Advances in genetic and genomic resources in Pacific whiteleg shrimp Penaeus vannamei: Towards modern and sustainable shrimp aquaculture

Genetic improvement of Pacific whiteleg shrimp Penaeus vannamei, the most economically important crustacean worldwide, is key to ensuring shrimp aquaculture's sustainability. Maximizing the potential of this industry requires implementing well-managed, genome-enabled breeding programs. This review discusses genetic and genomic resources available for shrimp production and their application, covering topics such as population genetics, reference genomes, linkage maps, genetic markers, genome-wide association studies, and genomic selection. The genetic characterization of shrimp requires the availability of genetic marker panels, whose density depends upon the applications. Several low- and high-density marker panels, from microsatellites to single nucleotide polymorphisms, are currently used in population genetic structure, diversity, and parentage assignment studies. The challenge is the low cost per individual panel for commercial aquaculture operations. The reference genome of P. vannamei has been recently improved with new genome assemblies. Nevertheless, there is still room for improvement in scaffold assembly, genetic mapping, and gene annotation. This information will be useful to integrate genomic information into breeding programs to improve desired economic traits. Wild and captive populations have been well-characterized, and the genetic architectures of commercially relevant traits (i.e. growth, immune response, sex) have been studied. Future work should focus on the underlying genomic basis of productive and adaptive traits, which can be applied to modern selective breeding strategies, such as genomic selection. Developments in these areas should accelerate shrimp genetic improvement and will be key in ensuring the industry's sustainability.