*4.5. Genotyping and Construction Bin Map*

The estimation of genotype calling parameters, determination of the recombination breakpoint, and construction of the bin map were carried out with minor modifications via the method of Sliding Window, as described by Huang et al. [19]. The genotype of each window was determined by the SNP ratio between the two parents; if the SNP ratio of SN265 to LTH was 15:5 or higher, the genotype was considered to be a homozygous SN265 genotype, if the ratio was lower, then it was designated as a homozygous LTH genotype. Moreover, if the SNP ratio between the two parents was between 5:15 and 15:5, the genotype was recognized as heterozygous. The genotype calling parameters were performed according to the methods described by Song et al. [22]. Adjacent 15 kb segments with the same genotypes were merged as one bin marker [46]. The linkage map was built using the *est.map* function with the R/qtl software [47].

#### *4.6. QTL Mapping for Low-Temperature Germinability*

In this study, we used the composite interval method (CIM) in the R/qtl package [47] to detect the QTLs for LTG. The threshold level of CIM was ensured by 1000 permutations, and the QTL confidence interval was estimated by using a 1.5 LOD-drop from the peak LOD. The germination rate (%) after 6 days under controlled temperature conditions of 15 ◦C was used for the QTL analysis.
