Demonstration for Integration of Genetic Linkage and Physical Maps of Catfish Using BAC-Anchored Microsatellites

Abstract

Catfish is the major aquaculture species in the United States. The development of genetic linkage maps with high marker densities and the development of physical maps are important steps toward genome-enable genetic improvements. The integration of genetic linkage map and physical map should further enhance genomic research. In this work, sex-specific linkage maps and a sex-averaged genetic linkage map of catfish was constructed using the BAC-anchored microsatellite markers. For female map, a total of 413 markers were used. Of these, 398 were assigned into 29 linkage groups. The total female map size spanned 964.4 cM. For male map, a total of 158 markers were used. Of these, 142 markers were assigned to 19 linkage groups. The total male map size spanned 276.1 cM. The sex-averaged map was constructed by using 435 microsatellite markers, of which 416 were assigned to 29 linkage groups. The estimated total length of sex-averaged map was 974.1 cM. It appeared that a greater recombination rate existed in the female than in the male. The female:male recombination ratio was 1.7:1. Mapping of the 416 BAC-anchored microsatellites allowed mapping of 191 contigs to the genetic linkage map, thereby placing these contigs on the genetic linkage map. Of these, 138 contigs were mapped with at least 2 microsatellite markers, thus allowing orientation of the contigs on the linkage map. Some of the microsatellites from the same contigs were actually mapped to different linkage groups, raising the question of the correctness of the physical map. Considering the duplicated genomes of teleost fish, mapping of BAC-anchored microsatellites will provide a great tool to verify the quality of the physical map, and allow the correction of any mistakes on the physical map. This work, therefore, serves as a pilot study for integration of genetic linkage map and physical map, contributes to the marker density of the linkage map, and provide guidance to genetic linkage and physical mapping.