Genome sequencing and genome-wide analysis uncover candidate genes and loci linked to key production traits in the Philippine black tiger shrimp (Penaeus monodon)

Abstract

<i>Penaeus monodon</i> (black tiger shrimp) is a key species in aquaculture globally and in the Philippines. The selection and development of stocks with desirable production traits, such as enhanced growth and disease resistance, are critical for improving production. In this study, we leveraged a newly assembled, high-quality genome sequence from a Philippine population to perform genome-wide scans for SNPs associated with key production traits. Using cohort-based extreme phenotype GWAS (XP-GWAS), we identified variants linked to resistance against white spot syndrome virus (WSSV), body weight, and carapace length-to-abdomen length (CL/AL) ratio. Candidate genes previously implicated in immune defense and growth regulation were located within 1-Mb regions surrounding these variants, reinforcing their likely functional involvement and providing biological support for the associations. These findings highlight genomic loci and gene candidates of direct relevance to selective breeding, offering molecular markers with potential utility in stock improvement programs for <i>P. monodon</i>. These genomic data, alongside the identified polymorphisms, constitute a valuable resource for enhancement of production and selective breeding strategies in the Penaeid species, contributing to the improvement of shrimp aquaculture.