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Originally published as Genetics Published Articles Ahead of Print on January 26, 2009.

Genetics, Vol. 181, 1649-1660, April 2009, Copyright © 2009
doi:10.1534/genetics.108.098855

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Huseyin Kucuktas*, Shaolin Wang*, Ping Li*, Chongbo He*, Peng Xu*, Zhenxia Sha*, Hong Liu*, Yanliang Jiang*, Puttharat Baoprasertkul*, Benjaporn Somridhivej*, Yaping Wang*, Jason Abernathy*, Ximing Guo{dagger}, Lei Liu{ddagger}, William Muir§ and Zhanjiang Liu*,1

* Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, {dagger} Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey 08349, {ddagger} W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and § Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907

1 Corresponding author: 203 Swingle Hall, Auburn University, Auburn, AL 36849.
E-mail: zliu{at}acesag.auburn.edu

A genetic linkage map of the channel catfish genome (N = 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3–18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.