Abstract: A recombinant inbred line population of rice(Oryza sativa L.)was directly seeded in plastic pots in a randomized complete block with two treatments,control(normal fertilizer level)and no fertilizer.Seedling height was measured at stages Ⅰ(25 days after seeding)and Ⅱ(50 days after seeding),respectively.Composite interval mapping was carried out using a high density linkage map based on the same population,leading to the identification of 8 main-effect QTL for seedling height,each explaining 4%-12% of the phenotypic variation.Comparing the QTL identified under two fertilizer levels resulted in a finding that most of the QTL showed effects on the trait only under one fertilizer level,indicating presence of significant QTL by fertilizer level interactions.Only one QTL(qSH-3-2)was found to produce consistent additive effect on the trait under two fertilizer levels.This QTL was located to the interval RM156-RM16 of chromosome 3 and its positive allele contributed by the parent Lemont.In addition.There were three QTL(qSH-1,qSH-3-3 and qSH-5)showing consistent additive effects at stages Ⅰ and Ⅱ.Breeding strategies for improvement of tolerance to low fertilizer stress in rice via marker-aided selection were discussed.