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United States Department of Agriculture

Agricultural Research Service

Research Project: CATFISH GENETICS, BREEDING, AND PHYSIOLOGY Title: Production and Utilization of a High-Density Oligonucleotide Microarray in Channel Catfish, Ictalurus punctatus

Authors
item Li, Robert
item Waldbieser, Geoffrey

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2006
Publication Date: June 1, 2006
Citation: Li, R.W., Waldbieser, G.C. 2006. Production and Utilization of a High-Density Oligonucleotide Microarray in Channel Catfish, Ictalurus punctatus. Biomed Central (BMC) Genomics 2006, vol. 7:134.

Interpretive Summary: Losses to disease is a major cause of production losses in the U.S. catfish industry. Understanding the genetic control of the catfish immune system will help researchers identify fish with superior genetic potential and use them as broodstock for improving disease resistance in commercial catfish populations. Toward this goal, we have created a microarray useful for simultaneously measuring levels of gene expression for almost 19,000 separate catfish genes. Channel catfish were injected with lipopolysaccharide, a component of bacterial cell walls that elicits immune responses, and total RNA from the spleen was removed 2, 4, 8, or 24 hours after injection. The microarray analysis showed 409 genes that were induced or repressed at least 2-fold by LPS exposure. Of these, 83 could be placed in one of six groups that demonstrated specific trends in expression over time. Measurement of gene expression by the microarray was highly correlated with measurement by quantitative real time PCR. The findings enable us to better understand recognition of LPS by host cells and the LPS-signaling pathway in fish, and further elucidate pathogen recognition pathways in the catfish.

Technical Abstract: A high-density oligonucleotide microarray for channel catfish (Ictalurus punctatus) was designed and produced with Maskless Array Synthesizer technology. The microarray contained 379,652 oligonucleotides (24-mer) covering 18,989 catfish unique sequences. Global expression profiling of the catfish spleens stimulated by lipopolysaccharide (LPS) for 2h, 4h, 8h and 24h was investigated with the microarray. In the spleen samples, 409 genes were induced or repressed greater than 2-fold by LPS treatment. “Self-organizing maps” clustering analysis was applied to interpret gene expression patterns, and 84 genes were clustered into six expression patterns. Real-time RT-PCR was used to verify the microarray results for 9 selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R2 = 0.87) with the results from the microarray. The findings enable us to better understand recognition of LPS by host cells and the LPS-signaling pathway in fish. The comparison between the LPS-signaling pathway in lower vertebrates and those well-documented in mammalian species such as humans and mice facilitates our understanding of the evolution of innate immunity.

Last Modified: 10/23/2014
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