Theses and Dissertations


Title: Development of type I markers of Ictalurid catfish

Name: Serapion, Jerry

Degree: MS

Chair: Zhanjiang (John) Liu

Resides:

University: Auburn University

Location: Auburn, Alabama

Date: 2003

Pages: 86

Keywords: Development,type I markers ,Ictalurid catfish

Abstract:

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution, and are required for comparative genomics. However, gene-derived markers are relatively more difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) for the identification of simple sequence repeats (SSR), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. Upon tagging microsatellites to genes, the microsatellites can then be used as gene markers. A biomformaties analysis of 15,565 ESTs in the GenBank identified 1672 ESTs containing microsatellites. Cluster analysis indicated that 853 of these ESTs fell into 204 contigs, and the remaining 819 ESTs were singletons. A total of 1,023 unique microsatellite-containing genes were identified. BLASTX similarity analysis revealed that 302 of the 1,023 unique genes corresponded to known genes. Of the 302 microsatellites associated with known genes, 241 harbored sufficient flanking sequences for primer design. Altogether, this project identified almost 900 useful microsatellites. The di-nucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among tri- and tetra-nucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. The approach of amplifying intron sequences using primers at flanking exons of known ESTs to identify intronic microsatellites was also studied. The rationale is that intronic sequences are more prone to mutations and therefore should harbor greater levels of polymorphism than exons, and so they would be more useful as genetic markers. In this project, 8 out of the 42 sequence-tagged sites (STS) contained intronic microsatellites. With a 19% success rate, this approach was useful for the development of microsatellite markers within known genes. Polymorphism was tested in the resource family F1-2 (female) x Channel catfish-6 (male). Our preliminary results indicated that the majority of the microsatellites were polymorphic and, therefore, are useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way and that will set the foundation for comparative genome analysis in catfish.

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