Genetic Differentiation Analysis of Three Glycyrrhiza Species via Whole-Genome Resequencing

Abstract Glycyrrhiza species are leguminous plants of significant medicinal value.Growing recognition of their medicinal and commercial importance has led to a substantial increase in market demand.Despite this demand, the genetic differentiation and adaptive evolutionary mechanisms at the whole-genome level among core species such as Glycyrrhiza uralensis , Glycyrrhiza glabra , and Glycyrrhiza inflata remain poorly understood.This study collected 45 samples of these three licorice species from Xinjiang, China, and performed whole-genome sequencing using the Illumina HiSeq platform. Using approximately 4.08 Gb of high-quality data, we conducted single-nucleotide polymorphism (SNP) detection, population genetic structure analysis (including phylogenetic tree construction, principal component analysis, and population structure modeling), selective sweep analysis, and gene functional enrichment analysis to systematically elucidate the genetic relationships and adaptive differentiation among the three species. Over 10 million high-quality SNPs were identified.Population genetic analysis revealed three genetically differentiated groups at the genomic level. Glycyrrhiza glabra and Glycyrrhiza inflata were most closely related (Fst = 0.169), while both showed higher differentiation from Glycyrrhiza uralensis (Fst > 0.182). Selective sweep analysis identified genomic regions under strong natural selection during species differentiation. Functional enrichment analysis of candidate genes within these regions showed significant enrichment in biological processes and pathways such as flavonoid biosynthesis, cellular redox homeostasis, and transmembrane signaling—functions closely linked to licorice’s secondary metabolism and environmental adaptability. This study demonstrates significant genetic differentiation among three medicinal licorice species at the whole-genome level and identifies potential functional genes associated with their adaptive evolution. These findings enhance our understanding of Glycyrrhiza evolutionary history and provide valuable genetic insights for medicinal germplasm improvement and resource conservation.