QTLs (2004) identified qLTG3-1 using backcross inbred lines

QTLs analyses for low-temperature germinability of rice revealed that polygenic genes control this trait (Table 4 and Fig 1). So far, more than 60 QTLs have been mapped over 12 chromosomes of rice for this trait (Sheng et al. 2001, Miura et al. 2001, Fujino et al. 2004, Zhang et al. 2005, Chen et al. 2006, Ji et al. 2008, Jiang et al. 2006, Wang et al. 2011, Li et al. 2013, Satoh et al. 2016, Yang et al. 2018). Majority of these QTLs were detected on chromosomes 2, 3, 7 and 8. However, only eight main effect QTLs were reported by different researchers (Table 4). Major QTLs like LTG3-1 (Fujino et al. 2008), qSV1 and qSV-5c (Xie et al. 2014) were fine mapped. Fujino et al. (2004) identified qLTG3-1 using backcross inbred lines (BILs) derived from a cross between Italica Livorno and Hayamasari as a major QTL for low-temperature germinability on chromosome 3, explaining 35% of the total phenotypic variation. A later study (Fujiano et al. 2008) with high-resolution marker density detected qLTG3-1 in a 4.8-kb window, which belongs only one gene (Os03g0103300) that encodes unknown function protein containing two known conserved domains, GRP (glycine-rich cell wall protein) and Tryp alpha amyl of the protease inhibitor/seed storage/LTP family. Using a genome-wide expression profiling analysis, Fujino and Matsuda (2010) identified 29 qLTG3-1 dependent genes with diverse functions. Several genes of these were involved in defense responses which were upregulated by qLTG3-1, indicating that qLTG3-1 expression is required for the expression of defense response genes in low-temperature germinability of rice. They showed that qLTG3?1 has a role in the upregulation of genes involved in phytoalexin biosynthesis. Further, qLTG3?1 was shown to increase the expression of probenazole?induced protein (PBZ1), which might induce programmed cell death. In genome-wide association mapping studies with diverse germplasm, Pan et al. (2015) and Sales et al. (2017) detected respectively 30 and 24 markers significantly associated with low-temperature germinability in rice.