Interspecific hybridization can induce extensive variation in genome sequences, including simple sequence repeat (SSR) regions. To determine the characteristics of SSR variation induced by interspecific hybridization and the possible effect of SSR variation on gene function, we constructed a Brassica napus doubled-haploid (DH) population from a cross between natural B. napus and resynthesized B. napus (B. oleracea × B. rapa) and identified, located, sequenced and functionally annotated SSR variants.The results showed that novel SSR variants were generated in the F generation and maintained in the introgressed DH population. Elimination of sequences carrying SSRs also occurred in the F hybrids, with three times as many sequences lost in the introgressed DH population compared to in the F hybrids, probably due to non-homologous recombination. The degree of SSR variation observed depended primarily on the number of SSR repeats and secondarily on the nucleotide composition of the SSR motifs.In the introgressed DH population, many genes containing SSRs exhibited frameshift mutations (62.5%) due to the expansion or contraction of the SSR motifs following deletion deletion (25%) or insertion (12.5%) mutations.Most genes harboring SSR variants were associated with vital metabolic processes, such as protein or DNA metabolic processes. The SSR variation induced by interspecific hybridization reflects an intrinsic property of species adaptability post-hybridization through variation. This study is beneficial to understanding the origin of SSRs and the effects of SSR mutation on polyploid genomes
