Silybum marianum (milk thistle) is among the top selling herbal products in the U.S., in Italy and in other countries. Despite its economic importance as an officinal and medicinal species, only few improved genotypes exist and the species is still marked by traits that are typical of non-domesticated plants. Based on this evidence, further genetic improvement is required for the complete exploitation of milk thistle as a crop species. The first step in order to allow further breeding programmes of the species is the setup of a reliable crossing protocol. The present paper, after a brief review of S. marianum flower anatomy, describes a crossing method for this plant. The correct phenological stage for emasculation is BBCH growth stage 54. If manual pollination is repeated two days after emasculation, a significant increase of F1 fruits can be obtained. By utilizing the proposed protocol, an average 70–90 florets per flower head are emasculated and percentage of success (F1 fruits harvested) usually ranges between 27 and 70%. The proposed crossing protocol will constitute an important tool in order to allow the further genetic improvement of this species.

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