Construction of high-density genetic linkage maps and QTL mapping in the golden pompano

The golden pompano (Trachinotus blochii) is an essential marine fish species of South China. In this study, a genetic map containing 24 linkage groups was compared with 102 F-1 generation individuals (full-sib). A total of 23,558 single-nucleotide polymorphisms (SNPs) have been identified via restriction-site associated DNA sequencing (RAD-seq). Among these, 12,358 high-quality SNPs were utilized to construct a linkage map and consequently, we present the first reported genetic map of T. blochii. The total lengths of female, male and sex average linkage maps were 2559.12 cm, 2827.48 cm and 3810.03 cm, respectively. These linkage maps were built via the application of quantitative trait loci (QTL) tags, which are related to the size and growth of T. blochii. We successfully detected 23 QTL of growth-related traits, including 4 QTL for body length, 5 QTL for body weight, and 14 QTL for body height. This newly developed, QTL facilitating, and high-resolution genetic map represents preliminary progress toward linking the traits of key conservation interest to DNA regions in T. blochii. Our research will provide guidance for the molecular breeding of the golden pompano.