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Background  Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown.    Results  Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the  Photoperiod-B1  ( Ppd-B1 ) and the  Vernalization-A1  ( Vrn-A1 ) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of  Vrn-A1  and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties’ region of origin and based on multi-location field trials show that  Ppd-B1  copy number has a substantial effect on the fine-tuning of flowering time.    Conclusions  In conclusion, our results show the importance of copy number variation at  Ppd-B1  and  Vrn-A1  for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0258-0) contains supplementary material, which is available to authorized users.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat