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Background  Cytoplasmic male sterility (CMS) conferred by the cytoplasm from  Gossypium harknessii  (D2) is an important system for hybrid seed production in Upland cotton ( G. hirsutum) . The male sterility of CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene  Rf1  transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood.    Results  In this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC 8 F 1 ) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the  Rf1 -carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results.    Conclusions  Through genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene  Rf1  and the CMS-D2 cytoplasm.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3841-0) contains supplementary material, which is available to authorized users.

Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton