Identification of SNPs and Candidate Genes Associated with Fecundity Trait Using BSA-seq and RNA-seq in Exopalaemon carinicauda.

Reproductive traits are of paramount importance as economic traits in shrimps, playing a vital role in enhancing commercial larval production within the aquaculture industry. Identifying genetic markers associated with reproductive traits is essential for implementing genomic and marker-assisted selection strategies to enhance reproductive performance. However, the existing knowledge of such genetic markers in Exopalaemon carinicauda remains relatively limited. In this study, we utilized next-generation sequencing coupled with bulked segregant analysis to identify molecular markers and candidate genes associated with reproductive traits in E. carinicauda using a F₂ population. A total of 31,048,793 SNPs and 3193 indels were identified between the two pools. Six candidate regions, spanning 72.24 Mb on chromosomes 6, 14, 15, 21, 23, and 35, were consistently identified through Euclidean distance and ΔSNP-index analyses, encompassing 609 genes. Kyoto Encyclopedia of Genes and Genomes analysis revealed significant associations with pathways such as ovarian steroidogenesis, oocyte meiosis, insulin signaling, GnRH signaling, and estrogen signaling. Among these, 22 genes showed strong links to ovarian development based on comparative transcriptomic analysis across 4 ovarian development stages. The integrated analysis of whole genome and transcriptome data showed that four genes (juvenile hormone esterase carboxylesterase, aurora kinase A, insulin-like peptide receptor, and Argonaute 3) might play important roles in regulating reproductive traits of E. carinicauda. Five SNP loci were validated employing a general linear model that are significantly associated with fecundity traits in the F₂ population. These findings not only offer valuable insights into the genetic underpinnings of reproductive traits but also provide a strong foundation for the development of genomic and marker-assisted selection strategies aimed at enhancing fecundity traits in E. carinicauda.