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Background  Litchi is a well-known subtropical fruit crop. However, irregular bearing attributed to unstable flowering is a major ongoing problem for the development of the litchi industry. In a previous study, our laboratory proved that litchi flowering was induced by low temperature and that a  FLOWERING LOCUS T  ( FT ) homologue gene named  LcFT1  played a pivotal role in this process. The present study aimed to understand the natural variation in  FT  among litchi germplasm resources and designed markers to verify easy- and difficult-flowering litchi germplasms. A grafting experiment was also carried out to explore whether it could shorten the seedling stage of litchi seedlings.    Results  Two types of  LcFT1  promoter existed in different litchi germplasm resources, and we named them the ‘easy-flowering type of  LcFT1  promoter’ and ‘difficult-flowering type of  LcFT1  promoter’, which resulted in three different  LcFT1  genotypes of litchi germplasm resources, including the homozygous easy-flowering type of the  LcFT1  genotype, homozygous difficult-flowering type of the  LcFT1  genotype and heterozygous  LcFT1  genotype of litchi germplasm resources. The homozygous easy-flowering type of the  LcFT1  genotype and heterozygous  LcFT1  genotype of the litchi germplasm resources completed their floral induction more easily than the homozygous difficult-flowering type of the  LcFT1  genotype of litchi germplasm resources. Herein, we designed two kinds of efficient molecular markers based on the difference in  LcFT1  promoter sequences and applied them to identify of the easy- and difficult-flowering litchi germplasm resources. These two kinds of molecular markers were capable of clearly distinguishing the easy- from difficult-flowering litchi germplasm resources at the seedling stage and provided the same results. Meanwhile, grafting the scion of seedlings to the annual branches of adult litchi trees could significantly shorten the seedling stage.    Conclusions  Understanding the flowering characteristics of litchi germplasm resources is essential for easy-flowering litchi breeding. In the present study, molecular markers provide a rapid and accurate approach for identifying the flowering characteristics. The application of these molecular markers not only significantly shortened the artificial crossbreeding cycle of easy-flowering litchi cultivars but also greatly saved manpower, material resources and land.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03309-7.

bmc plant biology

Development of molecular markers based on the promoter difference of LcFT1 to discriminate easy- and difficult-flowering litchi germplasm resources and its application in crossbreeding