Genetic structure analysis of Glycyrrhiza species and identification of SNP-loci associated with secondary metabolites in G. glabra

BACKGROUND: Glycyrrhiza spp. are medicinal legumes that produce a wide array of pharmacologically active secondary metabolites. This study generated a genomic resource by genotyping-by-sequencing 175 Glycyrrhiza accessions and populations to (1) characterize their genetic structure and assess population relationships, and (2) perform an association mapping for three medically important traits within G. glabra. RESULTS: We identified 38,393 high-quality single-nucleotide polymorphisms (SNPs). Genetic structure analysis revealed that G. glabra is mostly distinct from the other species, and identified one group of 66 plants from 33 Iranian G. glabra origins with moderate genetic differentiation. The association mapping identified in total 20 highly significant SNPs for three traits: 15 for glabridin in the cork layer of the root, of which 3 were also associated with glabridin in the fleshy texture of the root, and 5 for liquiritigenin in the cork layer of the root. Glabridin and liquiritigenin are described to be involved in biotic and abiotic stress responses. Candidate genes include: (1) MYB6 - a transcription factor that activates flavonoid-biosynthetic genes. (2) OCTOPUS-like - a regulator of primary root protophloem differentiation and root architecture. (3) WRKY transcription factors - modulators of phenylpropanoid, alkaloid and terpene pathways. (4) Aminodeoxychorismate synthase. CONCLUSIONS: Our study provided a comprehensive understanding of the genetic diversity of Glycyrrhiza spp. We identified genetic markers associated with important metabolites of the root, i.e. the flavonoids glabridin and liquiritigenin. These findings will facilitate the exploitation of genetic resources and inform future breeding programs, ultimately contributing to the development of improved Glycyrrhiza spp. varieties with enhanced medicinal properties.