GENOMIC SELECTION AND THE FUTURE OF BREEDING IN SHRIMP

The availability of SPF (Specific Pathogen Free) shrimp broodstock has had a significant impact on the aquaculture of shrimp; from reducing the incidence of disease to facilitating more traditional family-based breeding for shrimp. From a breeding perspective, one of the shortcoming of the SPF system is that for biosecurity reasons, it does not allow for genetics from the growing ponds to be incorporated into the breeding program. Similarly, selection for other traits such as disease resistance and carcass quality prevent broodstock on which a trait was measured from returning and contributing to the breeding nucleus. Thus, the only way to use this information for genetic improvement is to rely on family and sib-ship information. This approach is not ideal for several reasons, including 1) the requirement for enough members of every given family to be sampled to produce good phenotypic data, 2) the accuracy of selection is limited as within family genetic effects are not captured. Mass selection approaches suffer from the same short comings in biosecurity and suffer from the risk of inbreeding depression. Genomic selection was developed to increase the accuracy of selection, accelerate genetic gain, and consequently increase the genetic gains per generation while simultaneously allowing for the control of inbreeding on a whole-genome level. It relies on the estimation of genomic similarity to predict breeding values based on the determination of DNA sequence, rather than sib-ship relationship. It is a powerful tool for many reasons: 1) it allows for increases in selection accuracy; 2) it allows for selection of breeding candidates from different genetic backgrounds that are more likely to perform well; 3) it allows for the control of inbreeding (relatedness) in whole-genome wise fashion; 4) it allows the selection on phenotypes that cannot be measured on the candidates without depending solely on family information. This last point can have a great impact on shrimp breeding, as it would allow the accurate incorporation of genetic data from ponds without increasing biosecurity risks. Application of genomic selection is feasible when combining an economically efficient method for scanning the genome of broodstock for SNP (single nucleotide polymorphism) markers, and genomic imputation to reduce the overall burden of genotyping costs. With this system, the economic costs for incorporating genomic selection to accelerate shrimp breeding programs are no longer barriers to implementation.