Table 4. QTL detected in the two backcross introgression populations (Ce258-BILs and ZGX1-BILs) in 2009 in Nanning (NN09) and in 2010 in Sanya (SY10).
LOD(A) and LOD(AE) indicate LOD values for additive effects and additive by environment effects, respectively; PVE(A) and PVE(AE), phenotypic variances explained by additive effects and additive by environment effects, respectively; A, AE1 and AE2 indicate the additive effects and the additive by environment effects detected at NN09 and SY10, respectively.
| Ce258–BILs | ZGX1–BILs | Previously reported QTL or genes 5) | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Trait | QTL 1) | Chr. | Marker region 2) | LOD 3) (A) | LOD(AE) | PVE(A) | PVE(AE) | A 4) | AE1 | AE2 | LOD(A) | LOD(AE) | PVE(A) | PVE(AE) | A | AE1 | AE2 | |
| Fe | qFe1 # | 1 | RM302–RM486 | 7.4 | 8.0 | 0.706 | OsYSL18 [44] | |||||||||||
| qFe2 | 2 | RM154–RM211 | 5.4 | 7.5 | 0.271 | qFe2–1 [24] | ||||||||||||
| qFe6 # | 6 | RM3–RM340 | 9.8 | 5.0 | 18.3 | 10.9 | 0.633 | 0.315 | –0.338 | 6.7 | 10.2 | –0.134 | qFe6 [26] | |||||
| qFe7 # | 7 | RM134–RM1132 | 2.8 | 9.9 | 6.3 | 16.7 | 0.449 | –0.114 | 0.114 | |||||||||
| qFe11 & | 11 | RM441–RM202 | 4.5 | 5.5 | –0.127 | |||||||||||||
| Zn | qZn3 # | 3 | RM293–RM85 | 16.3 | 14.4 | 1.061 | 12.0 | 11.1 | 0.108 | |||||||||
| qZn6 # | 6 | RM3–RM340 | 31.7 | 24.8 | 1.743 | 4.6 | 7.3 | –0.562 | ||||||||||
| qZn7 # | 7 | RM134–RM1132 | 2.2 | 2.0 | 1.621 | 14.5 | 7.0 | 1.036 | LOC_Os07g43040 [17] | |||||||||
| qZn8 # | 8 | RM407–RM152 | 7.6 | 8.4 | 18.0 | 24.9 | 0.980 | 1.151 | –1.151 | 12.3 | 11.2 | 3.113 | qZn8–1 [24]; qZn8b [26]; qZn8 [25] | |||||
| qZn12 # | 12 | RM1337–RM3409 | 12.2 | 12.2 | 0.907 | qZn12–1 [24] | ||||||||||||
| Cd | qCd1 # | 1 | RM462–RM428 | 10.1 | 7.2 | –0.011 | 6.5 | 4.1 | 0.002 | |||||||||
| qCd3a | 3 | RM1324–RM489 | 8.3 | 11.2 | –0.003 | Segment_on_Chr3_for_Cd [[29]; OsNRAMP2 [45]; OsARD2 [46] | ||||||||||||
| qCd3b # , & | 3 | RM293–RM227 | 1.2 | 1.1 | 0.007 | 4.3 | 5.2 | –0.005 | qCdc3 [15] | |||||||||
| qCd4 | 4 | RM348–RM280 | 6.4 | 8.8 | 0.003 | qCd4–2 [49]; OsZIP3 [[50] | ||||||||||||
| qCd6 # | 6 | RM136–RM3 | 1.7 | 9.4 | 1.7 | 2.6 | 0.004 | –0.007 | 0.007 | 7.2 | 9.9 | –0.019 | Segment_on_Chr6_for_Cd [29]; OsLCT1 [41] | |||||
| qCd8 # | 8 | RM506–RM407 | 6.0 | 7.5 | 0.005 | 3.5 | 3.4 | 0.006 | Segment_on_Chr8_for_Cd [29] | |||||||||
| qCd11 & | 11 | RM332–RM441 | 2.9 | 2.6 | 1.7 | 0.7 | 0.011 | 0.009 | –0.009 | qCCBR–11a [51]; LOC_Os11g07980 [17] | ||||||||
| Pb | qPb4 # | 4 | RM241–RM280 | 18.8 | 8.8 | 0.009 | OsYSL13, OsYSL16 [47]; OsYSL12 [48] | |||||||||||
| qPb7 # | 7 | RM336–RM134 | 12.2 | 35.1 | –0.019 | 4.6 | 4.5 | 0.008 | LOC_Os07g43040 [17] | |||||||||
| qPb8a & | 8 | RM408–RM310 | 14.4 | 13.2 | –0.003 | 6.8 | 7.2 | 0.009 | ||||||||||
| qPb8b & | 8 | RM80–RM447 | 5.1 | 4.9 | 0.031 | 7.8 | 5.9 | 0.004 | ||||||||||
| qPb12 | 12 | RM20–RM4A | 19.2 | 16.5 | 0.011 | qPb12–2 [14] | ||||||||||||
QTL with symbols ‘#’ and ‘&’ are those stably detected in both the NN09 and SY10 environments in the Ce258 and ZGX1 backgrounds, respectively. Loci that passed the main-effect QTL confirmation test (See step 3 in the Materials and Methods) in at least one background are shown in bold.
Underlined markers are those closer to putative QTL.
Underlined numbers are the parameters of the QTL detected under the sub-threshold of 1.2 ≤ LOD ≤ the threshold estimated by permutation test as described in the Materials and Methods.
Additive effects resulting from the substitution of ZGX1 or Ce258 alleles by IR75862 alleles
Numbers in brackets are reference codes, as listed in the reference section.