Much of what is known about the process of technological innovation in agriculture has yet to be captured in the discussions of abiotic stress plant tolerance as well as rice cold tolerance. The development of research and technological solutions to minimize risks of current abiotic stresses to the plant can lead to two possible outcomes: increase in agricultural productivity and assist the future of plant breeding work. Research efforts about the role of technological development, driven by abiotic stress constraints, are pivotal in making any assertion about the likely tolerance of plant to abiotic stress. Drawing upon the hypothesis of QTL mapping, this research investigates on detection of QTLs for cold tolerance at the seedling stage in rice (Oryza sativa. L), QTLs identified from a BC1F2 breeding population derived from the cross between Chomrongdhan, a donor parent tolerant with Vary botry a susceptible parent, that lead to increase rice productivity in Madagascar. Using a controlled environment and molecular work, out of total 500 BC1F2 segregating plants, 144 plants were used for genotyping based on of visual seedling stage cold tolerance symptom. A total of 4606 SNP markers evenly spread throughout the whole 12 rice genome was used for parental polymorphism survey. The 34% polymorphic markers were used for QTL mapping for cold tolerance at seedling stage. QTL analysis using inclusive composite interval mapping detected four QTLs on chromosome 2 and 10 with phenotypic variances (R2) of 11.11, 7.55, 12.8 and 8.8%, respectively. The position of QTL on chromosome 2 was flanked by 2262412 and 2237404, three other QTLs were detected on chromosome 10 conferred cold tolerances for seedling growth and leaf growth at 14day after recovery and appear to be a novel QTLs. Selected tolerant plant in this research should be useful for the farmers and the markers flanking those identified QTLs should be useful for molecular marker assisted breeding for cold tolerance for the breeder. Keywords: QTL mapping, cold tolerance, seedling, rice
