# GWAS-Identified SNPs and Candidate Genes Influencing Sex in Loach (Misgurnus anguillicaudatus)

## TL;DR

This study identifies genetic markers and genes influencing sex in loach, which can help develop all-female breeding strategies to improve farming efficiency and economic value.

## Contribution

The study discovers sex-specific SNPs and candidate genes in loach, offering molecular tools for monosex breeding.

## Key findings

- 84 sex-associated SNPs were identified, with over half located on chromosome 6.
- Candidate genes like hemgn, foxl2a, and pard3ba were linked to sex regulation in loach.
- Signaling pathways such as TGF-β, FoxO, and mTOR are involved in sex regulation.

## Abstract

Loach (Misgurnus anguillicaudatus) has high nutritional value and is one of the important edible freshwater fish in East Asia. In particular, female loach is popular with consumers because of its large size. Thus, genetic improvements in all-female breeding of loaches better aligns with market demands. Elucidating the mechanism of sex regulation is critical to achieving monosex breeding in aquatic animals. However, the genetic basis for controlling the sex of loaches remains unclear at present. This study performed a genome-wide association study on male and female loaches, identifying sex-associated SNPs and important candidate genes. Notably, a sex-specific SNP marker that effectively identifies the genetic sex of loaches was developed. These findings will advance all-female loach breeding to enhance cultivation efficiency and economic value.

Loach (Misgurnus anguillicaudatus) is a small benthic fish favored by consumers in East Asia. Female loaches exhibit greater production value due to their larger size and higher meat yield. Therefore, controlling the sex of loach should be studied to implement an all-female breeding strategy. This study identified sex-related SNP markers and candidate genes in loach through GWAS. Genotyping male and female populations with WGRS revealed 84 SNPs labeled as associated with sex. Distinct SNP peaks appeared on Chr6 and Chr3, with over half of the sex-associated SNPs located on Chr6. Within these sex-associated regions, 15 key candidate genes related to sex and reproduction were identified, including hemgn and foxl2a. Among these genes, pik3cb on Chr3 and hhip, cntln, and pard3ba on Chr6 have multiple sex-associated haplotypes that can be utilized for subsequent monosex breeding. Notably, a highly male-linked SNP marker was identified on pard3ba, whose genotype is consistent with the male heterogamete (XX/XY). Through gene enrichment analysis and expression validation, signaling pathways such as TGF-β, FoxO, and mTOR were identified as being involved in sex regulation. This study provides molecular markers for sex-controlled breeding in loach, facilitating in-depth research into the mechanisms of sex regulation in loach.