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

Abstract

Introduction: Plectropomus leopardus, 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 P. leopardus are relatively lacking. Methods: 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 P. leopardus 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. Results: The results of these single-trait GWASs showed that 46 SNP loci (-log₁₀ p > 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 (-log₁₀ p > 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 taf7, ddx6, apoeb, sgk1, a2m, usf1, hsd3b7, dll4, xbp1, tet3, esr1, and gli3. 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. Discussion: In the present study, multiple genomic loci of P. leopardus 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 P. leopardus. Our results also can contribute to understanding the genetic basis of the sex differentiation mechanism and gonadal development process in grouper fish.

Keywords: Plectropomus leopardus; candidate genes; genome-wide association study; genomic loci; gonadal development; sex differentiation.

FIGURE 1

(A) Male gonad and (B) female gonad of P. leopardus.

FIGURE 2

Manhattan and QQ plots of genome-wide SNP significance for the traits of SDIF, GW, and GSI in P. leopardus. The X-axis shows all SNPs across chromosomes 1–24, and the Y-axis represents the -log₁₀ p. The gray dotted line indicates the genome-wide significant thresholds (p < 10E-7).

FIGURE 3

GO and KEGG analysis of the 156 potential candidate genes associated with sex differentiation and gonad development of P. leopardus. (A) Top 10 most significant GO terms (BP, biological process; CC, cellular component; and MF, molecular function) associated with the candidate genes; (B) top 20 most significant KEGG pathways associated with the candidate genes.