Identification of Quantitative Trait Loci for Alkaline Tolerance at Early Seedling Stage of Japonica Rice Under Alkaline Stress

Using an F2:3 population with 200 lines derived from a cross between the japonica rice (Oryza sativa L.) varieties Gaochan 106 and Changbai 9, quantitative trait loci (QTLs) for root number, root length, seedling height, and their relative alkaline damage rates at early seedling stage were identified under 0.15% Na2CO3 alkaline stress. A total of 26 QTLs associated with these traits were detected on chromosomes 1, 5, 6, 7, 8, 9, and 11, consisting of 4 QTLs for root number, 5 QTLs for relative alkaline damage rate of root number, 6 QTLs for root length, 2 QTLs for relative alkaline damage rate of root length, 5 QTLs for seedling height, and 4 QTLs for relative alkaline damage rate of seedling height. QTLs qRN6-1, qRN11, qRRN11-2, qRRL11-2, qSH1, qSH11-2, qRSH5, and qRSH6-2 accounted for 29.91, 13.42, 23.86, 21.06, 15.81, 16.53, 29.89, and 34.63% of the phenotypic variations, respectively. These QTLs, except for qRN6-1 with the marker flanking distance of 19.0 cM, were located with relatively large marker flanking distances over 26.3 cM. The positive alleles at 13 loci originated from the tolerant parent Changbai 9, and the positive alleles at other loci were from the sensitive parent Gaochan 106. Partial dominance and over dominance were the main effects at these loci.