Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in tiger puffer Takifugu rubripes

Abstract

The tiger puffer (Takifugu rubripes) is an important aquaculture species, and its low temperature tolerance breeding has a positive impact on the industry. However, genetic improvement of the species is still in its infancy. In order to promote the breeding process of tiger puffer, the construction of a genetic linkage map and the identification and validation of molecular markers associated with traits are the first steps towards marker-assisted selection (MAS). In this study, a high-density genetic linkage map of the tiger puffer was constructed by whole-genome resequencing. The map consisted of 4416 bin markers distributed over 22 linkage groups (LGs) with a total genetic coverage of 3147.8 cM and an average density of 0.76 cM. On this basis, quantitative trait locus (QTL) mapping results revealed that 14 QTLs associated with body weight, body length and total length were identified in five LGs at the genome-wide significance threshold, explaining 11.1–16.7% of the phenotypic variation. Among them, 10 QTLs were located in LG3, with the QTLs associated with body weight all located in LG3. There were four QTLs with overlapping regions which were associated with both body weight and total length. In addition, this study completed the QTL analysis of cold resistance traits of tiger puffer for the first time, and the results showed that eight QTLs were identified in six LGs, which explained 13.6–16.3% of the phenotypic variation. The linkage map and QTL for important economic traits obtained in this study provide useful tools for genetic research and molecular marker-assisted breeding of tiger puffer.