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Background  Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage.    Results  In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that  japonica  rice was more tolerant to cold at the bud burst stage than  indica  rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs ( P  < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs ( qSR2–2 ,  qSR3–1 ,  qSR3–2 ,  qSR3–3  and  qSR9 ) that were colocalized with those from previous studies and seven QTLs ( qSR2–1 ,  qSR3–4 ,  qSR3–5 ,  qSR3–6 ,  qSR3–7 ,  qSR4  and  qSR7 ) that were reported for the first time. Among these QTLs,  qSR9 , harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes ( LOC_Os09g12440 ,  LOC_Os09g12470 ,  LOC_Os09g12520 ,  LOC_Os09g12580  and  LOC_Os09g12720 ) were identified as candidates for  qSR9 .    Conclusion  This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03317-7.

Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS