Construction of a high-density genetic linkage map and QTL mapping for growth traits in Pseudobagrus ussuriensis

Abstract

Growth traits of fish are controlled by multiple gene loci called quantitative trait loci (QTLs). For identification of these QTLs, a high-density genetic linkage map is necessary. In the present study, a high-resolution genetic linkage map was constructed for the Ussuri catfish Pseudobagrus ussuriensis using SNPs generated using 2b-RAD technology in an F1 family. The consensus map of P. ussuriensis contained 7435 SNPs that were distributed among 26 linkage groups (LGs) and spanned 2656.718 cM with a resolution of 0.357 cM and a genome coverage rate of 98.926%. Both of the sex-specific maps had 26 LGs: 3914 SNPs were located in the female map with a map length of 2566.285 cM, an average interval resolution of 0.656 cM and a genome coverage rate of 98.913%, and the male map comprised 4411 SNPs spanning 2084.518 cM with a resolution of 0.473 cM and a genome coverage of 98.914%. The average recombination rate ratio of female to male was 1.293:1. Comparative genome mapping revealed 21 1:1 and five 1:2 syntenic relationships between P. ussuriensis LGs and channel catfish chromosomes. Based on the consensus map, 28 growth-trait-related QTLs (one genome-wide and 27 chromosome-wide) were identified in five LGs (LG1, LG4, LG5, LG16 and LG19) with a phenotypic variance explained (PVE) value range of 11.9–20.5%. The high-density genetic linkage map obtained in this study will provide important information for future genetic, genomic and evolutionary studies of P. ussuriensis, and the QTLs will be useful tools for growth mechanism analysis and marker assisted selection (MAS) breeding in this fish.