A review of catfish genomics: progress and perspectives

Abstract

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.

Artificial interspecific backcrosses between the hybrid of female Crassostrea hongkongensis × male C. gigas and the two parental species

“…The ratio of the H, HG and G locus types was approximately equal to 1:2:1 following the genetic segregation of Mendelian law. This result differed from several reports on the abnormal genetic patterns of fish F 2 hybrids analyzed using molecular methods (Liu, 2003;Liu et al, 1998;Stelkens et al, 2009). Collectively, the backcross progeny and F 2 hybrids showed a degree of genetic recombination and segregation despite using only one nuclear marker.…”

The Innate Immune-Related Genes in Catfish

“…Moreover, catfish remains to be the only fish species wherein clonal functionally of distinct lymphocyte cell lines have been established [29–31]. In catfish, innate immunity has built a set of complete defense system, proving beneficial in increasing resistance to pathogenic organisms [32], such as E. ictaluri and Flavobacterium columnare [33]. More recently, a large number of immune-relevant genes for innate immunity have been characterized in catfish, such as those encoding pattern recognition receptors, antimicrobial peptide, complements, lectins and cytokines [34–38] (Table 1).…”

A first generation BAC-based physical map of the channel catfish genome

“…Briefly, framework genetic linkage maps have been produced based on microsatellite loci [2] and Amplified Fragment Length Polymorphism (AFLP) loci [3]. Channel catfish Expressed Sequence Tags (EST) have been identified from several tissues [4,5] and clustered and annotated in the Gene Index Project [6]. A new EST project is underway through the Community Sequencing Program to sequence an additional 300,000 cDNA clones [7].…”