Genetic Characterization of Thai Indigo (Indigofera Tinctoria) by Data Single-Nucleotide Variants (SNVs) analysis.

Abstract

In the past, southern indigo was a highly sought-after local product for Portuguese traders, but the traditional knowledge and practices surrounding it have gradually faded over time. Meanwhile, in Northeastern Thailand, various types of indigo are widely cultivated, with Indigofera tinctoria L. (dye indigo) and Indigofera suffruticosa (wild indigo) being popular for producing a deep blue dye. Beyond its use as a dye, the indigo plant is also a source of bioactive compounds. This study aimed to investigate the genetic diversity of three indigo varieties: "Kram Thale" (sea indigo), "Kram Fak Khong" (curved-pod indigo), and "Kram Fak Trong" (straight-pod indigo). The research utilized single-nucleotide variants (SNVs) as molecular markers and analyzed the chemical composition of key compounds. The results showed that the nucleotide sequence data were of high quality, with an average quality score of 37–38. A total of 2,637,721 SNVs were initially detected, which was reduced to 1,801,689 SNVs after filtering. Genetic relationship analysis using a phylogenetic tree and Principal Component Analysis (PCA) revealed two main clusters. "Kram Thale" and "Kram Fak Khong" were found to be genetically similar, while "Kram Fak Trong" was distinctly separate. Population structure analysis also clearly divided the samples into three groups based on their variety. Furthermore, chemical analysis of the "Kram Thale" leaf extract using GC-MS identified several important compounds, including Phytol (6.73%), Hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl)ethyl ester (3.71%), 7-9-di+tert butyl-1-oxaspiro(4,5) deca-6,9-dinen-2,8-dione (3.62%), and 4-Acetyl-1,2,3,4-tetrahydro-2-oxoquinoline (3.41%). This study highlights the genetic differences between indigo varieties and the significant chemical composition of "Kram Thale," providing a foundation for future breeding programs and product development.