Table 3.
Main-effect QTL (M-QTL) affecting appearance quality traits in the reciprocal ILs derived from MH63 × 02428 across five locations
| ILs | Trait | M-QTL | Chr. | Position (Mb) | SZ | NJ | XZ | JZ | SY | Reported genes |
|---|---|---|---|---|---|---|---|---|---|---|
| MH63 | GL | qGL1.2 | 1 | 12.4–12.7 | 4.5/0.12/3.2 | |||||
| qGL1.3 | 1 | 39.5–40.2 | 4.4/0.13/2.5 | – | ||||||
| qGL3.1 | 3 | 16.2–17.2 | 43.7/−0.58/25.5 | 23.6/−0.88/10.3 | 21.2/−0.51/16.0 | 3.0/−0.10/1.9 | GS3 | |||
| qGL5 | 5 | 3.4–3.5 | 9.3/−0.17/4.7 | Chalk5, GS5 | ||||||
| qGL7 | 7 | 4.8–5.2 | 6.0/−0.26/8.3 | 12.0/−0.23/5.8 | ||||||
| qGL8 | 8 | 20.9–23.1 | 5.8/0.13/2.3 | 8.3/0.14/3.9 | ||||||
| qGL9.1 | 9 | 11.8–14.0 | 21.0/−1.02/55.6 | |||||||
| qGL11 | 11 | 11.0–15.5 | 15.8/−0.26/9.7 | |||||||
| GW | qGW2 | 2 | 27.1–27.8 | 2.9/0.04/2.5 | GS2/GL2 | |||||
| qGW3 | 3 | 31.8–31.9 | 7.8/0.06/6.2 | |||||||
| qGW4.1 | 4 | 27.0–27.9 | 3.4/−0.09/2.9 | |||||||
| qGW5.1 | 5 | 3.4–3.5 | 45.1/0.15/44.1 | 27.5/0.13/22.9 | 23.9/0.13/35.9 | 47.0/0.14/43.3 | Chalk5, GS5 | |||
| qGW5.2 | 5 | 24.8–25.2 | 8.4/0.08/14.5 | 6.7/0.05/6.7 | ||||||
| qGW11.1 | 11 | 0.0–0.3 | 3.6/−0.03/2.9 | |||||||
| qGW12.1 | 12 | 0.0–0.3 | 2.9/0.04/2.1 | |||||||
| qGW12.2 | 12 | 14.2–17.0 | 4.9/0.09/6.3 | |||||||
| LWR | qLWR1 | 1 | 14.6–15.4 | 11.2/0.1/7.3 | ||||||
| qLWR2.1 | 2 | 0.0–0.4 | 4.7/−0.04/1.8 | 3.9/−0.1/1.4 | ||||||
| qLWR2.2 | 2 | 19.9–20.5 | 3.1/−0.2/6.4 | |||||||
| qLWR3.1 | 3 | 16.2–17.2 | 18.1/−0.1/8.6 | |||||||
| qLWR3.2 | 3 | 34.9–35.4 | 8.5/−0.2/4.4 | |||||||
| qLWR4.1 | 4 | 7.2–11.4 | 3.2/−0.2/4.5 | |||||||
| qLWR4.2 | 4 | 22.4–22.6 | 4.3/−0.1/2.2 | GIF1 | ||||||
| qLWR5 | 5 | 3.4–3.5 | 42.7/−0.2/25.5 | 30.1/−0.2/15.1 | 23.8/−0.2/17.0 | 15.3/−0.2/18.6 | 34.0/−0.2/27.4 | Chalk5, GS5 | ||
| qLWR7 | 7 | 4.8–5.2 | 11.5/−0.1/6.4 | 8.3/−0.2/7.5 | ||||||
| qLWR9 | 9 | 14.8–15.1 | 7.7/0.1/3.2 | |||||||
| qLWR11 | 11 | 17.1–17.8 | 4.9/0.1/2.2 | |||||||
| qLWR12.1 | 12 | 0.0–0.3 | 4.6/−0.1/2.6 | |||||||
| qLWR12.2 | 12 | 24.7–25.4 | 3.8/−0.2/5.1 | |||||||
| PGWC | qPGWC4 | 4 | 7.2–11.4 | 4.5/19.6/15.0 | ||||||
| qPGWC5 | 5 | 3.4–3.5 | 22.2/13.8/25.2 | 9.3/10.1/12.7 | 24.0/9.6/30.9 | 13.5/11.7/16.2 | Chalk5/qPGWC5a/qPGC5–1/qPGWC5 | |||
| qPGWC7 | 7 | 4.8–5.2 | 6.4/12.7/23.1 | 20.6/6.8/6.4 | ||||||
| qPGWC11 | 11 | 10.7–15.5 | 6.2/17.0/16.9 | |||||||
| qPGWC12 | 12 | 24.7–25.4 | 11.7/33.7/15.4 | OsRab5a | ||||||
| DEC | qDEC4 | 4 | 27.0–27.9 | 5.1/5.6/7.4 | qWB4 | |||||
| qDEC5 | 5 | 3.4–3.5 | 24.3/5.6/31.3 | 14.9/3.3/7.0 | 30.4/4.2/39.4 | 4.8/3.2/5.4 | Chalk5/qDEC5a/qPGC5-1/qDEC5 | |||
| qDEC6 | 6 | 22.4–22.8 | 4.2/3.9/10.1 | |||||||
| qDEC7 | 7 | 4.8–5.2 | 12.5/3.6/14.1 | 5.7/5.2/1.1 | 4.6/2.8/4.7 | |||||
| qDEC8.2 | 8 | 9.8–10.2 | 41.9/10.4/25.5 | qPGC8-1 | ||||||
| qDEC9 | 9 | 11.8–14.0 | 6.0/14.3/10.9 | 12.5/8.9/20.0 | qDEC9 | |||||
| qDEC11 | 11 | 10.7–15.5 | 5.4/4.4/4.1 | |||||||
| 02428 | GL | qGL1.1 | 1 | 3.3–3.8 | 9.4/0.40/15.5 | |||||
| qGL3.1 | 3 | 16.2–17.2 | 7.5/0.30/12.6 | 6.2/0.30/13.9 | 4.3/0.20/9.8 | 3.9/0.20/9.1 | GS3 | |||
| qGL3.2 | 3 | 28.0–28.1 | 5.3/0.20/10.1 | GL3.1 | ||||||
| qGL4 | 4 | 29.9–30.2 | 4.3/−0.30/12.6 | |||||||
| qGL7 | 7 | 4.8–5.2 | 5.6/0.20/5.8 | 5.4/0.20/12.3 | 4.9/0.20/11.4 | 5.4/0.30/12.5 | 5.2/0.20/9.9 | |||
| qGL9.2 | 9 | 17.5–17.6 | 4.3/−0.30/10.3 | |||||||
| qGL10 | 10 | 12.0–12.2 | 4.2/0.20/5.1 | 4.9/0.30/12.8 | 5.2/0.30/13.0 | |||||
| GW | qGW4.2 | 4 | 29.9–30.2 | 3.9/−0.10/6.2 | Flo2 | |||||
| qGW5.1 | 5 | 3.4–3.5 | 4.6/−0.10/8.6 | 4.2/−0.10/9.7 | 5.1/−0.10/11.5 | 3.1/−0.10/7.3 | Chalk5, GS5 | |||
| qGW6 | 6 | 0.3–2.4 | 4.1/−0.10/5.2 | |||||||
| qGW7 | 7 | 29.1–29.4 | 4.3/−0.10/8.9 | |||||||
| qGW8 | 8 | 14.9–17.4 | 5.1/−0.10/8.6 | |||||||
| qGW11.2 | 11 | 11.7–12.7 | 6.3/−0.10/14.1 | 5.2/−0.10/12.1 | ||||||
| qGW12.3 | 12 | 24.8–25.2 | 18.9/−0.10/39.1 | 6.7/−0.10/11.2 | 5.1/−0.10/10.1 | |||||
| LWR | qLWR2.1 | 2 | 0.0–0.2 | 3.7/0.1/8.0 | ||||||
| qLWR4.3 | 4 | 32.3–32.6 | 5.4/0.1/9.7 | Flo2 | ||||||
| qLWR5 | 5 | 3.4–3.5 | 4.6/0.1/10.5 | Chalk5, GS5 | ||||||
| qLWR6 | 6 | 2.4–3.2 | 3.5/0.1/6.6 | |||||||
| qLWR7 | 7 | 4.8–5.2 | 3.8/0.1/7.8 | 5.5/0.1/12.5 | 5.9/0.1/13.4 | 5.2/0.1/11.7 | 4.2/0.1/7.5 | |||
| qLWR10 | 10 | 2.3–2.6 | 4.4/0.1/10.1 | |||||||
| PGWC | qPGWC3 | 3 | 10.0–10.1 | 5.9/−9.1/13.7 | 3.5/−7.5/6.7 | 4.8/−8.7/11.1 | ||||
| qPGWC6.1 | 6 | 2.4–3.2 | 4.3/−8.4/10.1 | qPGWC6 | ||||||
| qPGWC6.2 | 6 | 15.0–15.2 | 3.2/−7.7/7.5 | |||||||
| qPGWC7 | 7 | 4.8–5.2 | 5.3/−7.2/11.5 | 4.9/−6.8/8.1 | ||||||
| qPGWC8 | 8 | 19.9–20.3 | 3.4/−7.6/8.8 | qPGWC8b | ||||||
| DEC | qDEC6 | 6 | 22.4–22.8 | 3.3/−6.5/8.1 | ||||||
| qDEC7 | 7 | 4.8–5.2 | 5.3/−5.3/9.5 | 3.8/−5.2/6.8 | ||||||
| qDEC8.1 | 8 | 4.7–5.2 | 4.3/−6.3/9.5 | SSIIIa/Flo5 | ||||||
| qDEC8.3 | 8 | 19.9–20.3 | 4.5/−9.3/11.2 | qDEC8a/qDEC-8 | ||||||
| qDEC10 | 10 | 13.0–13.1 | 15.2/−13.7/33.1 | qDEC10/qPGC10–2 |
GL grain length, GW grain width, LWR length to width ratio, PGWC percentage of grains with chalkiness, DEC degree of endosperm chalkiness
SZ Shenzhen, NJ Nanjing, XZ Xuzhou, JZ Jingzhou, and SY Sanya. The values of LOD, additive effects, and the phenotypic variance explained of each QTLs were separated by “/”. The additive effects were estimated by the substitution the MH63 allele by the 02428 allele in MH63-ILs and 02428 allele by the MH63 allele in 024283-ILs
GS3 (Fan et al. 2006); Chalk5 (Li et al. 2014); qDEC5a, qDEC8a, qDEC10, qPGWC5a and qPGWC8b (Zhao, 2016); qDEC-8 (Wan et al. 2005), qDEC9 (Zhao et al. 2016; Wan et al. 2005); qPGC5-1, qPGC8-1, qPGC10-2 (Sun et al. 2015); qPGWC5 (Tan et al. 2000; Li et al. 2009); qPGWC6 (Tan et al. 2000; Li et al. 2009; Zhao et al. 2016); qDEC5 (Tan et al. 2000; Li et al. 2009); GS5 (Li et al. 2011); GS2 (Hu et al. 2015); GL2 (Che et al. 2015); GIF1 (Wang et al. 2008); OsRab5a (Wang et al. 2010); Flo2 (She et al. 2010); qWB4 (Kobayashi et al. 2013); SSIIIa (Fujita et al. 2007); GL3.1 (Qi et al. 2012; Zhang et al. 2012)