QTL mapping studies using various population (F2, DH, RILs, etc) involving different donor parents, particularly japonica type cold tolerant cultivars have detected the role of many genes and QTLs controlling cold stress tolerance during seedling stage of rice. So far, more than 170 QTLs for seedling stage cold tolerance have been mapped in different chromosomes (Table 2). These QTLs are distributed on almost all of the chromosomes, although chromosome 1, 2, 6, 8 and 11 represent a majority of them and contributed 4.8 – 42.3% phenotypic variation. However, only a few main effect QTLs were detected in these studies and some of them are common with differential marker intervals. Andaya and Mackill (2003a) reported 13 QTLs for seedling stage cold tolerance distributed over chromosomes 1, 2, 4, 6, 8, 10, 11 and 12 with a main effect QTL, qCTS12 on chromosome 12 at marker intervals of 35.3 – 38.4 cM explaining 40.6 % phenotypic variation. This QTL was fine mapped in later studies by Andaya and Tai (2006) in 55 kb window located on the BAC clone OSJNBb0071|17, which contains OsGSTZ1 and OsGSTZ2, the most likely candidate genes for cold tolerance at seedling stage. Kim et al. (2011) suggested that cold sensitivity in rice is strongly correlated with a naturally occurring Ile99Val mutation in the multifunctional glutathione transferase isoenzyme GSTZ2. In chromosome 2 at marker interval between RM561 and RM341, Lou et al. (2007) identified qCTS-2, a major QTLs with a 15.1 LOD and 27.4% R2 value in a double haploid population derived from of cross between a cold tolerant japonica variety, AAV002863 and cold susceptible indica rice variety Zhenshan97B. Liu et al. (2013) mapped another major QTL (qCTS2) overlapping the QTL (qCTS-2) mapped by Lou et al. (2007). Most probably both of them are the same QTLs, which could be confirmed through fine mapping. Koseki et al. (2010) identified a major QTL (qCsst11) with 20 LOD and 40.5% R2 value on chromosome 11 between S0605 and S0485, which was fine mapped and narrowed down to a 60 kb region, in which six genes have been predicted. Resequencing and expression studies revealed that either Os11g0615600 or Os11g0615900, or both, might control the seedling cold tolerance. Moreover, the deduced protein from the Os11g0615900 gene contains the NB-ARC (nucleotide-binding adaptor shared by APAF-1, R protein, and CED-4) domain, a conserved motif found in disease resistance proteins and involved in hypersensitive response (HR) (DeYoung and Innes 2006). The further functional studies of the Os11g0615900 gene under both cold stress and biotic stress would help to define the QTL qCtss11 and help discern whether the Os11g0615900 gene functions in signal transduction between biotic and abiotic stress. A comparison of the genetic location of qCtss11 and qCTS11-2 (identified by Andaya and Mackill 2003b) suggests that these loci are likely coincident and therefore, possibly allelic.
In a study with a RIL population derived from a cross of the cold-tolerant japonica cultivar Jinbubyeo and the cold-susceptible indica cultivar BR29, Kim et al. (2014) identified six QTLs including two QTL combinations (qSCT1 and qSCT11), which explained the critical threshold of 27.1 % for the R2 value determining cold tolerance at the seedling stage. These two QTLs (qSCT1 and qSCT11) were fine mapped and analyzed for candidate genes underlying them. Gene-based markers – In1-c3, derived from the open reading frame (ORF) LOC_Os01g69910 at qSCT1 region encoding calmodulin-binding transcription activator (CAMTA) on chromosome 1, and In11-d1, derived from ORF LOC_Os11g37720 (Duf6 gene) at qSCT11 region on chromosome 11, were found co-segregated with seedling cold tolerance. In another study with 151 BC2F1 mapping population of a cross between DX as a cold-tolerant donor and the indica variety Nanjing 11 (NJ) as a recurrent parent, Xiao et al. (2014) mapped two seedling cold-tolerant QTLs, named qRC10-1 and qRC10-2, on chromosome 10 by composite interval mapping. qRC10-1 (LOD = 3.1) was mapped at 148.3 cM between RM171 and RM1108, and qRC10-2 (LOD = 6.1) was mapped at 163.3 cM between RM25570 and RM304, which accounted for 9.4% and 32.1% of phenotypic variances, respectively. Xiao et al. (2014) also fined map the major locus qRC10-2 to a 48.5-kb region between markers qc45 and qc48. Two ORF, Os10g0489500 and Os10g0490100 in this 48.5 kb window showed different expression patterns between DX and NJ for low-temperature tolerance at seedling stage of rice. Low-temperature exposure affects the integrity of membrane stability through electrolyte leakage and inhibits photosynthesis. Bonnecarrene et al. (2015) identified 4 markers significantly associated with electrolyte leakage and one marker for photoinhibition (PSII). Further analysis showed that markers for electrolyte leakage were liked to LOC_Os07g44180 (OsLti6a), LOC_Os03g24380 (glutathione peroxidase), LOC_Os01g13030 (auxin-induced protein) and the marker for photoinhibition was associated with LOC_Os01g60020 (TF-NAC) gene.