Theses and Dissertations


Title: DEVELOPMENT OF GENOMIC RESOURCES AND cDNA MICROARRAY TECHNOLOGY FOR FUNCTIONAL GENOMICS OF CATFISH

Name: Kocabas, Arif Murat

Degree: PhD

Chair: Zhanjiang (John) Liu

Resides:

University: Auburn University

Location: Auburn, Alabama

Date: 2002

Pages: 93

Keywords: Channel catfish,gene expression,expressed sequence tag,myostatin,genomics

Abstract:

Myostatin is a recently discovered gene that inhibits muscle growth. Knockout of this gene alone might enhance carcass traits of animals and thereby significantly enhance production. Channel catfish (Ictalurus punctatus) myostatin gene was cloned, sequenced, and its expression was characterized. The myostatin gene has three exons encoding a protein of 389 amino acids. Comparison of the genomic sequences with those of the cDNA revealed that the myostatin cDNA was 1,673 base pair (bp) long with a 5'- untranslated region (UTR) and 3'-UTR of 180 bp and 323 bp, respectively. The deduced amino acid sequences of the catfish myostatin is highly conserved with those of other organisms. The myostatin locus is highly polymorphic in channel catfish because of the presence of several microsatellites and single nucleotide polymorphic sites. The myostatin gene was differentially expressed in various tissues and developmental stages, suggesting complex regulation of this gene and perhaps roles for myostatin in addition to those originally suggested. Expressed sequence tag (EST) analysis is an efficient approach not only for gene discovery and expression profiling, but also for development of molecular resources useful for functional genomics. ESTs were generated from channel catfish spleen cDNA library. A total of 1,208 spleen cDNA clones were analyzed. Of the 1,208 clones, 645 clones (54%) were identified as orthologues of known genes from other organisms by BLAST searches and 563 clones (46%) as unknown gene clones. There were 28 clones containing microsatellites that are useful as potential polymorphic markers for genome mapping studies. The identification of differential gene expression or differentially expressed genes (DEGs) between cells and tissues is a frequent goal in molecular biology research. White catfish (Ameiurus catus) grows more in winter than channel catfish, therefore, identifying DEGs that show different level of expression pattern in various conditions may have implications for genetic improvement of channel catfish. cDNA microarray technology was used to identify DEGs in the brain of cold acclimated white catfish. Two groups of white catfish were kept in different temperatures, 12±1°C and 24±1°C. Among the 660 genes studied, seven genes were up-regulated and 24 genes were down-regulated in the brain of white catfish that were kept at 12±1°C. These genes may be directly or indirectly involved in cold acclimation or cold tolerance, but the mechanism of their function needs to he further studied.

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