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Background    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.    Results  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.    Conclusion  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3534-8) contains supplementary material, which is available to authorized users.

bmc genomics

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