Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.)

Low temperature is a serious abiotic stress affecting rice production in subtropical and temperate areas. In this study, cold tolerance of rice at the germination and seedling stages were evaluated using one recombinant inbred line (RIL) population derived from a cross between Daguandao (japonica), with highly cold-tolerant at the seedling stage, and IR28 (indica), with more cold-tolerant at the germination stage, and the quantitative trait loci (QTL) mapping was conducted using the multiple interval mapping (MIM) approach. Continuous segregation in low temperature germinability (LTG) and cold tolerance at the seedling stage (CTS) were observed among the RIL populations. Most RILs were moderately susceptible or tolerant at the germination stage, but were susceptible at the seedling stage. No significant relationship was found in cold tolerance between the germination and seedling stages. A total of seven QTLs were identified with limit of detection (LOD) >3.0 on chromosomes 3, 8, 11 and 12, and the amount of variation (R2) explained by each QTL ranged from 5.5 to 22.4%. The rice LTG might be regulated by two minor QTLs, with the CTS controlled by one major QTL [qCTS8.1 (LOD = 16.1, R2 = 22.4%)] and several minor loci. Among these loci, one simultaneously controls LTG (qLTG11.1) and CTS (qCTS11.1). Several cold-tolerance-related QTLs identified in previous studies were found to be near the QTLs detected here, and three QTLs are novel alleles. The alleles from Daguandao at six QTLs increased cold tolerance and could be good sources of genes for cold tolerance. In addition, only one digenic interaction was detected for CTS, with a R2 value of 6.4%. Those major or minor QTLs could be used to significantly improve cold tolerance by marker-assisted selection (MAS) in rice.