Mapping of QTL Underlying Tolerance to Alkali at Germination and Early Seedling Stages in Rice

To detect quantitative trait loci (QTLs) associated with tolerance to alkali damage, 120 double haploid (DH) lines derived from the cross between TN1 (Oryza sativa L. subsp. indica) and Chunjiang 06 (O. sativa L. subsp. japonica) were used as mapping population. The seeds were treated with 0.15% Na2CO3 (alkali stress) and distilled water (control) and 10 traits were determined as indicators for alkali damage at germination and early seedling stages. The alkali damage rate in germination stage (ADG) positively correlated (P < 0.05) with the relative germination energy (RGE), relative germination rate (RGR), and relative germination index (RGI); and the alkali damage rate at early seedling stage (ADS) had significantly correlation with relative seedling height (RSH), relative root length (RRL), relative root number (RRN), and relative seedling dry weight (RDW). ADG and ADS could be used as indicators for alkaline tolerance in rice. Using QTLNetwork2.0 software, 14 additive QTLs and 13 pairs of epistatic QTLs controlling the tolerance to alkali were mapped. Two main-effect QTLs were detected in the region of RM251–RM3280 on chromosome 3, and 3 main-effect QTLs were mapped between RM3286 and RM1279 on chromosome 7. Epistatic loci, such as RM1–RM1195, RM1358–RM290, RM1279–RM505, and RM1246–RM519 on chromosomes 1, 2, 7, and 12, respectively, were important under alkali stress. The key loci under alkali stress may be pleiotropic or closely linked to each other. Some alkali resistance QTLs were likely to be in the same regions with salt resistance QTLs reported earlier. The QTLs detected in this study might be 2 types corresponding to resistances to ions (K+ or Na+) stress and high pH stress, respectively, and the latter probably plays an important role in the tolerance to alkali in rice.