Harnessing genomics to fast-track genetic improvement in aquaculture

Abstract

Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

Exploring genetic resistance to Infectious Salmon Anaemia Virus in Atlantic salmon by genome-wide association and RNA sequencing

“…Genetic improvement by selective breeding is limited by the existing additive genetic variation for the trait of interest in the population, and the ability to efficiently measure the trait, which limits the accuracy of selection and therefore genetic gain. The detection of functional genes and variants controlling disease resistance, as well as a better understanding of the genomic mechanisms underpinning disease resistance, can contribute to improve the efficiency of aquaculture breeding programmes by improvement of genomic selection methods [22]. Furthermore, this information can feed into genome editing efforts to enhance disease resistance, whether it is exploiting existing genetic variation or generating de novo mutations based on the functional basis of disease resistance [37,38].…”

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

“…Following the introduction of restriction‐site‐associated DNA sequencing (Baird et al., 2008), a wide range of related methodologies utilizing restriction enzymes have been introduced like genotyping by sequencing (Elshire et al., 2011), ddRAD‐seq (Peterson, Weber, Kay, Fisher, & Hoekstra, 2012), 2b‐RAD (Wang, Meyer, McKay, & Matz, 2012), ezRAD (Toonen et al., 2013), quaddRAD (Franchini, Monné Parera, Kautt, & Meyer, 2017), and 2RAD/3RAD (Bayona‐Vásquez et al., 2019). The aforementioned platforms have been used extensively in studies on aquatic organisms focusing both in population genetic aspects (Andrews, Good, Miller, Luikart, & Hohenlohe, 2016) and in studying traits of interest for farming purposes (Houston et al., 2020; You, Shan, & Shi, 2020). ddRAD‐seq is one of the most commonly utilized member of the reduced‐representation family combining simplicity and cost efficiency during library construction (Peterson et al., 2012).…”

Combining Multiple Approaches and Models to Dissect the Genetic Architecture of Resistance to Infections in Fish

“…The identification of the main mechanisms determining the resistance or susceptibility of a host to a pathogenic microbe is therefore extremely challenging, integrating the complexity of the variation of host genetics and the variability of pathogens and their capacity of fast evolution and adaptation. Genetic approaches such as QTL (quantitative trait loci) mapping make it possible to disentangle these complex interactions by providing information on the genetic determinism of host resistance and, ultimately, on the underlying genetic variations (and thus mechanisms) that make a host resistant or susceptible (Houston et al, 2020). Functional assays (comparative transcriptome analysis, in vitro culture models) also provide insights into mechanisms of interaction between the pathogen and its host and can help in identifying genes that play a key role in host response to infection.…”

“…Recent discoveries on probiotics raise hope for beneficial adjustment of gut microbiota, but no such treatment has been fully validated to date (Conti et al, 2014). Hence, genetic selection of fish with improved resistance to the main infectious diseases in a given environment remains a highly sought-after objective in aquaculture (Houston et al, 2020).…”