Cold stress at the booting stage in rice induces spikelet sterility because of aberrant microspore development, which often seriously damages seed production. Some breeding lines with high cold tolerance were developed by using tropical japonica variety Silewah as a donor of cold tolerance; however, the genetic factors that confer cold tolerance of this variety have not been comprehensively analyzed. In this study, phenotypic and molecular characterization of novel cold-tolerant strains derived from crosses with Silewah was performed to identify quantitative trait loci (QTLs) responsible for cold tolerance. Molecular marker analysis revealed that 2 cold-tolerant strains carried chromosomal segments of Silewah at the same genomic regions on chromosomes 3, 4 and 11. Single marker analysis in segregating population confirmed that the allele of Silewah on chromosome 3 (qCTB3-Silewah) conferred cold tolerance. The effect of qCTB3-Silewah was supported by the fact that this allele had been a target of selection during developing a breeding line by phenotypic selection from backcrossed progenies with an elite variety as a recurrent parent. qCTB3 is a different QTL from those reported for Silewah previously, suggesting that different QTLs might be exploited in different breeding programs depending on the genetic backgrounds and environmental conditions.
