World Aquaculture Magazine - June 2020

30 JUNE 2020 • WORLD AQUACULTURE • WWW.WA S.ORG Benchmark Genetics SPF PacificWhite Shrimp Breeding ProgramDeveloping SPR Population Using Genomic Selection Oscar Hennig During recent years Benchmark Genetics has developed a solid presence in aquaculture genetics through acquisitions of Akvaforsk Genetics (AFGC), a leading provider of advanced breeding program design and technical services to global aquaculture, and the breeding companies SalmoBreed and Stofnfiskur (Atlantic salmon) and Spring Genetics (tilapia). With the recent incorporation of Benchmark Genetics Colombia in 2016, Benchmark expanded its breeding business to Pacific white shrimp. Benchmark Genetics Colombia continues and expands the pioneering shrimp breeding program initiated by CENIACUA in Colombia in 1997, a program designed and supervised by Akvaforsk Genetics. In early 2000 the shrimp farming industry in Asia was faced with unstable results, mainly due to the introduction of diseases in the farm environment from the use of wild black tiger shrimp broodstock. The production of Pacific white shrimp, a non-native species in Asia went from 2,310 t in 2000 to over 3 million t today. That jump was based on the Asian shrimp farmers’ ability to take advantage of genet- ically improved, SPF Pacific white shrimp broodstock. That strategy worked but has not prevented a series of new disease epidemics. The shrimp farm sector will continue to experience new epidemics while depending on broodstock poorly adapted to local conditions. To break this vicious cycle there is the need of an alternative, integrated disease management strategy based on minimizing the risk of introduction of new diseases to the region; deployment of populations resistant to endemic diseases; and sanitary practices that minimize the likelihood of epidemics and delay infection. Benchmark Genetics has successfully introduced genomic tools, used routinely in the salmon industry, into its shrimp breeding program. Combining the SPF/SPR approach, Benchmark Genetics has successfully developed Pacific white shrimp populations with high levels of resistance to major diseases affecting the shrimp industry today such as WSSV, AHPND, NHP, TSV and vibriosis. Development of High Vigor Shrimp Using High-Throughput Shrimp Genotyping Robin Pearl The use of DNA-based markers in genetics programs has been widely adopted in many agricultural industries. Using DNAmarkers in a shrimp selection program, it is relatively easy to quantify survival (Fig. 4) and determine genetic distance from specific shrimp or families in actual production environments. The main limitation when applying this technology to shrimp genetic programs is the time and cost to do many samples. Therefore, the real benefit this technology offers has been limited. In 2019, API installed a High Throughput DNAGenotyping System that allows API to genotype thousands of shrimp samples daily using a fully automated system. This new high throughput genotyping system allows API to get the full benefit of conducting a DNA-based shrimp genetics program. The API genetic program is working to maximize the potential of this new technology. Shrimp broodstock companies have generally focused on marketing one or two lines of production shrimp, i.e. a fast-growth line and a disease-resistant line. Using high-throughput genotyping technology, it is now possible to develop custom-selected shrimp lines for particular production systems and/or environments. Genomic Selection in Shrimp John T. Buchanan The availability of SPF 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 shortcomings 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 return- ing 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 as the accuracy of selection is limited because within-family genetic effects are not captured. Mass selection approaches suffer from the same shortcomings in biosecurity, lose potential increases in genetic gain to reduced accuracy and suffer from the risk of inbreeding depression. Genomic selection was devel- oped to increase the accuracy of selection, accelerate genetic gain, and consequently increase genetic gain per generation while simultaneously allowing for the control of inbreeding on a whole-genome level (Fig. 5). It relies on the measurement of genomic similarity to predict breeding values, rather than a sib-ship relationship. This allows 1) increases in selection accuracy, 2) selection of breeding candidates from different genetic backgrounds that are more likely to performwell, 3) control of inbreeding (relatedness) in a genome-wide fashion, 4) selection on phe- notypes that cannot be measured on the breeding candidates without FIGURE 4. API Elite Breeders selection data showing individual harvest weights by family and family survival. FIGURE 5. Continuum of selective breeding methods.