Improvement of Disease Resistance in Livestock: Application of Immunogenomics and CRISPR/Cas9 Technology

Abstract

Disease occurrence adversely affects livestock production and animal welfare, and have an impact on both human health and public perception of food-animals production. Combined efforts from farmers, animal scientists, and veterinarians have been continuing to explore the effective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food-animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance.

Keywords: bioinformatics; disease resistance; genome editing; livestock; next generation sequencing; transcriptomics.

Figure 1

Schematic diagram showing the applications of immunogenomics and genome editing to produce disease-resistant animals. Severity and pathogenesis of disease depend on the interaction of the host immune system and the invading pathogens, where host genetic has potential influence. Immunogenomics employ the integrated bioinformatics tools to explore the influence of host genetic on the interaction between the host immune system and invading pathogens and subsequently identify the candidate gene (s) for disease resistance. The CRISPR/Cas9 mediated genome editing technology could subsequently be employed for targeted modification of the host genome to produce disease-resistant animals.

Figure 2

A working pipeline of (in vivo, in vitro, and in silico) immunogenomics for identification of disease resistance candidate gene/marker as prospective targets for genome editing. Isolation of single-cell population of a target from both phenotypic groups followed by RNA and DNA extraction separately. The RNA samples could be employed for proteomics and metabolomics profiling. On the other hand, DNA samples could also be subjected to single nucleotide polymorphisms (NSP) sequencing and genotyping, quantitative trait loci (QTL) mapping, and genome-wide association study, and epigenomics study targeting the disease resistance phenotype. Rigorous integrated bioinformatics application on all sets of omics data together enables us to identify the molecular biomarker for the target immunocompetence trait. After functional validation of the identified biomarkers in the independent population, those could be recommended as the targets for CRISPR/Cas9 mediated genome editing technology.

Figure 3

Nuclease-based genome editors. (A). Zinc Finger Nuclease (B). Transcription-Activator Like Effector Nuclease (TALEN). (C). Schematic diagram showing genome editing using CRISPR/Cas9 system. The Cas9 induces DNA double-strand break (DSB) which are repaired either by imperfect nonhomologous end-joining (NHEJ) to generate insertion or deletion (indels) or if a repair is provided, by homology-directed repair (HDR) (Adapted from Moore et al. [71], and Pellagatti et al. [9].