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<p><i>Andrographis paniculata</i>, 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 <i>A. paniculata</i> 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 <i>A. paniculata</i> cultivars for more efficient and sustainable cultivation.</p>

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Genetic analysis of seed germination rates in Andrographis paniculata using whole-genome resequencing and SNP marker development for breeding improvement

  • 期刊论文

  • 发表日期：

    2025年8月28日

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  • Patcharaporn Summat,
  • Keasinee Tongmark,
  • Sriprapai Chakhonkaen,
  • Numphet Sangarwut,
  • Natjaree Panyawut,
  • Wisuwat Thongphichai,
  • Suchada Sukrong,
  • Wanchana Aesomnuk,
  • Samart Wanchana,
  • Supatcharee Netrphan,
  • Amorntip Muangprom

摘要

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.