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Background  Polyploidy and hybridization are ubiquitous in  Rubus  L., a large and taxonomically challenging genus. Chinese  Rubus  are mainly concentrated into two major sections, the diploid  Idaeobatus  and the polyploid  Malachobatus . However, it remains unclear to be auto- or allo- polyploid origin of polyploids in  Rubus . We investigated the homoeologs and the structure of the  GBSS I-1 (granule-bound starch synthase I) gene in 140  Rubus  individuals representing 102 taxa in 17 (out of the total 24) subsections of 7 (total of 12) sections at different ploidy levels.    Results  Based on the gene structure and sequence divergence, we defined three gene variants,  GBSS I-1a,  GBSS I-1b, and  GBSS I-1c. When compared with  GBSS I-1a, both  GBSS I-1b and  GBSS I-1c have a shorter fourth intron, and  GBSS I-1c had an additional deletion in the fifth intron. For diploids, either  GBSS I-1a or  GBSS I-1b was detected in 56 taxa consisting of 82 individuals from sect.  Idaeobatus , while both alleles existed in  R. pentagonus  and  R. peltatus . Both homoeologs  GBSS I-1a and  GBSS I-1b were identified in 39 taxa (48 individuals) of  Malachobatus  polyploids. They were also observed in two sect.  Dalibardastrum  taxa, in one sect.  Chamaebatus  taxon, and in three taxa from sect.  Cylactis . Interestingly, all three homoeologs were observed in the three tetraploid taxa. Phylogenetic trees and networks suggested two clades (I and II), corresponding to  GBSS I-1a, and  GBSS I-1b/1c sequences, respectively.  GBSS I-1 homoeologs from the same polyploid individual were resolved in different well-supported clades, and some of these homoelogs were more closely related to homoelogs in other species than they were to each other. This implied that the homoeologs of these polyploids were donated by different ancestral taxa, indicating their allopolyploid origin. Two kinds of diploids hybridized to form most allotetraploid species. The early-divergent diploid species with  GBSS I-1a or -1b emerged before polyploid formation in the evolutionary history of  Rubus .    Conclusion  This study provided new insights into allopolyploid origin and evolution from diploid to polyploid within the genus  Rubus  at the molecular phylogenetic level, consistent with the taxonomic treatment by Yü et al. and Lu.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1915-7) contains supplementary material, which is available to authorized users.

Allopolyploid origin in Rubus (Rosaceae) inferred from nuclear granule-bound starch synthase I (GBSSI) sequences