High-Density Genetic Linkage Mapping in Hybrid Catfish Revealed Genomic Incompatibility Between Channel Catfish and Blue Catfish

Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform either of their parent species in a number of traits. Aquaculture of hybrid catfish is predominating the catfish industry nowadays. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array.  A total of 26,238 SNPs with 12,776 unique marker positions were mapped to 29 linkage groups. The linkage map spans approximately 3,240 cM with an average inter-marker distance of 0.25 cM.  A fraction of markers (986 of 12,776) exhibiting significant deviation from the expected Mendelian ratio of segregation were identified, which were clustered in major genomic blocks across 15 linkage groups, most notably on LG9 and LG15. The segregation distorted markers exhibited significant bias for the maternal alleles among the backcross progenies, suggesting the strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks provides insights into speciation as marked by incompatibilities between the two species. Such findings should have profound implications for understanding of genome evolution of closely related species, and for introgression hybrid production programs in aquaculture.