AUTHOR=Gao Jin , Wang Yongbo , Liu Jinye , Chen Fuxiao , Guo Yilan , Ke Hongji , Wang Xulei , Luo Ming , Fu Shuyuan 

TITLE=Genome-wide association study reveals genomic loci of sex differentiation and gonadal development in Plectropomus leopardus

JOURNAL=Frontiers in Genetics

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1229242

DOI=10.3389/fgene.2023.1229242

ISSN=1664-8021

ABSTRACT=<p><bold>Introduction:</bold><italic>Plectropomus leopardus</italic>, a commercially significant marine fish, is primarily found in the Western Pacific regions and along the coast of Southeast Asia. A thorough analysis of the molecular mechanisms involved in sex differentiation is crucial for gaining a comprehensive understanding of gonadal development and improving sex control breeding. However, the relevant fundamental studies of <italic>P. leopardus</italic> are relatively lacking.</p><p><bold>Methods:</bold> In this study, a genome-wide association study (GWAS) was conducted to investigate the genetic basis mechanism of sex differentiation and gonadal developmental traits in <italic>P. leopardus</italic> utilizing about 6,850,000 high-quality single-nucleotide polymorphisms (SNPs) derived from 168 individuals (including 126 females and 42 males) by the genome-wide efficient mixed-model association (GEMMA) algorithm.</p><p><bold>Results:</bold> The results of these single-trait GWASs showed that 46 SNP loci (-log<sub>10</sub><italic>p</italic> &gt; 7) significantly associated with sex differentiation, and gonadal development traits were distributed in multiple different chromosomes, which suggested the analyzed traits were all complex traits under multi-locus control. A total of 1,838 potential candidate genes were obtained by considering a less-stringent threshold (-log<sub>10</sub><italic>p</italic> &gt; 6) and ±100 kb regions surrounding the significant genomic loci. Moreover, 31 candidate genes were identified through a comprehensive analysis of significant GWAS peaks, gene ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, including <italic>taf7</italic>, <italic>ddx6</italic>, <italic>apoeb</italic>, <italic>sgk1</italic>, <italic>a2m</italic>, <italic>usf1</italic>, <italic>hsd3b7</italic>, <italic>dll4</italic>, <italic>xbp1</italic>, <italic>tet3</italic>, <italic>esr1</italic>, and <italic>gli3</italic>. These trait-associated genes have been shown to be involved in germline development, male sex differentiation, gonad morphogenesis, hormone receptor binding, oocyte development, male gonad development, steroidogenesis, estrogen-synthetic pathway, etc.</p><p><bold>Discussion:</bold> In the present study, multiple genomic loci of <italic>P. leopardus</italic> associated with sex differentiation and gonadal development traits were identified for the first time by using GWAS, providing a valuable resource for further research on the molecular genetic mechanism and sex control in <italic>P. leopardus</italic>. Our results also can contribute to understanding the genetic basis of the sex differentiation mechanism and gonadal development process in grouper fish.</p>