## 3 Results
### QTLs Detected in Ti52-2 Population  
A total of five, three and four QTLs for NGP, NSP, and SF were detected in Ti52-2 population, respectively and distributed on rice chromosome 3, 5, 6, 9, 11 and 12 (Table 3). No significant GE interaction was observed.  
Figure 3: Number of QTLs detected in three RIL populations for NGP (**a**), NSP (**b**) and SF (**c**), respectively.  
Ti52-2 was derived from TI carrying 13 segregating regions (Figure 4). In Ti52-2, those regions involving QTLs with major effects for NGP, NSP, and SF in TI and other two RIL populations had become homozygous, such as RG532-RM151 interval containing \(qNGP1.1\) and \(qNSP1\), RM6-RM240 interval containing \(qNGP2.2\) and \(qNSP2.2\), RM15303-RM16 interval containing \(qNGP3.1\) and \(qSF3.1\), RM276-RM549 interval containing \(qNGP6.2\) and \(qNSP6.2\), RM18038-RM18189 interval containing \(qSF5.2\). Therefore, Ti52-2 is a good candidate to detect minor-effect QTL for NGP, NSP, and SF.  
\begin{table}
\begin{tabular}{c c c c c c} \hline
**Trait** & **QTL** & **Interval** & **LOD** & \(A\)a ** & \(R^{2}\) (\%)b  \\ \hline NGP & \(qNGP3.3\) & RM232 & 3.2 & 2.29 & 4.1 \\  & \(qNGP5.5\) & RM18927-RM3321 & 4.1 & \(-\)2.46 & 4.9 \\  & \(qNGP6.1\) & RM469-RM589 & 5.8 & 2.31 & 9.9 \\  & \(qNGP9.1\) & RM5688-RM219 & 3.5 & \(-\)2.18 & 5.6 \\  & \(qNGP12.1\) & Pita-RM511 & 3.1 & 2.19 & 4.8 \\ \hline NSP & \(qNSP3.2\) & RM232 & 2.6 & 1.89 & 2.2 \\  & \(qNSP5.4\) & RM18927-RM3321 & 5.5 & \(-\)3.44 & 5.3 \\  & \(qNSP12\) & RM3246-Pita & 6.8 & 3.73 & 7.8 \\ SF & \(qSF3.4\) & RM14303-RM14383 & 3.8 & 0.53 & 7.3 \\ \hline  & \(qSF6.1\) & RM587-RM584 & 7.8 & 1.08 & 16.3 \\  & \(qSF9.2\) & RM5688-RM219 & 6.1 & \(-\)0.98 & 11.3 \\  & \(qSF11\) & RM224-RM5926 & 6.0 & 0.97 & 9.0 \\ \hline \end{tabular}
\end{table}
Table 3: QTLs detected for NGP, NSP, and SF in Ti52-2 population.  
Figure 4: Distribution of QTLs for NGP, NSP, and SF detected in Ti52-2 and TI populations.  
Both of _qNGP9.1_ and _qNGP9.1_ were validated in Ti52-2 and the direction of additive effects remained unchanged between TI and Ti52-2. Moreover, the \(R^{2}\) increased from 1.6 to 5.6% and 3.9 to 4.8%, respectively. In TI, _qNGP5.4_ was detected in the interval of RM274\(-\)RM334 on chromosome 5 and the IRBB52 allele increased NGP 3.81. In Ti52-2, the locus of RM334 had got homozygous, while RM274 remained be segregating. However, a QTL was found in the interval of RM18927\(-\)RM3321 upstream of _qNGP5.4_ with the TQ allele increasing NGP 2.46. Hence, the new QTL was named _qNGP5.5_. Among the five QTLs for NGP detected in Ti52-2, _qNGP6.1_ with the highest \(R^{2}\) was undetected previously in TI but mapped in the similar interval of RM508\(-\)RM190 in ZM, while _qNGP3.3_ with the lowest \(R^{2}\) was not identified in previous three RIL populations.  
Amid of the three QTLs for NSP detected in Ti52-2, _qNSP12_ was validated with the largest \(R^{2}\) of 7.8% and the enhancing allele was from IRBB52 in both TI and Ti52-2. _qNSP5.4_, a new QTL with an allelic effect in opposite direction to _qNSP5.3_ in the interval of RM274\(-\)RM334 detected in TI, was detected in the RM18927\(-\)RM3321 region. In addition, _qNSP3.2_ having the marginal LOD threshold and the smallest \(R^{2}\) was not previously detected in TI, ZM and XM.  
Out of the four QTLs for SF detected in Ti52-2, _qSF6.1_ with the highest \(R^{2}\) of 16.3% was mapped in RM586\(-\)RM584 region, which was undetected in TI and lay in a similar interval of RM190\(-\)RZ516 detected in XM. The others, _qSF9.2, _qSF3.4_, and _qSF11_, were not identified previously in three RIL populations. Either position or additive effect direction of _qSF9.2_ was different from _qSF9_ identified in ZM. Thus _qSF9.2_ was a new QTL and _qSF9_ was renamed as _qSF9.1_.