Table 4. QTLs identified for LLS and plant-type-related traits through single-environment QTL mapping using high density SNP-based map.
| Trait | QTLa | Chr.b | Marker interval | Range (cM) | Env.c | Position | Additived | PVEe (%) | LOD |
|---|---|---|---|---|---|---|---|---|---|
| LLS | qLLSA1-1 | A1 | Ahsnp978-Ahsnp275 | 30.3–33.5 | NC13 | 32.01 | 0.46 | 5.12 | 3.47 |
| qLLSA1-2 | A1 | Ahsnp517-Ahsnp422 | 38–43.4 | NC13 | 39.11 | 0.48 | 5.63 | 3.89 | |
| qLLSA1-3 | A1 | Ahsnp1339-Ahsnp819 | 45.3–52 | WH13 | 46.51 | 0.64 | 5.07 | 2.58 | |
| NC13 | 48.51 | 0.49 | 5.11 | 3.32 | |||||
| qLLSA4-1 | A4 | Ahsnp1681-Ahsnp1897 | 50.4–52.7 | NC13 | 51.51 | 0.52 | 5.29 | 3.66 | |
| qLLSA5 | A5 | Ahsnp1180-Ahsnp78 | 20.6–28.1 | NC13 | 25.81 | 0.38 | 3.64 | 2.56 | |
| qLLSA6-1* | A6 | Ahsnp629-Ahsnp1883 | 11.4–14.6 | NC12 | 13.71 | 0.39 | 3.41 | 2.85 | |
| qLLSA6-2 | A6 | Ahsnp1843-Ahsnp1521 | 19.2–24.2 | WH12 | 21.61 | 0.47 | 4.31 | 2.57 | |
| qLLSA6-3 | A6 | Ahsnp419-Ahsnp418 | 31–35.8 | WH12 | 33.61 | 0.67 | 7.6 | 3.96 | |
| qLLSA8 | A8 | Ahsnp320-Ahsnp919 | 57–76.1 | NC12 | 66.41 | 0.39 | 3.69 | 3.09 | |
| qLLSA10 | A10 | Ahsnp1559-Ahsnp809 | 27.5–31.1 | NC11 | 31.01 | 0.69 | 10.26 | 6.37 | |
| qLLSB1* | B1 | GM1331-Ahsnp1805 | 0–8.8 | WH12 | 4.41 | 0.64 | 8.22 | 5.06 | |
| qLLSB4-1* | B4 | Ahsnp505-Ahsnp471 | 11.4–32.9 | NC11 | 22.54 | 0.52 | 5.75 | 3.38 | |
| qLLSB6-1* | B6 | Ahsnp295-AHGS1422 | 31.8–40.1 | NC11 | 35.36 | 0.74 | 13.89 | 8.17 | |
| qLLSB6-2 | B6 | Ahsnp539-Ahsnp136 | 44.5–47 | NC12 | 45.81 | 0.75 | 11.66 | 8.92 | |
| NC11 | 45.81 | 0.74 | 12.9 | 7.81 | |||||
| qLLSB6-3 | B6 | Ahsnp1070-Ahsnp1665 | 56–57.6 | NC12 | 57.01 | 0.6 | 7.16 | 4.23 | |
| qLLSB6-4 | B6 | Ahsnp676-Ahsnp231 | 62.18–64.62 | NC13 | 63.61 | 0.89 | 18.47 | 10.79 | |
| qLLSB6-5 | B6 | Ahsnp231-AHGS1431 | 64.9–67.8 | WH13 | 65.31 | 0.69 | 6.33 | 2.9 | |
| qLLSB6-6 | B6 | AHGS1431-Ahsnp163 | 68.4–71.5 | NC13 | 71.01 | 0.91 | 19.12 | 11.25 | |
| qLLSB6-7 | B6 | Ahsnp1166-Ahsnp996 | 73.3–78 | WH13 | 74.51 | 1.03 | 14.18 | 6.85 | |
| qLLSB10 | B10 | Ahsnp1458-Ahsnp299 | 5.3–8.6 | NC11 | 7.51 | 0.44 | 4.1 | 2.73 | |
| HMS | qHMSA5-1 | A5 | Ahsnp1180-Ahsnp1133 | 21.6–25.7 | NC13 | 23.71 | -5.64 | 15.28 | 4.88 |
| qHMSA5-2 | A5 | Ahsnp1338-Ahsnp213 | 33.6–38 | NC13 | 35.61 | -4.81 | 10.66 | 3.46 | |
| qHMSA9-1 | A9 | Ahsnp1103-Ahsnp1059 | 0–2.2 | NC13 | 0.01 | -3.91 | 10.73 | 4.98 | |
| qHMSA9-2* | A9 | Ahsnp902-Ahsnp1167 | 71.6–82.2 | WH12 | 73.11 | -3.08 | 5.39 | 3.06 | |
| WH13 | 75.11 | -3.36 | 5.22 | 2.68 | |||||
| qHMSA10-1 | A10 | Ahsnp77-Ahsnp787 | 7.8–8.8 | WH12 | 7.91 | -3.22 | 5.26 | 2.98 | |
| qHMSA10-2 | A10 | Ahsnp712-GM692 | 14.4–19.9 | WH12 | 17.81 | -3.31 | 6.14 | 3.49 | |
| qHMSB2 | B2 | Ahsnp1331-Ahsnp1308 | 1.6–12.1 | NC13 | 5.01 | 3.97 | 8.94 | 4.24 | |
| qHMSB3-1 | B3 | Ahsnp586-Ahsnp1194 | 48–52.2 | WH13 | 50.21 | -3.39 | 5.39 | 2.93 | |
| qHMSB3-2* | B3 | Ahsnp1236-Ahsnp1549 | 59.7–61.8 | WH13 | 60.81 | -4.02 | 7.99 | 4.63 | |
| qHMSB6* | B6 | Ahsnp227-Ahsnp295 | 12.1–32.3 | WH13 | 24.11 | -3.22 | 4.76 | 2.78 | |
| LLB | qLLBA9-1 | A9 | Ahsnp1103-Ahsnp1059 | 0–2.4 | NC13 | 0.01 | -3.7 | 10.59 | 5.09 |
| qLLBA9-2 | A9 | Ahsnp902-Ahsnp1167 | 72.2–82.2 | WH13 | 77.11 | -4.05 | 5.55 | 2.75 | |
| WH12 | 77.11 | -5 | 11.45 | 5.8 | |||||
| qLLBB1 | B1 | Ahsnp966-Ahsnp1373 | 28.2–31.1 | WH12 | 30.91 | -3.61 | 5.17 | 3.02 | |
| qLLBB3 | B3 | Ahsnp1236-Ahsnp1549 | 59.3–61.8 | WH13 | 60.81 | -3.61 | 4.73 | 2.68 | |
| qLLBB6* | B6 | Ahsnp227-Ahsnp295 | 16.6–31.1 | WH12 | 27.81 | -2.93 | 4 | 2.55 | |
| qLLBB8-1 | B8 | AHGS1388-Ahsnp1644 | 11.5–16 | NC12 | 14.71 | -2.86 | 6.86 | 3.25 | |
| qLLBB8-2* | B8 | Ahsnp779-Ahsnp732 | 62.6–73.4 | WH12 | 66.31 | -3.25 | 4.28 | 2.71 | |
| TNB | qTNBA3 | A3 | Ahsnp965-Ahsnp1014 | 35.7–39.2 | WH12 | 36.81 | -1.78 | 6.19 | 3.25 |
| qTNBA5 | A5 | Ahsnp926-Ahsnp236 | 15.7–17.8 | WH12 | 17.51 | -1.78 | 5.22 | 2.87 | |
| qTNBA6-1 | A6 | Ahsnp418-AHGS0153 | 37.2–43.6 | WH12 | 42.11 | 1.8 | 4.59 | 2.66 | |
| qTNBA6-2 | A6 | Ahsnp19-Ahsnp1889 | 51.5–57.5 | WH12 | 55.51 | 1.97 | 6.05 | 2.87 | |
| qTNBA8* | A8 | Ahsnp1305-Ahsnp1244 | 23.4–41.9 | NC12 | 32.71 | -2.32 | 5 | 2.76 | |
| NC13 | 28.41 | -1.63 | 5.34 | 3.06 | |||||
| NC13 | 40.71 | -1.6 | 4.96 | 2.7 | |||||
| qTNBA10 | A10 | ARS775-Ahsnp1387 | 0–6.8 | NC12 | 0.01 | -2.61 | 6.96 | 3.81 | |
| qTNBB1* | B1 | GM1331-Ahsnp642 | 0–2 | WH13 | 0.01 | -2.67 | 5.58 | 3.3 | |
| qTNBB3 | B3 | AHGS1201-AHGS2526 | 12.6–25.9 | WH13 | 17.51 | 3.98 | 5.32 | 3.56 | |
| qTNBB4-1 | B4 | Ahsnp781-Ahsnp1160 | 46.8–47.8 | WH13 | 46.81 | -2.88 | 5.76 | 3.4 | |
| qTNBB4-2 | B4 | Ahsnp207-Ahsnp232 | 54.7–56.6 | WH13 | 55.61 | -3.29 | 9.54 | 5.82 | |
| qTNBB4-3 | B4 | Ahsnp282-Ahsnp1066 | 64.9–68.3 | WH13 | 67.81 | -3.67 | 11.85 | 6.48 | |
| qTNBB6-1 | B6 | Ahsnp425-Ahsnp349 | 48.9–62.2 | NC13 | 54.51 | -2.32 | 9.8523 | 4.77 | |
| qTNBB6-2 | B6 | Ahsnp1309-Ahsnp64 | 62.6–65 | WH13 | 63.61 | -3.58 | 10.35 | 5.92 | |
| qTNBB6-3* | B6 | AHGS1431-Ahsnp690 | 69.5–71.5 | NC13 | 71.01 | -2.05 | 8.1 | 4.74 | |
| WH13 | 71.01 | -4.05 | 13.44 | 7.95 | |||||
| qTNBB8 | B8 | Ahsnp1700-Ahsnp1055 | 10.1–14.2 | WH12 | 10.81 | -2.05 | 7.55 | 4.16 |
a The nomination of QTL is comprised of four parts. The first part “q” stands for QTL. The second part is the abbreviation of traits. The third part, the number stands for chromosome. The fourth part is the serial number of QTL on the same chromosome. The names followed by * were QTLs simultaneously detected by joint QTL analysis among all environments.
b Chr. indicates chromosome.
c Env. indicates environment. NC11, NC12, NC13 WH12 and WH13 represent Nanchong in 2011, Nanchong in 2012, Nanchong in 2013, Wuhan in 2012 and Wuhan 2013, respectively.
d.Additive effect of the QTL.
e The phenotypic variation explained of corresponding QTL.