Resequencing insights into the genetic characteristic and development of molecular markers for Chi-Nan germplasm (Aquilaria sinensis)

Aquilaria sinensis is a subtropical tree species known for producing agarwood, which is widely used in traditional medicines and renowned for its incense qualities. The Chi-Nan germplasm (CNG), a new chemotype of A. sinensis , has a high capacity for agarwood production and has recently been discovered in the wild, with extensive cultivation through grafting in China. However, the origin and genetic characteristics of CNG remain unclear. To address this, we resequenced the genomes of 191 accessions including CNG and ordinary A. sinensis (OAS). Population genetic revealed that CNG and OAS were closely related but had genetic differentiation at some extend. Pairwise Sequentially Markovian Coalescent (PSMC) predicted a similar evolutionary strategy occurred between CNG and OAS, and they were diverged approximately 0.1 million years ago. Selective sweep analyses identified KEGG pathways, transcription factor families, and genes related to sesquiterpene and chromone biosynthesis, highlighting potential differences in agarwood formation between CNG and OAS. Additionally, 4 Kompetitive allele-specific PCR (KASP) markers were developed based on SNP loci in selective regions to accurately identify CNG. This study provides valuable genetic resources and insights into enhancing agarwood production and breeding varieties of A. sinensis . • The relationship of Chi-Nan germplasm and ordinary A. sinensis is close. • It have genetic differentiation between two germplasms in A. sinensis. • Two germplasms might diverged at ∼0.1 million years ago. • The variant pathways and genes related to agarwood biosynthesis were identified. • Molecular markers were creatively developed for Chi-Nan germplasm identification.