## 2 Results
### Fine Mapping and Candidate Gene Analysis of the Strong Culm and Lodging Resistance QTL \(q\)SCM4  
The strong culm and lodging resistance QTL \(q\)SCM4 was localized in the 1.53 Mb range by multi-year (Figure 2a, Table 2). A fine mapping of \(q\)SCM4 was performed using a RHL derived segregating population containing 1781 single plants, whose progeny segregated as strong culms (1317) and weak culms (464) = 2.84:1.00 (\(\chi^{2}\) = 0.4593, \(p>0.05\)) conforming to a 3:1 segregation ratio. Combining the four newly-developed polymorphic molecular markers in the target region narrowed the localization of \(q\)SCM4 from 1.53 Mb to 320.6 kb between SSR1-RMS511 (Figure 2c). Using the constructed BC\({}_{3}\)F\({}_{2}\) backcrossing segregation populations containing 3216 individuals, the physical interval of \(q\)SCM4 was finally narrowed to 58.5 kb by the screening of key recombinant individuals combined with phenotypic identification (Figure 2d).  
\begin{table}
\begin{tabular}{l l l l l l l l l} \hline
**Groups** & **Location** & **Trait** & **Year** & **Chr. a** & **Interval** & **LOD b** & **Add. c** & **Var (\%) d** \\ \hline F2 & Shenyang & BS & 2008 & 4 & RM470– & 4.80 & \(-\)160 & 23.4 \\ F2 & Shenyang & CT & 2008 & 4 & RM470– & 3.19 & \(-\)0.11 & 20.8 \\ F2 & Shenyang & CD & 2008 & 4 & RM470– & 3.34 & \(-\)0.15 & 16.2 \\ F2 & Shenyang & GPP & 2008 & 4 & RM470– & 3.21 & \(-\)6.1 & 16.8 \\ F2 & Shenyang & PBN & 2008 & 4 & RM470– & 5.90 & \(-\)1.6 & 26.4 \\ F2 & Shenyang & SBN & 2008 & 4 & RM470– & 3.40 & \(-\)2.5 & 16.1 \\ RILs & Shenyang & BS & 2010 & 4 & RM225– & 5.21 & \(-\)135 & 31.5 \\ RILs & Shenyang & CT & 2010 & 4 & RM225– & 4.12 & \(-\)0.18 & 24.5 \\ RILs & Shenyang & CD & 2010 & 4 & RM349 & 4.36 & \(-\)0.11 & 20.5 \\ RILs & Shenyang & GPP & 2010 & 4 & RM225– & 3.21 & \(-\)12.12 & 14.6 \\ RILs & Shenyang & PBN & 2010 & 4 & RM225– & 13.34 & \(-\)1.1 & 43.2 \\ RILs & Shenyang & SBN & 2010 & 4 & RM225– & 4.56 & \(-\)5.47 & 26.6 \\ RILs & Harbin & BS & 2012 & 4 & RM225– & 3.92 & \(-\)157 & 28.7 \\ RILs & Harbin & CT & 2012 & 4 & RM225– & 4.12 & \(-\)0.18 & 24.5 \\ RILs & Harbin & CD & 2012 & 4 & RM225– & 3.76 & \(-\)0.14 & 22.7 \\ RILs & Harbin & GPP & 2012 & 4 & RM225– & 3.37 & \(-\)8.72 & 20.4 \\ RILs & Harbin & PBN & 2012 & 4 & RM225– & 3.19 & \(-\)0.98 & 19.4 \\ RILs & Harbin & SBN & 2012 & 4 & RM470– & 3.56 & \(-\)2.76 & 19.5 \\ \hline \end{tabular}  
* \({}^{\mathrm{a}}\) Chr., chromosome; b Logarithm (base 10) of the odds for the corresponding QTL peak; c Additive effect of the corresponding QTL; d Percentage of the phenotypic variation explained by the corresponding QTL.  
\end{table}
Table 2: QTL for panicle and basal culm related traits on chromosome 4 using F\({}_{2}\) population (176 plants) and RIL population (144 lines) of SN265-\(11/\)LTH in Shenyang and Harbin in 2008, 2010 and 2012, respectively.  
The candidate gene annotation analysis of _qSCM4_ in the rice genome using the RAP-DB database ([[http://rapidb.dna.affrc.go.jp/](http://rapidb.dna.affrc.go.jp/)]([http://rapidb.dna.affrc.go.jp/](http://rapidb.dna.affrc.go.jp/)), accessed on 27 December 2022) revealed that the 58.5 kb range contained 11 annotated genes (Figure 2e). According to the annotation function of 11 genes and the re-sequencing date of the RIL parents (NCBI, PRJNA587802) [38]. Only _Os04g0615000_, which encoding a functional protein with serine and cysteine structural domains, was identified having biparental DNA sequence differences among these genes. There were 13 DNA sequence changes in LTH, compared to SN265 in this gene, including a fragment deletion, two base changes in the 3' UTR region, six base changes in the exons, and four base changes in the introns. Four of these DNA sequence variations caused amino acid mutations including Val-Ala in exon 1, Arg-His in exon 3, Ala-Val and Val-Ile in exon 5, and two synonymous mutations on exon 1. The Arg-His mutation on exon 3 occurred at the active center of the functional structural domain and was likely to result in a change in protein function (Figure 2f).