Table 2.
Quantitative trait loci for seed coat deficiency (SCD) in the mapping populations
| Popa | Envb | QTL namec | Position (cM) | Chrd | Flanking markerse | GI (cM)f | Wm82.a2.v1 Physical interval (bp)g | LODh | PVE(%)i | Addj | Methodk |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Pop 1 | 2016 | qSCD14 | 28 | 14 | Gm14_6024101-Gm14_4956317 | 26.5–29.5 | 6,135,158–5,040,727 | 3.4 | 4.6 | − 1.9 | CIM |
| qSCD15 | 12 | 15 | Gm15_511387-Gm15_4751337 | 8.5–13.5 | 511,864–4,770,814 | 4.5 − 6.1 | 6.6 − 10.1 | − 2.8 to − 2.9 | CIM, IM, SMA | ||
| qSCD20 | 48 | 20 | Gm20_35625615-Gm20_36002148 | 46.5–50.5 | 36,720,824–37,097,315 | 7.3 − 8.4 | 7.5 − 11.3 | − 3.0 to − 3.1 | CIM, IM, SMA | ||
| 2017 | qSCD3 | 4 | 3 | Gm03_241447-Gm03_715393 | 0–8.5 | 239,949–714,448 | 4.5 − 7.2 | 4.2 − 5.3 | − 4.4 to − 6.1 | CIM, IM, SMA | |
| qSCD10 | 25 | 10 | Gm10_11518881-Gm10_26188429 | 22.5–25.5 | 11,710,604–16,707,334 | 3.4 − 4.5 | 4.1 − 5.0 | − 4.3 to − 6.1 | CIM, IM, SMA | ||
| qSCD15 | 23 | 15 | Gm15_5312718-Gm15_6066709 | 22.5–23.5 | 5,331,364–6,085,794 | 5.0 − 5.7 | 5.3 − 7.0 | − 5.0 to − 6.9 | CIM, IM, SMA | ||
| qSCD20 | 45 | 20 | Gm20_34881595-Gm20_35625615 | 44.5–46.5 | 36,021,058–36,720,824 | 14.1 − 15.2 | 12.2 − 23.8 | − 9.3 to − 10.4 | CIM, IM, SMA | ||
| 2018 | qSCD5 | 98 | 5 | Gm05_36671535-Gm05_41740936 | 95.5–98 | 36,962,030–38,597,425 | 3.1 | 4.9 | − 2.7 | CIM | |
| qSCD6 | 51 | 6 | Gm06_17258654-Gm06_38499465 | 46.5–56.5 | 17,303,937–39,188,086 | 5.5 − 5.9 | 9.3 − 9.5 | − 3.6 to − 4.6 | CIM, IM, SMA | ||
| qSCD7 | 72 | 7 | Gm07_17030454-Gm07_16979586 | 71.5–72.5 | 17,116,283–17,065,562 | 3.1 | 4.8 | − 2.6 | CIM | ||
| qSCD15 | 23 | 15 | Gm15_5312718-Gm15_6066709 | 22.5–23.5 | 5,331,364–6,085,794 | 6.3 − 7.4 | 10.2 − 10.4 | − 3.7 to − 4.9 | CIM, IM, SMA | ||
| qSCD20 | 52 | 20 | Gm20_36002148-Gm20_36095037 | 51.5–52.5 | 37,097,315–37,190,252 | 6.1 − 6.7 | 9.4 − 9.7 | − 3.7 to − 4.7 | CIM, IM, SMA | ||
| AVE | qSCD6 | 51 | 6 | Gm06_17258654-Gm06_38499465 | 46.5–56.5 | 17,303,937–39,188,086 | 5.2 − 7.3 | 7.3 − 7.8 | − 3.0 to − 4.7 | CIM, IM, SMA | |
| qSCD10 | 26 | 10 | Gm10_23967467-Gm10_12080275 | 22.5–27.5 | 20,275,514–12,272,454 | 3.1 − 3.8 | 3.8 | − 3.3 | IM, SMA | ||
| qSCD14 | 30 | 14 | Gm14_5603904-Gm14_5655487 | 29.5–30.5 | 5,714,996–5,766,579 | 2.9 | 3.5 | − 2.1 | CIM | ||
| qSCD15 | 23 | 15 | Gm15_5312718-Gm15_6066709 | 22.5–23.5 | 5,331,364–6,085,794 | 7.3 − 7.8 | 7.5 − 9.5 | − 3.5 to − 4.6 | CIM, IM, SMA | ||
| qSCD20 | 52 | 20 | Gm20_36002148-Gm20_36095037 | 51.5–52.5 | 37,097,315–37,190,252 | 13.7 − 15.1 | 12.9 − 20.8 | − 5.1 to − 6.0 | CIM, IM, SMA | ||
| Pop 2 | 2016 | qSCD1_1 | 15 | 1 | Gm01_1887205-Gm01_49322760 | 13.5–16.5 | 1,887,609–50,206,347 | 4.6 | 5.3 | − 4.3 | IM, SMA |
| qSCD1_2 | 25 | 1 | Gm01_1653315-Gm01_50262496 | 24.5–26.5 | 1,653,600–51,147,675 | 5.4 − 7.2 | 6.8 − 17.4 | − 3.7 to − 5.2 | CIM, IM, SMA | ||
| qSCD1_3 | 50 | 1 | Gm01_31906055-Gm01_7052156 | 46.5–55.5 | 33,203,133–7,071,117 | 4.9 | 4.1 | − 3.9 | IM, SMA | ||
| qSCD13 | 21 | 13 | Gm13_29677928-Gm13_28206014 | 20.37–22.37 | 30,875,555–29,399,384 | 5.5 | 4.3 | − 3.8 | IM, SMA | ||
| qSCD15 | 6 | 15 | Gm15_5312718-Gm15_6272006 | 5.5–6.5 | 5,331,364–6,291,081 | 4.8 | 3.9 | − 4.1 | IM, SMA | ||
| qSCD18_1 | 21 | 18 | Gm18_15324039-Gm18_7348168 | 20.5–21.5 | 15,066,204–7,370,390 | 4.1 | 3.3 | − 3.5 | IM, SMA | ||
| qSCD20 | 32 | 20 | Gm20_35625615-Gm20_36002148 | 29.5–36.5 | 36,720,824–37,097,315 | 4.7 | 3.6 | − 3.7 | IM, SMA | ||
| 2017 | qSCD1_3 | 51 | 1 | Gm01_31906055-Gm01_7052156 | 48.5–55.5 | 33,203,133–7,071,117 | 4.0 − 5.5 | 4.8 − 14.0 | − 6.7 to − 8.6 | CIM, IM, SMA | |
| qSCD15 | 5 | 15 | Gm15_5312718-Gm15_6272006 | 1.5–7.5 | 5,331,364–6,291,081 | 4.9 | 3.9 | − 8.3 | IM, SMA | ||
| qSCD16 | 2 | 16 | Gm16_103052-Gm16_1755870 | 0–7.5 | 102,882–1,772,720 | 4.2 | 3.6 | − 7.5 | IM, SMA | ||
| qSCD18_2 | 5 | 18 | Gm18_122382-Gm18_1308443 | 0–5.5 | 122,380–1,308,798 | 5.5 | 4.9 | − 8.5 | IM, SMA | ||
| qSCD19 | 67 | 19 | Gm19_41918030-Gm19_50486916 | 65.5–68.5 | 42,120,908–50,607,336 | 5.3 | 5.8 | − 9.5 | IM, SMA | ||
| qSCD20_2 | 18 | 20 | Gm20_26785339-Gm20_25063646 | 15.5–21.5 | 27,947,431–26,214,468 | 4.8 | 3.8 | − 8.0 | IM, SMA | ||
| qSCD20 | 33 | 20 | Gm20_36095037-Gm20_36153048 | 31.5–34.5 | 37,190,252–37,248,263 | 4.1 − 5.4 | 4.3 − 13.8 | − 6.8 to − 8.4 | CIM, IM, SMA | ||
| 2018 | qSCD15 | 5 | 15 | Gm15_5312718-Gm15_6272006 | 2.5–6.5 | 5,331,364–6,291,081 | 3.8 | 10.4 | − 5.1 | CIM, IM, SMA | |
| AVE | qSCD1_2 | 25 | 1 | Gm01_1653315-Gm01_50262496 | 24.5–26.5 | 1,653,600–51,147,675 | 3.6 | 3.1 | − 5.0 | IM, SMA | |
| qSCD1_3 | 50 | 1 | Gm01_31906055-Gm01_7052156 | 46.5–55.5 | 33,203,133–7,071,117 | 4.2 − 6.0 | 4.1 − 15.5 | − 4.5 to − 5.6 | CIM, IM, SMA | ||
| qSCD15 | 5 | 15 | Gm15_5312718-Gm15_6272006 | 2.5–6.5 | 5,331,364–6,291,081 | 4.9 | 3.1 | − 5.3 | IM, SMA | ||
| qSCD20_2 | 12 | 20 | Gm20_827937-Gm20_12318232 | 7.5–14.5 | 824,049–8,318,718 | 5.7 | 4.3 | − 5.8 | IM, SMA | ||
| qSCD20 | 33 | 20 | Gm20_36095037-Gm20_36153048 | 31.5–34.5 | 37,190,252–37,248,263 | 4.9 | 3.0 | − 5.0 | IM, SMA |
Bold letters or values are QTLs names or the least or the maximum percentage of variance explained by corresponding QTL, respectively, mentioned in the text
aPop 1 and Pop 2 were developed from the crosses of V11-0883 × V12-1626 and V11-0883 × V12-1885, respectively
bEnv: the individual years and across years (AVE) in which the QTL was detected
cThe name of each QTL is a composite of SCD followed by the chromosome number, QTLs detected in different methods with the same or overlapping maker interval were designated as on QTL
dChr: chromosome
eFlanking markers: the markers flanking the QTL
fGI: genetic interval
gPhysical interval according to genome position at Wm82.a2.v
hLOD: logarithm of odds, data showed the range of the values detected across methods
iPVE: percentage of variance explained, data showed the range of the values detected across methods
jAdd: additive effect, data showed the range of the values detected across methods
kMethods: by which the QTL was detected, data presented were the range of different methods