Construction of a high-density high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Abstract

Catfish is the leading aquaculture specie in the United States of American. However, the catfish industry is facing great challenges due to devastating diseases, high production cost, high feed and energy cost and international competition. Exploiting fish genetics and genomics can greatly contribute to production efficiency and enhancing performance. Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K SNP array. A total of 54,342 SNPs were placed on the linkage map, the highest marker density among all aquaculture species. The estimated genetic size was 3,505 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495 cM in females and 2,594 cM in males, representing a ratio of 1.7:1 between female and male in recombination rate. After integration with previously established physical map, over 87% of physical map contigs were anchored to the linkage groups which covered a physical length of 867 Mb, accounting for about 90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole genome assembly, and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.