Genetic diversity and population structure of the endangered Japanese sea cucumber (Apostichopus japonicus) in natural seas of northern China

Abstract

Overfishing and habitat destruction have decimated wild sea cucumber (Apostichopus japonicus) stocks, causing this species to become endangered. Several conservation measures have been implemented to assist in the recovery of A. japonicus. Due to the low efficiency of conventional domestication methods and the current prevalence of bottom-sowing culture in marine ranches, it is urgent to evaluate the genetic diversity and population structure of sea cucumber geographical groups in the natural seas of northern China using genome-wide molecular markers. In this study, six sea cucumber geographical groups were collected from marine ranches in Shandong, Hebei, and Liaoning provinces. A total of 18,191 high-quality genome-wide single nucleotide polymorphisms (SNPs) were identified in 70 A. japonicus individuals using 2b-RAD technology. These SNPs were used to assess the genetic diversity and population structure of the six groups. Compared with previous studies, these six geographical groups showed much lower levels of genetic diversity both among and between groups, with all individuals clustering into one population. These findings demonstrate the necessity of continuous genetic monitoring of A. japonicus in the natural seas of northern China. Furthermore, this study serves as a valuable reference for future genome-assisted breeding and germplasm improvement in this economically critical species.

Keywords

• Genetic diversity
• Population structure
• Apostichopus japonicus
• Natural seas