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Background  Asia minor bluegrass ( Polypogon fugax, P. fugax ), a weed that is both distributed across China and associated with winter crops, has evolved resistance to acetyl-CoA carboxylase (ACCase) herbicides, but the resistance mechanism remains unclear. The goal of this study was to analyze the transcriptome between resistant and sensitive populations of  P. fugax  at the flowering stage.    Results  Populations resistant and susceptible to clodinafop-propargyl showed distinct transcriptome profiles. A total of 206,041 unigenes were identified; 165,901 unique sequences were annotated using BLASTX alignment databases. Among them, 5904 unigenes were classified into 58 transcription factor families. Nine families were related to the regulation of plant growth and development and to stress responses. Twelve unigenes were differentially expressed between the clodinafop-propargyl-sensitive and clodinafop-propargyl-resistant populations at the early flowering stage; among those unigenes, three belonged to the ABI3VP1, BHLH, and GRAS families, while the remaining nine belonged to the MADS family. Compared with the clodinafop-propargyl-sensitive plants, the resistant plants exhibited different expression pattern of these 12 unigenes.    Conclusion  This study identified differentially expressed unigenes related to ACCase-resistant  P. fugax  and thus provides a genomic resource for understanding the molecular basis of early flowering.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4324-z) contains supplementary material, which is available to authorized users.

Transcriptomics analysis of the flowering regulatory genes involved in the herbicide resistance of Asia minor bluegrass (Polypogon fugax)