Objective The study was conducted to clarify the genetic structure characteristics, genetic diversity level and molecular variation of different geographical populations of Conopomorpha sinensis Bradely, with an aim to provide scientific evidence for the study of its origin and evolution and provide reference information for the control of this pest in different regions.

Method Using the C. sinensis from5production areas in southern China as materials, using GBS (Genotyping-by-sequencing) technology was used for samples genotyping, then SNP locus was identified with SAMTOOLS software, and phylogenetic tree was constructed according to SNP genotyping results. Finally, principal component analysis was performed.

Result Sequencing of C. sinensis from5regions was conducted by GBS technology. A total of 27.39 Gb of high-quality effective data were obtained, with an average of 5.48 Gb per sample. A total of 11 767 high-quality single nucleotide polymorphism (SNPs) loci were obtained. Phylogenetic tree analysis showed that the genetic relationship of Luzhou population was far from that of other populations. The results of principal component analysis showed that C. sinensis was divided into2groups in5regions, and the Luzhou population was significantly different from the other4populations. Both principal component analysis and phylogenetic tree analysis revealed that there were obvious differences in genetic level among C. sinensis from different geographical origins. The results of genetic diversity analysis showed that the observed heterozygosity was 0.2099-0.2531, the expected heterozygosity was 0.1937-0.2203, π was 0.2495-0.2748, indicating that the genetic diversity level of C. sinensis population was low. The results of AMOVA analysis showed that the genetic variation between populations (0.87%) was smaller than that within populations (99.13%), indicating that the variation mainly came from within populations rather than between populations.

Conclusion The genetic diversity level of C. sinensis in different geographical populations was low, while the genetic differentiation degree of Luzhou population in Sichuan was high, and its genetic relationship was distant with other populations.