2.3 | –2.2 | 0.5 | –0.1 | 0.9 | Confirmed | Confirmed | E1 | “ | |||
| qRP_Gm16 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm16@54.5 | Satt596 | s014300091-2 | Satt596 | 5.7** | 2.1 | 2.3 | 0.5 | –0.5 | 1.0 | –– | –– | GmFT5a | “ | |||
| qRP_Gm17 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm17@46.0 | T001709449l | T001710954m | T001709449l | 4.5** | 1.6 | –2.3 | 0.5 | 1.1 | 0.9 | Confirmed | –– | qRP_Gm17 | “ | |||
| qRP_Gm01 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm01@44.8 | Satt221 | Satt370 | Satt221 | 4.4** | 1.6 | 2.1 | 0.5 | –2.0 | 0.9 | –– | –– | qRP_Gm01 | “ | |||
| PH | qPH_Gm19_1d | Gm19@114.0 | Satt664 | C19-BARC- 030101-06809 | Satt664 | 30.4** | 42.7 | 15.5 | 1.1 | 0.5 | 1.6 | Gm19@101.0 | Sat_286 | FT3-751 | FT3-751 | 129.8** | 45.7 | 14.4 | 0.5 | –3.5 | 1.0 | Confirmed | Confirmed | Dt1 | “ | ||
| qPH_Gm19_2d | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm19@102.0 | Sat_286 | FT3-751 | FT3-751 | 78.7** | 27.6 | 7.0 | 0.6 | 7.2 | 1.1 | Confirmed | –– | E3 | “ | |||
| qPH_Gm10 | Gm10@117.2 | FT2-300H01d | s005205820-2 | FT2-300H01d | 6.3* | 6.4 | 5.8 | 1.1 | 4.1 | 1.6 | Gm10@102.0 | Satt331 | FT2-300H01d | FT2-300H01d | 17.4** | 5.3 | 4.0 | 0.5 | –0.4 | 0.9 | Confirmed | Confirmed | E2 | “ | |||
| qPH_Gm06 | Gm06@103.0 | s005700017 | s007100484 | s005700017 | 16.6** | 19.3 | –10.5 | 1.1 | 3.8 | 1.6 | Gm06@106.4 | sF3H | FT1SSR9 | FT1SSR9 | 15.9** | 4.8 | –3.8 | 0.5 | 1.1 | 0.9 | Confirmed | Confirmed | E1 | “ | |||
| NP | qNP_Gm19 | Gm19@116.0 | C19-BARC- 030101-06809 | Satt229 | C19-BARC- 030101-06809 | 15.0** | 26.4 | 84.4 | 9.7 | 17.0 | ## | Gm19@101.0 | Sat_286 | FT3-751 | FT3-751 | 148.2** | 39.3 | 80.0 | 3.5 | 30.0 | 6.8 | Confirmed | Confirmed | Dt1/E3 | “ | ||
| qNP_Gm12 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm12@50.0 | s024200450 | s023500372 | s024200450 | 33.9** | 6.8 | 31.6 | 3.0 | 6.7 | 6.0 | Confirmed | –– | qDFF_Gm12 | “ | |||
| qNP_Gm10 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm10@109.0 | FT2-300H01d | T001045537m | FT2-300H01d | 27.7** | 5.4 | 28.3 | 3.1 | 5.3 | 5.6 | –– | –– | E2 | “ | |||
| qNP_Gm06 | Gm06@103.0 | s005700017 | s007100484 | s005700017 | 11.5** | 19.3 | −73.0 | 9.5 | 9.2 | ## | Gm06@104.4 | Satt277 | sF3H | sF3H | 23.5** | 4.6 | –29.7 | 3.2 | 5.1 | 5.8 | Confirmed | Confirmed | E1 | “ | |||
| qNP_Gm11 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm11@61.5 | GMES0766 | T001111280m | T001111280m | 15.3** | 2.9 | –21.2 | 2.8 | 1.7 | 5.4 | Confirmed | –– | qDFF_Gm11 | “ | |||
| qNP_Gm16 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm16@69.5 | GMES4751 | s026800043 | s026800043 | 7.4* | 1.4 | –18.5 | 3.2 | 16.3 | 6.1 | –– | –– | GmFT5a | “ | |||
| TSW | qTSW_Gm19 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm19@102.0 | Sat_286 | FT3-751 | FT3-751 | 155.5** | 37.3 | 37.9 | 1.7 | 18.3 | 3.2 | –– | –– | Dt1/E3 | “ | ||
| qTSW_Gm12 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm12@50.0 | s024200450 | s023500372 | s024200450 | 44.2** | 8.0 | 18.1 | 1.5 | 1.7 | 2.9 | Confirmed | –– | qDFF_Gm12 | “ | |||
| qTSW_Gm11 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm11@61.0 | GMES0766 | T001111280m | T001111280m | 36.2** | 6.5 | –16.3 | 1.4 | 1.4 | 2.6 | Confirmed | –– | qDFF_Gm11 | “ | |||
| qTSW_Gm06 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm06@105.4 | Satt277 | sF3H | sF3H | 35.7** | 6.4 | –17.4 | 1.5 | 3.2 | 2.6 | Confirmed | –– | E1 | “ | |||
| qTSW_Gm10 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm10@110.0 | FT2-300H01d | T001045537m | FT2-300H01d | 20.9** | 3.6 | 10.7 | 1.5 | 5.2 | 2.8 | Confirmed | –– | E2 | “ | |||
| qTSW_Gm16 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm16@68.5 | GMES4751 | s026800043 | GMES4751 | 8.7** | 1.5 | –9.7 | 1.5 | 9.4 | 2.9 | Confirmed | –– | GmFT5a | “ | |||
| qTSW_Gm20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Gm20@99.0 | T002042675s | Sct_189 | T002042675s | 6.8** | 1.1 | –9.4 | 2.0 | 1.5 | 3.9 | Confirmed | –– | qTSW_Gm20 | Seed yield 15–15 | Kabelka et al. 2004 | ||
| SWH | qSWH_Gm08 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm08@46.0 | GMES1620 | AY262686B | AY262686B | 33.3** | 10.1 | –2.8 | 0.2 | 1.9 | 0.4 | Confirmed | –– | qSWH_Gm08 | Seed weight 4–5 | Maughan et al. 1996 (close to I locus) | |
| qSWH_Gm06 | Gm06@98.4 | Satt277 | C06-BARC- 014491-01562 | Satt277 | 8.9** | 17.1 | –2.4 | 0.4 | 1.7 | 0.5 | Gm06@106.4 | sF3H | FT1SSR9 | FT1SSR9 | 29.1** | 8.8 | –2.3 | 0.2 | 1.1 | 0.4 | Confirmed(partially) | Confirmed | E1 | “ | |||
| qSWH_Gm11 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm11@59.0 | GMES0766 | T001111280m | T001111280m | 22.3** | 6.6 | –1.8 | 0.2 | 0.0 | 0.4 | Confirmed | –– | qDFF_Gm11 | “ | |||
| qSWH_Gm17 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm17@51.0 | T001709449l | T001710954m | T001710954m | 15.1** | 4.4 | –2.0 | 0.3 | 0.5 | 0.5 | Confirmed | –– | qSWH_Gm17 | Seed yield 5-2 | Renyna and Sneller 2001 | ||
| qSWH_Gm19 | Gm19@118.9 | FT3-751 | C19-BARC- 018175-02533 | FT3-751 | 8.4** | 15.9 | 2.4 | 0.4 | 1.1 | 0.5 | Gm19@107.1 | Sat_286 | FT3-751 | FT3-751 | 10.7** | 3.1 | 1.1 | 0.2 | 0.1 | 0.3 | Confirmed | Confirmed | Dt1/E3 | “ | |||
| qSWH_Gm20 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm20@98.0 | T002042675s | Sct_189 | T002042675s | 6.6** | 1.9 | –1.5 | 0.3 | 1.1 | 0.5 | Confirmed(partially) | –– | qSWH_Gm20 | “ | |||
| qSWH_Gm13 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm13@16.0 | Satt146 | Satt252 | Satt252 | 6.6** | 1.9 | –1.1 | 0.2 | 0.0 | 0.5 | Confirmed(partially) | –– | qDFF_Gm13 | “ | |||
| qSWH_Gm02 | –– | –– | –– | –– | –– | –– | –– | –– | –– | –– | Gm02@22.0 | Sat_096 | Sat_351 | Sat_351 | 5.9** | 1.7 | –0.9 | 0.2 | –0.4 | 0.5 | Confirmed | –– | qSWH_Gm02 | “ | |||
NA, the trait was not evaluated in the F2 population; LOD, logarithm of odds of the presence of a QTL; PVE, percentage of variance explained by the QTL.
a
Sowing date of F2 population and BC3F3 population were 30 May 2007 and 24 June2011, respectively.
b
Indicated as chromosome name and position in cM separated by @.
c
‘Confirmed partially’ indicates that a singificant difference was observed between Enrei and a CSSL habouring several donor choromosomal fragments.
d
Effects of the QTLs corresponding to E3 and Dt1 loci were calculated separately.
*
Significant at P < 0.05 after 1,000 permutation; **Significant at P < 0.01 after 1,000 permutation.