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Published on: November 9, 2013
Genetic analysis of seed germination rates in Andrographis paniculata using whole-genome resequencing and SNP marker
Patcharaporn Summat1,2, Keasinee Tongmark1, Sriprapai Chakhonkaen1
1National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Khlong Luang, Pathum Thani, 12120 Thailand.
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.
