## 3 Results
### QTLs Detected in Three RIL Populations  
A total of 58 QTLs were detected in three RIL populations and distributed on all 12 rice chromosomes, including 22 for NGP, 17 for NSP, and 19 for SF (Table 2). Figure 2: Correlation between different traits using mean value in Teqing/IRBB lines (TI) population (**a**), Zhenshan 97/Milyang 46 (ZM) population (**b**) and Xieqingzao/Milyang 46 (XM) population (**c**). The upper panel contains the correlation coefficients, and the lower panel contains the distributions of the three traits. * and *** represent significant level at 0.05 and 0.001, respectively. \begin{table}
\begin{tabular}{c c c c c c c c c c c c c} \hline \hline  
\begin{table}
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**Tait** & **QTL \({}^{\ast}\)** & **TI Population** & & \multicolumn{6}{c}{**ZM Population**} & \multicolumn{6}{c}{**XM Population**} \\ \hline  & **Interval** & _LOD_ & _A_b [FOOTNOTE:b]Footnote b: A, additive effect of replacing a maternal allele with a paternal allele. \({}^{\ast}\)\(R^{2}\), proportion of phenotypic  
For NGP, 12, 11, and four QTLs were identified in TI, ZM, and XM, respectively. Among them, five QTLs were shared between two populations and 17 were identified in single population (Table 2 and Figure 3a). In TI, \(q\)_NGP2.2_ and \(q\)_NGP3.1_ explained the highest two proportions of phenotypic variance with the value of 20.6% and 11.4%, respectively. The other 10 QTLs had the phenotypic variance explanation ranging from 1.5 to 3.9%, of which three QTLs: \(q\)_NGP1.2_, \(q\)_NGP4_, and \(q\)_NGP5.2_ were shared with ZM. In ZM, \(q\)_NGP1.1_ and \(q\)_NGP6.2_ were revealed to have the highest two \(R^{2}\) of 15.2% and 12.4%, which were also detected in XM. The \(R^{2}\) values of other QTLs were much smaller ranging as 2.5-5.4%. In XM, all four QTLs showed small \(R^{2}\) values ranging from 2.6 to 6.6%. No QTL was found in both of TI and XM. The overall \(R^{2}\) for NGP were much higher in TI and ZM than in XM, which were 59.0%, 56.3%, and 17.4%, respectively. Significant genotype-by-environment (GE) interaction was observed for \(q\)_NGP1.1_ and \(q\)_NGP6.2_ only in ZM (Table S3). For NSP, ten, eight and eight QTLs were detected in TI, ZM and XM, respectively. Among them, one QTL was shared within all three populations, seven QTLs were contributed by two populations and nine QTLs were identified in single population (Table 2 and Figure 3b). \(q\)_NSP5.1_, the only one stably detected in three populations, lay in the interval of RM164-RM18927 on chromosome 5 in TI and showed minor effect in all populations. \(q\)_NSP2.2_ displayed the largest R\({}^{2}\) of 22.1% in TI but nearly the smallest \(R^{2}\) of 2.1% in ZM, indicating divergent effects produced in different genetic background. In ZM, \(q\)_NSP1_ and \(q\)_NSP6.2_ had the highest two R\({}^{2}\) of 15.1% and 13.6%, the other six QTLs had \(R^{2}\) ranging from 2.0 to 4.6%. In XM, \(q\)_NSP1_ also had the highest contribution of 11.1%, and the other seven QTLs had \(R^{2}\) ranging from 2.9 to 6.5%. The overall \(R^{2}\) of the QTLs were 55.9%, 45.8% and 45.1% in TI, ZM and XM, respectively. Except \(q\)_NSP2.3_, \(q\)_NSP10_, and \(q\)_NSP11.2_, all QTLs for NSP were simultaneously shared the same intervals as QTLs for NGP, in accordance with high positive correlation between NGP and NSP in three populations. In addition, one significant GE interaction was found for \(q\)_NSP1_ in ZM (Table S3). For SF, ten, six and five QTLs were identified in TI, ZM and XM, respectively. Only two QTLs were shared between two populations (Table 2 and Figure 3c). \(q\)_SF3.3_ was simultaneously identified in ZM and XM, of which the \(R^{2}\) reached almost the highest with value of 7.4% and 7.6%, respectively. \(q\)_SF6.2_ was detected in TI and ZM, with minor effect to SF in both populations. In TI, \(q\)_SF5.2_ appeared the highest \(R^{2}\) of 13.9% and the remaining 16 QTLs had the \(R^{2}\) ranging from 2.9 to 8.2%. The overall \(R^{2}\) of the QTLs were 51.1%, 27.3% and 30.1% in TI, ZM and XM, respectively.