Vol.:(0123456789) 1 3 Molecular Genetics and Genomics https://doi.org/10.1007/s00438-017-1388-z ORIGINAL ARTICLE Haplotype analysis of the germacrene A synthase gene and association with cynaropicrin content and biological activities in Cynara cardunculus Ana Margarida Ferro 1,2  · Patrícia Ramos 1,3  · Ângela Guerra 1,3  · Paula Parreira 1  · Teresa Brás 1,4  · Olinda Guerreiro 1,5  · Eliana Jerónimo 1  · Carmen Capel 6  · Juan Capel 6  · Fernando J. Yuste‑Lisbona 6  · Maria F. Duarte 1  · Rafael Lozano 6  · M. Margarida Oliveira 2  · Sónia Gonçalves 1,7 Received: 23 January 2017 / Accepted: 27 October 2017 © Springer-Verlag GmbH Germany 2017 Abstract Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropic- rin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from dif- ferent origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities. Using high-resolution melting, nine haplotypes were identifed. The putative impact of the identifed allelic variants in GAS protein was evaluated by bioinformatic tools and polymorphisms that putatively lead to protein conformational changes were described. Additionally, cynaropicrin and main pentacyclic triterpenes contents, and antithrombin, antimicrobial and antiproliferative activities were also determined in C. cardunculus leaf lipophilic-derived extracts. In this work we identifed allelic variants with putative impact on GAS protein, which are signifcantly associated with cynaropicrin content and antiproliferative activity. The results obtained sug- gest that the identifed polymorphisms should be explored as putative genetic markers correlated with biological properties in Cynara cardunculus. Keywords Cynara cardunculus · Germacrene A synthase · Single nucleotide polymorphisms · Cynaropicrin · Biological activities · Association analysis Abbreviations a.a Aminoacid CDS Coding sequence Cc Cynara cardunculus L. DMSO Dimethyl sulfoxide EI-MS Electron impact mass spectra GC–MS Gas chromatography–mass spectrometry GAS Germacrene A synthase HPLC–UV High-Performance Liquid Chromatogra- phy–Ultraviolet-Visible analysis HRM High-resolution melting Communicated by S. Hohmann. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00438-017-1388-z) contains supplementary material, which is available to authorized users. * Sónia Gonçalves sonia.goncalves@cebal.pt 1 Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908 Beja, Portugal 2 Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, 2781-901 Oeiras, Portugal 3 CICECO, Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal 4 LAQV, REQUIMTE, FCT, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal 5 Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, ULisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal 6 Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120 Almeria, Spain 7 Present Address: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SA, UK