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Background  Heading time is an important adaptive trait in durum wheat. In hexaploid wheat,  Photoperiod-1  ( Ppd ) loci are essential regulators of heading time, with  Ppd-B1  conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome  Ppd-D1  locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat.    Results  In this study, we employed a panel of 328 diverse European durum genotypes that were evaluated for heading time at five environments. Genome-wide association mapping identified six putative QTL, with a major QTL on chromosome 2B explaining 26.2% of the genotypic variance. This QTL was shown to correspond to copy number variation at  Ppd-B1 , for which two copy number variants appear to be present. The higher copy number confers earlier heading and was more frequent in the heat and drought prone countries of lower latitude. In addition, two other QTL, corresponding to  Vrn-B3  ( TaFT ) and  Ppd-A1 , were found to explain 9.5 and 5.3% of the genotypic variance, respectively.    Conclusions  Our results revealed the yet unknown role of copy number variation of  Ppd-B1  as the major source underlying the variation in heading time in European durum wheat. The observed geographic patterns underline the adaptive value of this polymorphism and suggest that it is already used in durum breeding to tailor cultivars to specific target environments. In a broader context our findings provide further support for a more widespread role of copy number variation in mediating abiotic and biotic stress tolerance in plants.    Electronic supplementary material  The online version of this article (10.1186/s12863-019-0768-2) contains supplementary material, which is available to authorized users.

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat