**3. Discussion**

#### *3.1. Seed Dormancy QTL Analysis*

Seed dormancy in rice is generally a complex trait and is controlled by multiple genes. In our study, the genetic architecture of seed dormancy was examined in the NIP/ZS97 CSSL population with each line carrying one or a few different introgressed segments from NIP and otherwise sharing the uniform genetic background of ZS97. Each introgression segment was defined by high-density SNP markers. The CSSL population has several advantages over other mapping populations such as F2, BC1, and RIL [38–40]. First, the detection power of QTLs in CSSLs was higher than that of other mapping populations reported. In total, 36 QTLs for seed dormancy were identified in this CSSL population using six germination parameters (Table 2) and the six germination parameters explained from 50.5% to 77.9% of phenotypic variance. However, only four seed dormancy QTLs were detected in a double haploid (DH) population [41]. Four [42] and nine [15] seed dormancy QTLs were identified by two different RIL populations, respectively. Second, it is easier to develop a secondary F2 population derived from a cross between a CSSL line containing the target QTL and the recurrent parent for fine mapping [38,43]. In our study, by developing an F2 segregation population, one of the novel seed dormancy QTLs, namely *qDOM3.1*, was delimited to 90 kb (Figure 5).

Among all 36 QTLs, 10 were detected or cloned previously for seed dormancy (Table 2). The results implied that our NIP/ZS97 population and QTL analysis method turned out to be efficient to detect seed dormancy QTLs across the whole genome. The first cloned seed dormancy gene in rice *Sdr4* was only detected in T50 (*qDOM7.5*), implying that our population had mild seed dormancy level. *qDOM7.4* covered the gene *SD7-1*/*Rc* and was detected in all six parameters except Gmax. *SD7-1*/*Rc* was a pleiotropic gene that most likely controlled the dormancy and pigment traits by regulating ABA and flavonoid biosynthetic pathways, respectively [22]. *OsFbx352*, which was located under *qDOM10.3*, was detected in all six parameters. It was involved in the regulation of glucose-induced suppression of seed germination by targeting ABA metabolism [36]. Besides the QTLs co-located with the previous study, there were 26 new QTLs identified in the present study; therefore, both the plant material and abundant QTL information will facilitate the use of the dormancy alleles in other breeding programs or other research studies.
