*3.7. QTLs for Coleoptile Length*

QTL analysis of coleoptile length was carried out for two scoring dates (9 and 10 DAI) considering that the two parental lines had the greatest difference in coleoptile length (Table 3). A total of three QTLs associated with coleoptile length were detected and they were colocalized with the LTG QTLs (*qLTG1*, *qLTG3*, and *qLTG8*). At 9 DAI, *qCCL3* (qLTG3-1\_18D) and *qCCL8* (RM22689-RM22705) were identified and they explained 12.0 and 6.4% of the phenotypic variance, respectively. The *qCCL1* on chromosome 1 between markers RM220 and CRM22 was not significant (*p* = 0.059) at 9 DAI (data not shown).

At 10 DAI, *qCCL1*, *qCCL3,* and *qCCL8* were detected (Table 4). The QTLs explained 6.4%, 9.2%, and 7.1% of the total phenotypic variance, respectively. No QTL was detected on the other *O. rufipogon* introgression segments on chromosomes 9 and 10 at 9 and 10 DAI. *O. rufipogon* alleles are partially recessive at *qCCL1* and *qCCL8* loci, and dominant at the *qCCL3* locus similar to the case in LTG (Tables 2 and 4). *qLTG8* in this study was colocalized with the *qCCL8* for coleoptile length under cold stress in the study [6] and the allelic relationship between two QTLs remains to be clarified.
