Transcribed Dinucleotide Microsatellites and Their Associated Genes from Channel CatfishIctalurus punctatus

Liu, Zhanjiang; Tan, G.; Li, Ping; Dunham, Rex A.

doi:10.1006/bbrc.1999.0751

Cited by 54 publications

(31 citation statements)

References 32 publications

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“…Several hundred microsatellite markers have been developed in catfish [5,11,21,26,27,33,35]. Microsatellite markers are very useful markers.…”

Section: Development and Evaluation Of Molecular Markersmentioning

confidence: 99%

A review of catfish genomics: progress and perspectives

Liu

2003

Comp Funct Genom

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Catfish is one of the lower teleosts whose genome research is important for evolutionary genomics. As the major aquaculture species in the USA, its genome research also has practical and economical implications. Much progress has been made in recent years, including the development of large numbers of molecular markers, the construction of framework genetic linkage maps, the identification of putative markers involved in performance traits, and the development of genomic resources. Repetitive elements have been identified and characterized in the catfish genome that should facilitate physical analysis of the catfish genome. A large number of genes or full-length cDNAs have been analysed using genomic approaches, providing information on gene structure, gene evolution and gene expression in relation to functions. Catfish genome research has come to a stage when physical mapping through BAC contig construction is greatly demanded, in order to develop regional markers for QTL analysis and for large-scale comparative mapping. The current effort in large-scale EST analysis and type I marker mapping should further enhance research efficiency through comparative mapping. Candidate gene identification is being accelerated through the use of cDNA microarrays.

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“…Several hundred microsatellite markers have been developed in catfish [5,11,21,26,27,33,35]. Microsatellite markers are very useful markers.…”

Section: Development and Evaluation Of Molecular Markersmentioning

confidence: 99%

A review of catfish genomics: progress and perspectives

Liu

2003

Comp Funct Genom

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“…Traditionally, SSR isolation has relied on the screening of genomic libraries using repetitive probes and sequencing of positive clones in order to develop locus-specific primers, which is obviously a tedious task but can result in numerous SSRs being obtained. Moreover, detection of polymorphic microsatellites located within genes and ESTs provides a possibility of connecting microsatellites with genes of known function and are more useful for comparative gene mapping to study evolution (Vignal et al 2002;Liu et al 1999).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite marker isolation and cultured strain identification in Carassius auratus gibelio

Guo

Gui

2008

Aquacult Int

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Microsatellites have become the preferred molecular markers for strain selection and genetic breeding in fish. In this study a total of 105 microsatellites were isolated and identified in gibel carp (Carassius auratus gibelio) by microsatellite sequence searches in GenBank and other databases and by screening and sequencing of positive clones from the genomic library enriched for AG and GATA repeats. Moreover, nineteen microsatellites were randomly selected to design locus-specific primer pairs, and these were successfully used to identify and discriminate different cultured strains of gibel carp including strains A, D, L, and F. Three different types of microsatellite pattern were distinguished by the number and length of fragments amplified from the 19 primer pairs, and some microsatellite primer pairs were found to produce different microsatellite patterns among strains and strain-specific fragments. In addition, some duplicated alleles were also detected in two microsatellite patterns. Therefore, the current study provides direct molecular markers to discriminate among different cultured strains for selective breeding and aquaculture practice of gibel carp.

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“…The catfish cDNA sequences are unique in that they appear to contain a large proportion of microsatellite-containing EST's compared to other species (21-23). Liu et al (22) and Karsi et al (21) reported finding microsatellites in 7% and 9% of brain and skin ESTs, respectively. This is much higher than that found in mammalian ESTs and even more than twice the rate in zebrafish ESTs (Table 2).…”

Section: Discussionmentioning

confidence: 97%

Isolation and Enrichment of Abundant Microsatellites from a Channel Catfish (Ictalurus punctatus) Brain cDNA Library

Nonneman

Waldbieser

2005

Animal Biotechnology

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Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5 0 -UTR, 72% contained repeats in the 3 0 -UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid, single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.

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Transcribed Dinucleotide Microsatellites and Their Associated Genes from Channel CatfishIctalurus punctatus

Cited by 54 publications

References 32 publications

A review of catfish genomics: progress and perspectives

A review of catfish genomics: progress and perspectives

Microsatellite marker isolation and cultured strain identification in Carassius auratus gibelio

Isolation and Enrichment of Abundant Microsatellites from a Channel Catfish (Ictalurus punctatus) Brain cDNA Library

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