Abstract
Andrographis paniculata, a traditional medicinal herb, is widely cultivated in Asia. This study investigates the genetic basis of seed germination rates using whole-genome resequencing (WGR) and SNP analysis. Germination rates of 40 A. paniculata accessions revealed two groups: low germination (0-20%) with 33 accessions and high germination (81-100%) with seven accessions. WGR was performed on 23 accessions, and SNPs were analyzed for genetic diversity, population structure, and QTL-seq. The genetic diversity and population structure analysis showed that most accessions were clustered together, while two exhibited distinct clustering patterns. QTL-seq identified regions across five chromosomes linked to germination, with 24 SNPs associated with this trait. Five SNP markers were developed using Tetra-Primer ARMS PCR and validated across all 40 accessions. Three markers-1-5362280, 1-5679230, and 16-3668893-showed the highest correlation with high germination rates, with marker 1-5362280 offering the strongest predictive accuracy (71.43%). These findings provide valuable molecular tools for marker-assisted selection, aiding in the development of improved A. paniculata cultivars for more efficient and sustainable cultivation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-025-01643-w.