Supplementary Fig. 1 Genetic linkage map for the IL population developed from the cross Sasanishiki×Habataki showing location of quantitative trait loci for tiller number and effective panicle.
Supplementary Fig. 1
Supplementary Table 1 Analysis of variance (F value) and broad-sense heritability (%) of the mean performance for tiller number and effective panicle of the set of ILs across three environments (E1, E2 and E3).
Lines b / 37 / 2.28** / 5.57** / 28.07** / 20.63** / 13.10** / 21.11**
Environments / 2 / 6.23** / 48.49** / 610.81** / 1053.46** / 956.78** / 201.77**
Lines x Environments / 74 / 2.41** / 4.58** / 15.01** / 11.20** / 4.51** / 5.18**
Broad-sense heritability (%) d
E1 / 51.96 / 29.87 / 75.32 / 71.64 / 63.37 / 81.98
E2 / 21.48 / 46.81 / 93.17 / 85.13 / 71.71 / 59.87
E3 / 55.23 / 79.2 / 90.45 / 92.01 / 82.24 / 88.92
Joint environments / 10.71 / 18.23 / 21.96 / 14.09 / 11.63 / 36.91
a. SOD, sources of difference
b. **Significance levels of 0.01
c. DAT, days after transplanting
d.. Broad-sense heritability (%) in ILs in each environment separately and across three environments taken together.
Supplementary Table 2 Correlation coefficients between tiller number (15 DAT, 22 DAT, 29 DAT, 36 DAT and 43 DAT) and effective panicle in E1, E2 and E3, respectively.
Environment / 15 DAT a / 22 DAT / 29 DAT / 36 DAT / 43 DATE1 / 0.308 / 0.167 / 0.363* / 0.678** / 0.440**
E2 b / 0.397* / 0.457* / 0.401* / 0.418* / 0.629**
E3 / 0.313 / 0.357* / 0.597** / 0.702** / 0.803**
a. DAT, days after transplanting
b. *Significance levels of 0.05, **Significance levels of 0.01
Supplementary Table 3 Quantitative trait loci (QTLs) for tiller number in the IL population in E1
QTL a / Chr. / Flanking markers / IL / 15 DAT b / 22DAT / 29 DAT / 36 DAT / 43 DATLOD c / Add(a) d / PVE(%) e / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%)
qTN1.2 / 1 / RM7124-RM1297 / SL402 / 3.418 / -0.185 / 7.068
qTN1.3 / 1 / RM6581-RM7600 / SL403 / 4.977 / -0.235 / 11.4 / 8.886 / -0.695 / 7.361
qTN1.4 / 1 / RM1387-RM8137 / SL404 / 4.977 / -0.235 / 11.4
qTN2.1 / 2 / RM2770-RM7562 / SL405 / 4.691 / -0.836 / 7.768
qTN2.3 / 2 / RM1211-RM3858 / SL407 / 5.388 / -0.249 / 5.52 / 14.986 / 1.1 / 25.56
qTN4.1 / 4 / RM7585-RM5633 / SL412 / 11.828 / 0.476 / 10.405 / 7.441 / 0.605 / 5.567
qTN4.2 / 4 / RM3534-RM2431 / SL414 / 6.873 / 1.089 / 13.19 / 14.581 / 1.206 / 15.792
qTN6 / 6 / RM1370-RM5463 / SL421 / 6.415 / -1.036 / 11.93 / 16.862 / -1.295 / 25.547 / 8.272 / -0.719 / 5.613
qTN7.1 / 7 / RM4584-RM7479 / SL422 / 8.309 / 0.351 / 5.662
qTN7.2 / 7 / RM1364-RM7601 / SL424 / 3.877 / -0.2 / 8.259
qTN10.1 / 10 / RM3882-RM4455 / SL431 / 3.377 / 0.661 / 9.444
qTN11.2 / 11 / RM2191-RM2064 / SL436 / 9.271 / 0.627 / 11.663
a. Individual QTLs are shown with the italic abbreviation of the trait and the chromosome number.
b. DAT, days after transplanting.
c. Threshold values of logarithm of odds (LOD) for panicle related traits.
d. Additive effect, a positive value indicates superiority of Habataki allele.
e. % of variance explained.
Supplementary Table 4 Quantitative trait loci (QTLs) for tiller number in the IL population in E2
QTL a / Chr. / Flanking markers / IL / 15 DAT b / 22DAT / 29 DAT / 36 DAT / 43 DATLOD c / Add(a) d / PVE(%) e / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%)
qTN2.3 / 2 / RM1211-RM3858 / SL407 / 5.948 / 0.518 / 17.012 / 4.879 / 0.931 / 16.858 / 6.657 / 2.481 / 29.184 / 15.415 / 2.877 / 48.759 / 6.394 / 1.446 / 13.624
qTN4.2 / 4 / RM3534-RM2431 / SL414 / 4.822 / 1.356 / 6.152
qTN5.2 / 5 / RM7118-RM6742 / SL416 / 4.355 / -1.267 / 5.374
qTN8 / 8 / RM5767-RM5891 / SL427 / 3.267 / 0.993 / 6.424
qTN10.2 / 10 / RM3882-RM4455 / SL431 / 5.49 / 0.501 / 15.926 / 3.139 / 0.968 / 6.099
a. Individual QTLs are shown with the italic abbreviation of the trait and the chromosome number.
b. DAT, days after transplanting.
c. Threshold values of logarithm of odds (LOD) for panicle related traits.
d. Additive effect, a positive value indicates superiority of Habataki allele.
e. % of variance explained
Supplementary Table 5 Quantitative trait loci (QTLs) for tiller number in the IL population in E3
QTL a / Chr. / Flanking markers / IL / 15 DAT b / 22DAT / 29 DAT / 36 DAT / 43 DATLOD c / Add(a) d / PVE(%) e / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%) / LOD / Add(a) / PVE(%)
qTN1.1 / 1 / RM6887-RM3233 / SL401 / 3.524 / -1.347 / 5.927
qTN1.3 / 1 / RM6581-RM7600 / SL403 / 3.223 / -0.437 / 5.237 / 5.168 / -1.722 / 9.686
qTN2.1 / 2 / RM2770-RM7562 / SL405 / 6.219 / -1.62 / 12.517 / 7.137 / -2.697 / 18.306 / 3.882 / -2.409 / 11.423 / 4.172 / -1.497 / 7.32
qTN2.2 / 2 / RM5699-RM1234 / SL406 / 3.611 / -0.468 / 6.019 / 4.371 / -1.274 / 7.743 / 5.74 / -2.279 / 13.069
qTN2.3 / 2 / RM1211-RM3858 / SL407 / 2.702 / 1.067 / 7.236
qTN4.2 / 4 / RM3534-RM2431 / SL414 / 6.619 / 2.048 / 13.688
qTN5.1 / 5 / RM1248-RM6517 / SL415 / 6.128 / 0.663 / 12.07
qTN7.2 / 7 / RM1364-RM7601 / SL424 / 2.653 / 1.914 / 7.21 / 3.23 / 1.278 / 5.329
qTN8 / 8 / RM5767-RM5891 / SL427 / 3.022 / 1.701 / 11.079
qTN9 / 9 / P414D03-RM7481 / SL429 / 2.824 / 0.43 / 5.246
qTN10.2 / 10 / RM1859-RM6737 / SL432 / 4.5 / 0.538 / 7.947 / 5.332 / 1.455 / 10.108
qTN11.1 / 11 / RM286-RM7283 / SL434 / 4.393 / 1.28 / 7.823
qTN12 / 12 / Bb77A02-RM3747 / SL437 / 5.191 / 1.728 / 9.744
a. Individual QTLs are shown with the italic abbreviation of the trait and the chromosome number.
b. DAT, days after transplanting.
c. Threshold values of logarithm of odds (LOD) for panicle related traits.
d. Additive effect, a positive value indicates superiority of Habataki allele.
e. % of variance explained.
Supplementary Table 6 QTL analysis for tiller number and effective panicle by F2 progeny of a cross between SL414 and Sasanishiki
Trait / Marker interval / LOD b / Add c / PVE(%) dTiller number (43 DAT) a / RM5478-RM2431 / 3.32 / 2.34 / 14.47
Effective panicle / RM5478-RM2431 / 3.99 / 2.67 / 19.13
a. DAT, days after transplanting
b. Threshold values of logarithm of odds (LOD) for panicle related traits.
c. Additive effect, a positive value indicates superiority of Habataki allele.
d. % of variance explained.