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BMC Genomics. 2017 Feb 17;18(1):183. doi: 10.1186/s12864-017-3534-8.

Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities.

Author information

Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908, Beja, Portugal.
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2781-901, Oeiras, Portugal.
Centre for Research in Ceramics and Composite Materials (CICECO) and Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal.
Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, University of Lisbon, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal.
Centro de Investigación en Biotecnología Agroalimentaria (BITAL), Universidad de Almería, 04120, Almeria, Spain.
Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, 7801-908, Beja, Portugal.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB101SA, Cambridge, UK.



Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities.


In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3'-hydroxylase (C3'H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3'H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3'H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms.


In this work we identified allelic variants with putative impact on C3'H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.


Antioxidant activity; Antithrombin activity; Association analysis; C3′H; Chlorogenic acid; Cynara cardunculus; HQT; Haplotype; High-resolution melting; SNPs

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