Genome re-sequencing and PCR amplification based simple and rapid sexing method for Procambarus clarkii

Procambarus clarkii is a valuable commercial aquatic species in China. Like many commercial crustaceans, P. clarkii exhibits significant sex dimorphism, with females containing more flesh than males of the same weight. The genomic data generated by high-throughput sequencing technology provides crucial information for the development and application of sex-specific markers in a multitude of aquatic animals. In this study, whole genome re-sequencing was performed on 15 individuals each of female and male P. clarkii from the ZS population (sampled from Zhisheng, Chongqing). The total clean data from the female and male samples were 74.23 Gb and 71.43 Gb, respectively. Thus far, according to our analysis results, 187 primers have been designed for developing sex-specific markers, and three of them showed exclusively male-specific bands by PCR amplification. Further validation showed that these three sex-specific markers located on LG38 could effectively distinguish between male and female P. clarkii , with a sex discrimination rate ranging from 98.8 % to 100 % in five geographical regions. This PCR amplification-based approach to developing sex-specific markers is not only efficient and simple, but also serves as a useful reference that can be extended to other crustacean species based on next-generation sequencing data. The markers identified in this study may be useful for increasing yield through sex-control breeding in the P. clarkii aquaculture industry. • The sex-determination candidate region was located on LG 38 of P. clarkii . • Three male sex-specific markers located on LG 38 were developed. • P. clarkii was confirmed to use a male heterogametic system (XX/XY).