Black tiger shrimp (Penaeus monodon) are the second most cultured shrimp species globally, with over 700,000 tons produced per annum. However, like many aquaculture species the underlying drivers of economically important traits in black tiger shrimp are poorly understood, and the observed performance across individuals is highly variable. In particular, it is critical to uncover the genomic architecture of economically important traits to facilitate advanced selective breeding approaches (i.e. marker assisted selection or genomic selection). Such approaches are reliant upon a robust understanding of the placement and contribution of individual genetic markers in the prediction of an individual’s performance or merit (genomic estimate breeding value).
In this study, we utilised 2,745 individuals obtained from 19 families in an Australian commercial breeding population to construct a high-density genomic map containing 5,100 SNP markers obtained using genotype by sequencing. Overall, the genome-wide distribution of the SNP markers was confirmed with 43 linkage groups identified and through comparative mapping were subsequently anchored to, and then used to correct assembly errors in the Thai reference genome and further scaffold a Australian genome assembly. By combining genotype data and phenotypic records obtained at harvest, we undertook quantitative trait mapping (QTL) and genome-wide association studies (GWAS) for the primary production traits, growth and sex. In both QTL and GWAS analysis, a single sex-associated region was identified (Fig 1.), confirming earlier studies undertaken with divergent Indian and Mozambique black tiger shrimp breeding populations and the white leg shrimp, Litopenaeus vannamei. Current studies of genetic drivers of growth are underway; with preliminary results indicate a highly polygenic trait architecture with moderate heritability (h2 ≈ 0.24). Understanding the genomic architecture of commercial traits is critical to inform genetic improvement strategies for black tiger shrimp and lays the foundation for advanced methods of selective breeding.