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Background  Artificial synthesis of octoploid rapeseed double haploid (DH) induction lines Y3380 and Y3560 was made possible by interspecific hybridization and genome doubling techniques. Production of pure lines by DH induction provides a new way to achieve homozygosity earlier in  B.napus . Previously, the mechanism of induction, and whether the induction has obvious maternal genotypic differences or not, are not known so far.    Results  In this study, different karyogene and cytoplasmic genotype of  B.napus  were pollinated with the previously reported DH inducers e.g. Y3380 and Y3560. Our study presents a fine comparison of different cytoplasmic genotypes hybridization to unravel the mechanism of DH induction. Ploidy identification, fertility and SSR marker analysis of induced F 1  generation, revealed that ploidy and phenotype of the induced F 1  plants were consistent with that type of maternal, rather than paternal parent. The SNP chip analysis revealed that induction efficiency of DH inducers were affected by the karyogene when the maternal cytoplasmic genotypes were the same. However, DH induction efficiency was also affected by cytoplasmic genotype when the karyogenes were same, and the offspring of the  ogura  cytoplasm showed high frequency inducer gene hybridization or low-frequency infiltration.    Conclusion  The induction effect is influenced by the interaction between maternal karyogene and cytoplasmic genotype, and the results from the partial hybridization of progeny chromosomes indicate that the induction process may be attributed to the selective elimination of paternal chromosome. This study provides a basis for exploring the mechanism of DH inducer in  B.napus , and provides new insights for utilization of inducers in molecular breeding.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02981-z.

Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus