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Background    Verticillium  wilt (VW) caused by  Verticillium dahliae  ( Kleb ) is one of the most destructive diseases of cotton. The identification of highly resistant QTLs or genes in the whole cotton genome is quite important for developing a VW-resistant variety and for further molecular design breeding.    Results  In the present study, BC 1 F 1 , BC 1 S 1 , and BC 2 F 1  populations derived from an interspecific backcross between the highly resistant line Hai1 ( Gossypium barbadense  L.) and the susceptible variety CCRI36 ( G. hirsutum  L.) as the recurrent parent were constructed. Quantitative trait loci (QTL) related to VW resistance were detected in the whole cotton genome using a high-density simple sequence repeat (SSR) genetic linkage map from the BC 1 F 1  population, with 2292 loci covering 5115.16 centiMorgan (cM) of the cotton (AD) genome, and the data concerning VW resistance that were obtained from four dates of BC 2 F 1  in the artificial disease nursery and one date of BC 1 S 1  and BC 2 F 1  in the field. A total of 48 QTLs for VW resistance were identified, and 37 of these QTLs had positive additive effects, which indicated that the  G. barbadense  alleles increased resistance to VW and decreased the disease index (DI) by about 2.2–10.7. These QTLs were located on 19 chromosomes, in which 33 in the A subgenome and 15 QTLs in the D subgenome. The 6 QTLs were found to be stable. The 6 QTLs were consistent with those identified previously, and another 42 were new, unreported QTLs, of which 31 QTLs were from  G. barbadense . By meta-analysis, 17 QTL hotspot regions were identified and 10 of them were new, unreported hotspot regions. 29 QTLs in this paper were in 12 hotspot regions and were all from  G. barbadense .    Conclusions  These stable or consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying VW resistance. This study provides useful information for further comparative analysis and marker-assisted selection in the breeding of disease-resistant cotton. It may also lay an important foundation for gene cloning and further molecular design breeding for the entire cotton genome.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3128-x) contains supplementary material, which is available to authorized users.

Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense