*3.2. Mapping QTLs for Low-Temperature Germinability*

We used low-temperature germination rate of the F2 population at 6 and 7 DAI for the QTL analysis because we observed larger differences among the parental lines (CR1517 and CR1518) at the periods. The F2 population exhibited nearly normal distribution of the LTG rate at 6 DAI (skewness = −0.4277) and was skewed to the left at 7 DAI (skewness = −1.0609) (Figure 2). Using QTL-linked SSR markers and one InDel marker, we consistently detected *qLTG1* and *qLTG3* 6 and 7 DAI, respectively. *qLTG1* was detected between RM220 and CRM22 markers, while *qLTG3* was detected on qLTG3-1\_18D marker on chromosomes 1 and 3, respectively. The *qLTG1* explained 16.0% and 12.0% phenotypic variation 6 and 7 DAI, respectively, while *qLTG3* explained 23.8% and 22.1% phenotypic variation 6 and 7 DAI, respectively. Based on gene action analysis 6 DAI, the additive effect (*a*) and dominant effect (*d*) of *O. rufipogon* allele on *qLTG1* locus (RM220–CRM22) were 10.0 and 0.2, respectively. *O. rufipogon* allele

of *qLTG1* had 7.7 and 2.1% of the additive and dominant effects, respectively, 7 DAI. In the *qLTG3* locus (qLTG3-1\_18D), *O. rufipogon* allele accounted for 9.6 and 8.1% of the additive effects 6 and 7 DAI, respectively. The dominant effect was 9.7% on both days. Degrees of dominance were 1.0 and 1.2 at 6 and 7 DAI, respectively (Table 2). In addition, we detected two minor QTLs on chromosome 8 and 10. No QTLs were detected between markers RM72 and RM22705 (*p* = 0.086) on chromosome 8 at 6 DAI. *qLTG8* was detected when the significant difference had a *p* value of 0.014 at 7 DAI. The phenotypic variation explained by *qLTG8* was 5.45%. In addition, we identified other QTLs on chromosome 10. The QTLs were detected on the most distal end of the short arm of chromosome 10 by RM25633 and RM333-RM591, respectively. The phenotypic variation explained by *qLTG10.1* was 4.6% at 7 DAI. *qLTG10.2* explained 4.2 and 6.6% of the phenotypic variation at 6 and 7 DAI, respectively. In addition, additive and dominant effects of *O. rufipogon* alleles at the *qLTG8* locus (RM72-RM22705) were 4.9 and 2.4% at 7 DAI, respectively. *qLTG10.1* had 2.9 and −1.9% additive and dominant effects, respectively, at 7 DAI. The additive effects of *qLTG10.2* were −4.2 and −5.3% at 6 and 7 DAI, and the dominant effects of the QTL were 5.1 and 5.5% at 6 and 7 DAI, respectively. Although two QTLs, *qLTG10.1* and *qLTG10.2*, were linked on the short arm of chromosome 10, the effect for LTG of *O. rufipogon* allele was different. *O. rufipogon* introgression had a −0.6 degree of dominance at the *qLTG10.1* locus at 7 DAI, while −1.2 and −1.0 degrees of dominance were observed at *qLTG10.2* at 6 and 7 DAI, respectively (Table 2). The gene actions of *O. rufipogon* are different in the five QTLs. The *O. rufipogon* allele is partially dominant at *qLTG8* and *qLTG10.2*, partially recessive at *qLTG10.1*, completely dominant at *qLTG3*, and completely recessive at *qLTG1* with regard to regulating LTG (Table 2).

**Figure 2.** Frequency distribution of germination rate in 154 F2 plants at 6 and 7 days after incubation (DAI) at 13 ◦C. Germination rate was measured at 4–8 (DAI). Arrows indicate mean germination rate of CR1517 and CR1518 lines.


**Table 2.** List of QTLs identified for low-temperature germinability in F2 population.

(x) LTG: low-temperature germination. (y) R2: Coefficient of determination. (z) *a*: Additive effect = (*O. rufipogon* homozygote − Hwaseong homozygote)/2, *d*: Dominant effect = Heterozygote − (*O. rufipogon* homozygote + Hwaseong homozygote)/2, *d*/*a*: degree of dominance.
