Genomic Approaches to Characterization of the Innate Immune Response of Catfish to Bacterial Infection

Abstract

Genetic selection for disease resistance encoded in the genomes of blue catfish and channel catfish continues to hold the greatest potential for long-term solutions to aquaculture-based disease outbreaks. Progress towards this goal requires the development of genomic resources for catfish, including expressed sequence tags (ESTs). In the context of catfish immune research, ESTs provide a foundation for both research on individual immune-related genes and microarray-based transcriptome analysis following infection. Both approaches are needed to advance our knowledge of teleost immunity and move closer to identification of genetic sources of disease resistance. My research, as presented here, encompasses these two complementary approaches to EST research with in-depth studies of the catfish CC chemokine family and development and utilization of a high-density oligonucleotide microarray for expression analysis following E. ictaluri infection. Twenty-six CC chemokines from catfish were mapped to BAC clones. Through a combination of hybridization and fluorescent fingerprinting, 18 fingerprinted contigs were assembled from BACs containing catfish CC chemokine genes. The catfish CC chemokine genes were found to be not only highly clustered in the catfish genome, but also extensively duplicated at various levels. The catfish CC chemokine family is the largest characterized CC chemokine family to-date, and it serves as a reference for chemokine studies in teleost fish as well as for studies of gene duplication patterns in catfish. ESTs were also utilized in the development of a 28K in situ oligonucleotide microarray composed of blue catfish (Ictalurus furcatus) and channel catfish (Ictalurus punctatus) transcripts. Initial microarray analyses in channel catfish and blue catfish liver following an infection with E. ictaluri captured a high number of unique, differentially expressed transcripts and indicated the strong upregulation of several pathways involved in the inflammatory immune response. The construction and utilization of high-density oligonucleotide microarrays from channel catfish and blue catfish ESTs represent a strong foundation for future, widespread use of microarrays in catfish research.