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Background  Apple ( Malus  ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between  M. domestica  cultivars ‘Jonathan’ and ‘Golden Delicious’ were used.    Results  A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251  Malus  accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7–71.4% of the 331 bud sports derived from ‘Fuji’, ‘Red Delicious’, ‘Gala’, ‘Golden Delicious’, and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that  M. domestica  showed higher genetic diversity than the other species.  Malus  underwent a relatively high level of wild-to-crop or crop-to-wild gene flow.  M. sieversii  was closely related to both  M. domestica  and cultivated Chinese cultivars.    Conclusions  The identity signatures of  Malus  accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among  Malus  species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02744-2.

Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions