RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer

Abstract

Golden mahseer (Tor putitora) is a critically endangered fish with significant economic importance. However, its reproductive challenges in a captive environment pose a limitation to the successful domestication and aquaculture potential of this species. To understand the role of various genes in gonad maturation and reproduction in golden mahseer, we conducted an RNA-sequencing (RNA-Seq) study on the brains of mature male and female specimens. Altogether, 20.6 and 21.5 million reads were generated from the brains of the male and female fish, respectively. A total of 26,989 and 55,600 cDNA coding sequences (CDS) were identified from the male and female brains, respectively, among which 26,258 CDS from the male brain and 53,446 CDS from the female brain demonstrated homology to known protein database sequences. A comprehensive analysis revealed a total of 1187 distinct differentially expressed upregulated genes (DEGs), encompassing 953 DEGs anticipated to exhibit upregulation in the female brain and 234 DEGs in the male brain. Furthermore, in the brain of female and male golden mahseer, a significant downregulation was observed in 492 and 744 genes, respectively, resulting in a cumulative count of 1236 downregulated genes. Validation of the RNA-Seq results was performed by quantitative real-time PCR (qPCR) using 24 genes. Sixteen candidate genes with differential expression levels between the male and female fish were then selected and analyzed via qPCR. The results confirmed that amh, foxl3, dax1, kif20, and tkt were upregulated in the male golden mahseer brain, while cyp19a1a, dmrt2a, gdf9, sox9b, wt-1a, and aqp1 were upregulated in the female golden mahseer brain. Our study elucidates the distinct gene expression profiles in male and female golden mahseer brains and thus offers valuable insights for potential reproductive manipulation strategies in this fish species.