A High-Density Genetic Linkage Map of Channel Catfish for the Assembly of Reference Whole Genome Sequences

Genetic linkage maps are essential for mapping quantitative trait loci (QTL), identifying causative genes, facilitating whole genome sequence assembly, and conducting comparative genome analyses. However, progress has been hindered by the lack of efficient markers. Taking advantage of the catfish 250K SNP array, here we report the construction of a high-density and high-resolution genetic linkage map for channel catfish, Ictalurus punctatus, a dominant aquaculture species in the United States. A total of 62,870 informative SNPs were mapped by genotyping three families of 576 individuals using the catfish 250K SNP array. The sex-averaged map spanned a genetic length of 7088.5 cM, with an average inter-marker spacing of 0.4 cM across the 29 linkage groups. The female and male maps were estimated to be 7502.7 cM and 5421.7 cM, respectively, indicating a higher recombination rate in the female (1.38:1). This linkage map facilitates the building of chromosome-level assembly of the whole genome sequence by anchoring sequence scaffolds and contigs to linkage groups. A total of 86% of the catfish scaffolds from catfish genome assembly were anchored onto the 29 chromosomes. The linkage map is also useful in validating the whole genome sequence assembly. Eighty four problematic scaffolds were detected and corrected based on the linkage map. With exception of zebrafish, the catfish genetic linkage map contains the highest density of markers among aquatic animals, which provides a framework for constructing and validating the reference whole-genome sequence assembly, and provides the basis for whole genome comparative studies.