1. Introduction
Infectious diseases cause substantial economic losses in the aquaculture sector [
1]. Estimating the exact figure with high accuracy is challenging; for example, an estimated annual revenue loss globally because of viral diseases is approximately
$3-5 billion for the shrimp sector alone [
2]. Predictions suggest that the impact of disease outbreaks on the aquaculture sector will become more severe due to the unprecedented effects of changing environments [
3,
4]. Apparently, climate change can exacerbate the impact of diseases on animal health by altering the behaviour of pathogens, hosts, disease vectors, transmission rates, or the distribution of competitors, predators, and parasites within ecosystems [
5]. Elevated water temperatures, for instance, can accelerate the development of highly infectious pathogens, potentially leading to disease outbreaks with severe financial repercussions [
6].
Controlling diseases in aquaculture is crucial to ensure healthy animals and maximize yields. Common methods and strategies used to manage and control diseases in agriculture include biosecurity measures, sanitation, quarantine, chemical treatments, and therapeutic approaches such as diets, probiotics, or improved farming practices like crop rotation and vaccines [
7]. Sanitation involves cleaning and disinfecting to prevent the transfer of pathogens. Quarantine measures are essential to prevent the introduction of new diseases and protect pathogen-free farms. Chemical treatments, such as antibiotics, have raised concerns due to their potential impacts on human health and the natural environment, as well as the development of resistance [
8].
While vaccines have shown promise in controlling diseases in aquaculture species, their effectiveness can vary depending on several factors, including disease and species specificity [
9,
10]. There is a growing interest in controlling infectious diseases in an environmentally sustainable manner. Integrated farming systems, such as those involving fish, shrimp, and aquatic plants, or crop plants like rice, as well as the rotation of these species, can disrupt the life cycle of many disease-causing pathogens and reduce their build-up in aquaculture farms [
11]. However, these measures are often temporary and may not always be cost-effective and sustainable in the long term.
Genetics and genomics hold promise for providing sustainable solutions through the development of disease-resistant strains [
12,
13]. Specifically, quantitative genetic theory [
14] provides the framework for systematically improving disease resistance in host populations, both through selective breeding and, more recently, the integration of genomic data [
15,
16]. This approach has been successfully applied in various fields, including agriculture and animal breeding, to enhance disease resilience in animal and plant populations [
17]. Conventional genetic improvement programs combine phenotypic measurements with pedigree information. Phenotypic measurements involve measuring traits such as disease incidence, severity, or pathogen load in host populations [
18]. A pedigree is a family tree that keeps records over multiple generations and is maintained through physical tagging methods, such as PIT tags for fish and visible elastomer tags for crustaceans or DNA markers. Analysis of pedigree and phenotypic information is often conducted to obtain genetic parameters (heritability, correlations), providing primary inputs for genetic improvement programs and estimating individual genetic merits, known as estimated breeding values (EBVs) for selection. Across species, heritability for disease resistance traits to various pathogens (bacteria, viruses, parasites, or other pathogens) is moderate to high (h
2 = 0.09 – 0.41), indicating that genetic factors play a significant role in determining the trait and it can respond to artificial selection [
19,
20]. In addition to population parameters, genetic evaluation of pedigree and disease phenotypes is conducted to estimate EBVs for all individuals in the pedigree [
21]. Based on these EBVs, individuals with higher genetic resistance to the disease are selected as parents for the next generation. This approach has achieved significant genetic gain, ranging from 4% to 15% for economically important traits including disease resistance to various pathogens in fish, crustaceans, and molluscs [
22,
23]. Despite these successes, genetic improvement programs for aquaculture species often focus solely on improving resistance to a specific pathogen or selecting a single trait. Breeding objectives should be broadened by incorporating disease resistance alongside commercial traits like growth rate, meat quality, and reproductive performance. Furthermore, infectious disease resistance can be influenced by environmental factors, making it essential to evaluate resistance under different environmental conditions relevant to the target population.
Recently, omics technologies, when integrated with pedigree and phenotypes, have enhanced our understanding of the genetic basis of infectious diseases, guided the development of novel therapeutics and vaccines, and enabled more precise and personalized approaches to disease management and prevention [
24]. Specifically, genomics involves the study of an organism's entire genome, including its genes and non-coding sequences. Sequencing the genomes of infectious agents (e.g., bacteria, viruses, parasites) helped understand their genetic diversity, transmission pathways, evolution, and disease dynamics [
25]. More importantly, genome sequencing of aquaculture species helped understand the genetic factors in the host that influence susceptibility, resistance, and immune response to infectious diseases. In this context, genome sequencing also enables the selection of individuals based on their DNA information. This approach is known as genomic selection [
26], which involves using genome-wide markers or sequencing data, to predict their risks to diseases and their genomic breeding values for desirable traits, such as disease resistance. Studies in aquaculture species employing various algorithms, from mixed models to machine or deep learning, have shown that recent high-throughput genome sequencing platforms can provide genomic information to achieve moderate to high levels of prediction accuracy for disease traits [
27,
28]. After the prediction model is trained, breeders can apply it to individuals whose disease resistance is unknown, such as young animals. There are several benefits of genome-based selection for disease resistance, mainly including early identification and selection of disease-resistant individuals to reduce the generation time, increase accuracy to achieve faster improvements, reduce the cost of data recording, and improve genetic diversity [
29]. In short, genome-based selection is a powerful tool for enhancing disease resistance of aquaculture species, contributing to sustainable agriculture and improved animal health.
There are also other omics techniques [
30]. Transcriptomics studies differential gene expression between individuals or groups with different disease outcomes to discover genetic factors that contribute to resistance or susceptibility or identify genes that are upregulated or downregulated in response to infection. Proteomics assists in identifying host proteins or protein signatures that can serve as biomarkers for disease diagnosis, prognosis, or monitoring. Metagenomics [
31] studies the composition and functional potential of microbiomes to understand their role in infectious diseases and identify ways to manipulate the microbiome for therapeutic purposes [
32]. Functional genomics involves manipulating genes to understand their functions. This can include techniques like CRISPR-Cas9 gene editing to study the impact of specific genes on disease susceptibility or pathogen virulence [
33,
34].
This study is not intended to offer an exhaustive review of the existing literature on these subjects. A more comprehensive exploration of these themes can be found in recent review articles [
35,
36]. The current paper aims to emphasize the key discoveries derived from our research employing genetic and genomics methodologies to enhance disease resistance, focusing on three principal aquaculture species: white leg shrimp (
Litopenaeus vannamei), striped catfish (
Pangasianodon hypophthalmus) and yellowtail kingfish (
Seriola lalandi). Furthermore, this discussion encompasses emerging technologies, including precision agriculture systems, AI algorithms, and future research directions aimed at expediting genetic enhancements for our targeted species.
3. Alternative selection criteria to enhance disease resistance.
Genetic selection aimed at enhancing disease resistance remains a formidable challenge in aquaculture species, primarily due to the involvement of pathogen challenge tests that are both costly and time-consuming. Recent research endeavours [
45] have explored alternative selection criteria, such as viral titre or viral load, as means to develop disease-resistant lines within white shrimp species. Although heritable genetic components for viral titres related to infectious diseases, specifically hepatopancreatic parvovirus (HPV) in banana shrimp [
45] and White Spot Virus (WSSV) in
L. vannamei [
38], have been identified, accurately measuring this trait requires examination of the hepatopancreas in sacrificed breeding candidates. Furthermore, while there is a positive genetic association between viral titre and WSSV resistance, this correlation significantly deviates from unity, implying that these are distinct traits and that selecting for reduced viral titre cannot encapsulate the full spectrum of genetic expression associated with WSSV resistance, as observed by Trang et al. in 2019a. Given these challenges, there has been a growing interest in leveraging immunological parameters within selective breeding programs to bolster disease resistance across aquaculture species. In our research, we sought to acquire initial genetic parameters for immunological traits in our target species. Due to the limited sample sizes used for analysing these immunological parameters, heritability estimates for these traits were not published due to their low reliability. Nevertheless, studies in other species have provided evidence of genetic variability in immune responses, with heritability (h
2) estimates ranging from 0.2 to 0.3 for lysozyme in rainbow trout and h
2 estimates of 0.16 to 0.20 for antibody titres in Atlantic salmon [
52]. Furthermore, in various fish species, positive correlations have been established between disease resistance and non-specific immune factors, such as the correlation between
Aeromonas hydrophila resistance and immunity traits in bighead catfish (
rg = 0.05 - 0.27) [
53] or
Vibrio anguillarum and
A. salmonicida resistance and specific antibodies in rainbow trout [
54]. Also note that the correlation of resistance against
A. hydrophila with different immunological factors exhibited both negative and positive associations (
rg = -0.48 to 0.51) [
55]. The findings from these studies collectively suggest that immunological parameters hold promise as indirect selection criteria within selective breeding programs, ultimately enhancing overall disease resistance in aquaculture species, as highlighted by Van Sang et al., 2023. Currently, we are expanding our sample size to ensure a reliable estimation of genetic parameters within the populations of white leg shrimp and striped catfish under investigation.
4. Genetic variants for disease resistance
Traditional quantitative genetic selection has delivered a spectacular response, averaging 12.9% per generation, in bolstering resistance to different pathogens [
23]. Nevertheless, this conventional approach relies on challenge tests, which present significant practical challenges, including concerns related to biosecurity, labour-intensiveness, time consumption, and high costs. Considering these obstacles, we have identified molecular genetic markers that can facilitate gene- or marker-assisted selection for traits that are inherently challenging and costly to measure, such as disease resistance. To advance in this direction, we conducted Restricted sites associated DNA sequencing (RAD-seq) on a cohort consisting of 752 Yellowtail Kingfish (YTK) and 560 Striped Catfish individuals.
In YTK, our investigation yielded no markers associated with the animals’ susceptibility to skin flukes [
56]. This outcome may be attributed to multiple factors, including the limited representation of diseased fish in our study (only 4%), the utilization of shallow sequencing strategies, potential recombination during the course of line development, or insufficient linkage disequilibrium (LD) between markers and the genes responsible for disease susceptibility [
48]. In contrast, our analysis of Striped Catfish identified numerous SNPs significantly linked to disease resistance traits, as illustrated in
Figure 1. However, these SNPs collectively accounted for only a modest proportion (close to zero) of the trait's variation. Our further examination of these significant SNPs revealed no direct associations with genes of established functions. Surprisingly, SNPs linked to molecular mechanisms governing immune response and disease resistance, which one might expect, did not attain statistical significance. These findings further underscore the limitations of RAD-seq in terms of gene identification, primarily due to the provision of relatively short sequences, with an average length of only 68 base pairs.
To surmount these limitations, we are contemplating a comprehensive strategy involving the re-sequencing of a larger number of individuals to increase sequencing depth and sample size. This expanded approach aims to enhance our prospects of detecting genes that exert major effects on disease resistance traits within our studied populations of white shrimp, striped catfish and yellowtail kingfish.
5. Genomic prediction to enable genome-based selection
In the preceding section, we presented the outcomes of our genome-wide analysis, which reveal that numerous genetic variants additively influence disease resistance traits, with each variant exerting a relatively modest impact. Instead of searching for individual genes or variants, our approach involves simultaneously estimating their cumulative effects, leading to enhanced predictions of genetic susceptibility or genetic merit concerning disease-related phenotypes. Importantly, there are possibilities for uncovering causative mutations. Additionally, if our predictive models prove accurate, it may obviate the need for collecting phenotype data. The elimination of data recording for disease traits is particularly critical in the context of farmed and aquatic animal species, as this process entails significant time and cost implications. Furthermore, many economically significant traits are either expensive or challenging to measure, such as disease resistance, which often necessitates challenge tests involving pathogens, or eating quality traits, which require the slaughter of animals. Obviously, genomic prediction has become a pivotal component of genetic improvement programs, specifically geared towards forecasting susceptibility to infectious diseases within our studied species. The primary objective of genomic prediction is to leverage genome-wide markers or DNA sequences to forecast phenotypes, specifically in our studies to predict genetic predispositions to infectious diseases, thereby facilitating genome-based selection within our target species.
In these studies, we have employed several advanced statistical methodologies to estimate genomic breeding values (gEBVs). These comprise regression techniques, Best Linear Unbiased Prediction (BLUP), Bayesian approaches (such as Bayes A, B, C, Cpi, and R), as well as deep learning and machine learning algorithms powered by artificial intelligence [
57,
58]. Regardless of the method employed, the accuracy of genomic prediction is gauged by the correlation between predicted and actual phenotypes, with a correlation approaching one indicating a high level of accuracy. For instance, our predictions exhibited moderate to high accuracy for disease traits assessed in challenge test experiments [
59], whereas accuracy was lower for disease resistance recorded under field (or farm) conditions [
41]. A summary of the prediction accuracy for disease resistance traits, including survival rate and time to death, employing various statistical methods and algorithms, is shown in
Table 4.
Across our studied species, a consistent trend emerged indicating that multivariate analysis increased the precision of genomic prediction for disease-related traits [
59,
60]. The imputation of missing genotypes also contributed to an enhanced predictive capacity by 5-18% [
41]. Conversely, the utilization of SNP subsets obtained from Genome-Wide Association Studies (GWAS) yielded similar or lower prediction accuracies for these traits [
59]. Generally, BLUP-based methods (e.g., GBLUP or single-step GBLUP) exhibited comparable predictive performance to common Bayesian methods (i.e., Bayes A, B, C, and Cpi). However, Bayes R marginally outperformed GBLUP and other Bayesian techniques. Both deep learning and machine learning approaches surpassed GBLUP and Bayes R to some extent; nevertheless, the advantages of AI algorithms are contingent upon the specific populations and traits under consideration [
41,
60]. Their benefits become more pronounced when modelling intricate interaction networks and variables (Nguyen et al., unpublished).
In summary, our findings suggest the prospects of genome-based selection to enhance disease resistance within our target populations. Also note that prediction accuracy is influenced by various factors [
61], including the size of the reference population, trait heritability, structure and/or genetic composition of populations, gene or marker effects, the extent of linkage disequilibrium within populations, and the type of genotype data or sequencing platforms used (e.g., whole genome, whole exon, or reduced sequencing methods). In our studies, we performed reduced sequencing due to their affordable costs, which consistently provided informative markers to attain a reasonable level of prediction accuracy for disease traits. However, genomic selection for disease-related traits under field or on-farm conditions remains challenges, necessitating extensive, large-scale routine data collection pertaining to the disease status of animals during natural disease outbreaks. This indicates the continued importance of phenotype data in advancing genetic improvement for traits recorded under field (farm) environments. Furthermore, the availability of a robust genome assembly for these species holds the potential to accelerate progress in genomic selection and furnish reference information essential for comprehending the biological factors underlying genetic variations in disease traits among YTK and striped catfish populations.
8. Concluding remarks and suggestions
Our research has yielded valuable insights into the control of infectious diseases in white leg shrimp, striped catfish, and yellowtail kingfish. We have achieved this by developing disease-resistant strains that can thrive in diverse production systems. Despite our initial successes, it is evident that advancing genetic progress in these populations requires integrated, multidisciplinary research efforts.
In forthcoming studies, we aim to address emerging topics in the fields of genetics and genomics of infectious diseases. Exemplary questions are:
Which genes or genetic mutations have the most significant impact on variations in disease severity and outcomes among host individuals?
What are the genetic determinants governing immune responses to infectious agents, and how do these responses differ among individuals?
What molecular interactions occur between highly infectious pathogens and host cells, and how does host genetics influence these interactions? Can we leverage this knowledge for genetic improvement?
What genetic mutations are responsible for changes in pathogen virulence, transmissibility, and disease dynamics?
What are the most effective strategies for integrating host and pathogen genomics to gain a comprehensive understanding of the biological factors controlling complex infectious diseases?
By addressing these questions, our future research could further enhance our ability and knowledge to combat infectious diseases in aquaculture and promote sustainable and resilient production systems.