The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization

Abstract

Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. “Omics” based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from “omics” studies has not yet been completely realized. Integration between the multiple “omics” resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging “omics” based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of “omics” resources in penaeid aquaculture.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

“…While the penaeid industry has seen dramatic growth for the past few decades, industrial production of P. monodon proved to be unsustainable due to a lack of biological and genetic knowledge to achieve its desirable traits such as fast growth, disease resistance, reproductive maturation without reliance on wild brooders (Guppy et al, 2018). Recently, the L. vannamei breeding and domestication programs can be expeditely improved due to the available genome sequence, which allows selective breeding and helps in overcoming industrial challenges (Zhang et al, 2019).…”

Thermal challenge of the Indian shrimpPenaeus indicus

“…Successful breeding programs have significantly improved productivity, efficiency and stability of global aquaculture production of P. vannamei and P. monodon (Coman, 2014;Flegel, 2019;Moss, Moss, Arce, Lightner, & Lotz, 2012). Recent advances in 'omics' research and genomics breeding (Guppy et al, 2018) could allow us to realize these potential benefits of P. indicus much faster.…”

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

“…Likewise, Wang [45] found 3200 SNPs for L. vannamei would be sufficient for accurate GRM calculations when assessing an independent commercial population. While the genome sizes of P. monodon and L. vannamei are similar, and karyotypes are identical [2.2 Gb vs 1.7 Gb; 44 chromosomes; Guppy [46]], the lower required number of markers for GRMs in L. vannamei may be due to both studies utilising samples from established breeding programs (many generations removed from wild) with large full-sib/half-sib family structures rather than wild individuals from two distinct regions in this study [47]. Effectively, a large full-sib/half-sib family dataset structure requires fewer markers to completely tag each segregating portion of the genome, and as such results in lower variation in GRM estimates at lower marker densities [48][49][50].…”