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Background  Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice.    Results  A novel major QTL,  qPSST6 , controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of  qPSST6 . Two genes,  LOC_Os06g39740  and  LOC_Os06g39750 , were annotated as “response to cold” by gene ontology (GO) analysis. qRT-PCR analysis revealed that  LOC_Os06g39750  was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of  LOC _ Os06g39750  in regulating the PSST of rice, suggesting that it was the candidate gene of  qPSST6 .    Conclusions  The information obtained in this study is useful for gene cloning of  qPSST6  and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).    Electronic supplementary material  The online version of this article (10.1186/s12284-018-0218-1) contains supplementary material, which is available to authorized users.

Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy