Genetic diversity analysis of wild population based on SNP developed from transcriptome sequencing of spot-fin porcupine fish (Diodon hystrix)

Abstract

Diodon hystrix is widely distributed in tropical and subtropical coastal waters. Owing to its delicious taste, the annual catch of this fish in the South China Sea has been on the rise. It is urgent to assess the population status of D. hystrix. Molecular markers are often used to evaluate the population status of the important and rare fishery resource, however, there was still no suitable markers of D. hystrix with overfishing in recent years. This study totally obtained 7.2 Mb clean reads with 94.92 % of Q20 bases and 4179 variants of 2276 unigenes by Illumina sequencing platform. Additionally, 64 amplifiable variants of 36 unigenes were obtained by PCR amplification, and 25 available SNPs showing polymorphism were confirmed from these amplifiable variants. By assessing the index of association, we ultimately identified 14 SNPs after removing 10 SNPs with linkage disequilibrium and 1 SNP with Hardy-Weinberg disequilibrium. Using these 14 SNPs, we can evaluate the wild population of D. hystrix as a sexually reproducing population and speculate that this population was relatively stable (HWE. p = 0.525) with moderate genetic diversity (PIC = 0.328). In conclusion, transcriptomic sequencing can quickly obtain the SNPs as molecular markers which can be used for population genetic diversity. It provides necessary help for the conservation biology and resource evaluation of D. hystrix.