Mapping QTL associated with rice allelopathy using the rice recombinant inbred lines and specific secondary metabolite marking method

Quantitative trait loci (QTL) mapping was done using population of 147 recombinant inbred lines from a cross between most allelopathic cultivar Zhong-156 and least allelopathic cultivar Gumei-2. The map contained 168 DNA markers, covering all 12 chromosomes with 1447.9cM spans. The AI (Allelopathic Index) determined by the special secondary metabolite marking method was used to evaluate the allelopathic effects of rice lines. Three main-effect QTLs, mapped on chromosomes 5, 5 and 11, explained 13.6% phenotypic variation. One QTLs on chromosome 11 had the largest effect on the expression of allelopathic rice and explained 10.6% phenotypic variation. A multiple QTL model estimated that three QTLs with LOD scores > 2.0 were 10.02, 11.23 and 16.51, respectively. Five pairs of digenic epistatic loci were also found, which collectively explained 41.5% of the phenotypic variation. Two of those main-effect QTLs participated in digenic epistatic loci. The main QTLs and epistatic loci totally explained 55.1% of the phenotypic variation of allelopathic activity.