# Whole-Genome Resequencing Analysis Reveals Insights into Sex Determination and Gene Loci Associated with Sex Differences in Procambarus clarkii

## TL;DR

This study identifies the sex-determining region and genes in Procambarus clarkii, offering insights into crustacean sex determination and potential applications for genetic improvement.

## Contribution

The study identifies a sex-determining region on Chr38 and specific genes linked to sex determination in Procambarus clarkii for the first time.

## Key findings

- The XY sex determination system is located on Chr38: 6,000,000–21,100,000 bp.
- A 21 bp female-specific insertion was identified as a sex-specific molecular marker.
- Genes like SOAT, NPC1, and PTGS2 are linked to sex determination and validated through RT-qPCR.

## Abstract

Since the molecular mechanisms underlying sex determination in Procambarus clarkii are still unclear, it is important to investigate the genetic basis of sex determination in crustaceans. Currently, the molecular mechanisms of sex determination and the gender-specific markers in this species remain poorly understood. In this study, a total of 14,046,984 SNPs and 2,160,652 InDels were identified through genome-wide resequencing of 89 individuals (45 females and 44 males). Further analysis confirmed that the candidate chromosome was Chr38, the sex determination system was identified as XY, and the sex determination region was located at Chr38: 6,000,000–21,100,000 bp. A pair of sex-specific molecular markers has been identified based on a 21 bp female-specific insertion within the candidate sex-determining region. Additionally, SOAT, NPC1, PTGS2, FANCD1, and VAlRS were identified as candidate sex-determining genes through the screening of candidate genes and RT-qPCR validation analysis. These findings provide a robust foundation for investigating sex-determining mechanisms in crustaceans. Through the integration of genome-wide association studies (GWAS), selection signals, and transcriptome analysis, we identified, for the first time, genes associated with sex determination, growth, and immunity. These genes represent promising candidates for further functional studies and genetic improvement in Procambarus clarkii.