Study of the origin and evolution of Isatis indigotica fortune via whole-genome resequencing

Isatis indigotica Fortune is a plant with significant medicinal and dye value, and its characteristics are important for agricultural production and industrial uses. Therefore, elucidating the origin and evolutionary path of I. indigotica is crucial for increasing its economic value. Whole-genome resequencing was performed on 94 cultivated samples of I. indigotica . Principal component analysis and phylogenetic tree analysis revealed that Group 1 (g1) included I. indigotica found in regions in Northwest China and Northern China, whereas Group 2 (g2) included I. indigotica growing in other major Chinese production zones. Assessment of linkage disequilibrium in the genomes of g1 and g2 revealed that g1 has been subjected to more significant selective pressure than was g2. SNP-based structure and gene flow analyses highlighted the origin of I. indigotica in Northwest China and indicated that it subsequently spread to Northeast, Eastern, and Central China. Additionally, the use of single-nucleotide polymorphisms and morphological data in genome-wide association studies revealed significant differences in traits between g1 and g2. QTLs reveal genes that affect key traits on different chromosomes. Furthermore, KEGG and GO analyses revealed genes that affect metabolic pathways such as glutathione metabolism, pentose and glucuronate interconversion, and the biosynthesis of plant secondary metabolites. Generally, the WGR and GWAS of I. indigotica disclosed its origin, evolutionary route, population distribution, selective pressure, trait variances, and the genes influencing key traits. In the future, through functional validation and molecular marker-assisted breeding, candidate genes associated with target traits can be used to cultivate superior varieties of I. indigotica . • Whole genome resequencing was performed on 94 samples of Isatis indigotica cultivation. Through PCA and phylogenetic tree analysis, the samples were divided into two groups including g1 and g2. • SNP based structural and gene flow analysis indicates that I. indigotica originated in the northwest region of China and subsequently spread to the northeast, east, and central regions.