*2.6. QTL Mapping and Data Analysis*

The lengths of the substituted segments in CSSLs were assayed according to the previously established method [10]. A chromosomal segmen<sup>t</sup> flanked by two donor markers was considered to be 100% donor type, and the length of the segmen<sup>t</sup> was considered to be the minimum length of a substituted segmen<sup>t</sup> (L-min). A chromosome segmen<sup>t</sup> flanked by two recipient markers was considered as 0% donor type, and the length of the segmen<sup>t</sup> was considered to be the maximum length of a substituted segmen<sup>t</sup> (L-max). A chromosome segmen<sup>t</sup> flanked by one marker of donor type and one marker of recipient type was recognized as 50% donor type. The length of each substituted segmen<sup>t</sup> in the CSSLs was calculated as the estimated length (L), which is the average of L-min and L-max.

Genotypic graphics and chromosome genetic maps of the CSSLs were generated using the Graphic Geno-Types 2 software (GGT2.0) [10]. A putative QTL was declared at the significance level of *p* ≤ 0.001 in a CSSL. If several CSSLs with overlapping substituted segments shared the same QTL, a substitution mapping approach was employed to localize the QTL to a smaller genomic interval [33]. QTL nomenclature was performed according to McCouch and CGSNL: each QTL name is italicized and starts with a lowercase letter "q" to indicate that it is a QTL, followed by a two to five letter standardized "trait name", a number designating the rice chromosome on which it occurs (1–12), a period (".") and a unique identifier to differentiate individual QTLs for the same trait that resides on the same chromosome [34]. The linkage map of QTLs was constructed using MapChart 2.2 [35]. The statistical analysis of the phenotypic and genotypic data of the DP30-CSSL populations was performed by QTL IciMapping 4.1.0 software [36]. Base on the permutation test to set LOD value ≥2.5 as the thresholds for QTL analysis. The chromosomal genetic map was constructed using MapChart 2.3 software.

The genetic effect of different QTLs according to the previously established following formulas [13]:

