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Background  We previously reported the development of a set of  Gossypium hirsutum-G. australe  alien chromosome addition lines. Naturally, however,  G. hirsutum - G. australe  chromosome exchanges were very limited, impeding the stable transference of useful genes from  G. australe  (G 2 G 2  genome) into the most cultivated cotton,  G. hirsutum  (AADD).    Results  In the present report, the pollen from a pentaploid (2n = AADDG 2 ) of  G. hirsutum-G. australe  was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of  G. hirsutum  over three consecutive years. Irradiation greatly increased the genetic recombination rates of the  G. hirsutum  and  G. australe  chromosomes and a total of 107 chromosome introgression individuals in 192 GISH-negative (with no GISH signal on chromosome) survived individuals, 11 chromosome translocation individuals (containing 12 chromosome translocation events) and 67 chromosome addition individuals were obtained in 70 GISH-positive (with GISH signal(s) on chromosome(s)) survived individuals, which are invaluable for mining desirable genes from  G. australe . Multicolor genomic in situ hybridization results showed that there were three types of translocation, whole arm translocation, large alien segment translocation and small alien segment translocation, and that all translocations occurred between the G 2 -genome and the A-subgenome chromosomes in  G. hirsutum . We also found that higher doses induced much higher rates of chromosome variation but also greatly lowered the seed viability and seedling survivability.    Conclusions  Irradiation has been successfully employed to induce chromosome introgressions and chromosome translocations and promote chromosome exchanges between cultivated and wild species. In addition, by balancing the rates of chromosome introgression and translocation to those of seed set, seed germination, and seedling rates in the M1 generation, we conclude that the dosage of 20 Grays is the most suitable. The established methodology may guide the utilization of the tertiary gene pool of  Gossypium  species such as  G. australe  in cotton breeding in the future.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4398-7) contains supplementary material, which is available to authorized users.

Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum