High-density genetic linkage map and QTL fine mapping of growth and sex in snakehead (Channa argus)

Abstract

High-density genetic linkage maps are essential for quantitative trait locus (QTL) mapping, candidate gene identification, marker-assisted selection, genome assembly and comparative genomic analysis in aquaculture species. Snakehead (Channa argus) is an important aquaculture species in China, but the genetic improvement of this species is still in its infancy. In this study, a high-density genetic linkage map was constructed for snakehead using 2b-RAD sequencing technology. The consensus map contains 3151 single nucleotide polymorphism (SNP) markers assigned to 24 linkage groups (LGs) and spanning 2728.9 cM with an average marker interval of 0.87 cM. Comparative genomics revealed a 1:1 syntenic relationship between snakehead LGs and chromosomes of medaka and European seabass. Fourteen chromosome-wide QTLs associated with body weight and body length were identified in five LGs, explaining 9.6–12.8% of the phenotypic variation. Potential candidate growth-related genes, such as SATB homeobox 2 (satb2), were identified within the QTL intervals. A single major locus for sex determination was identified in LG5 that explained 97.4–100% of the phenotypic variation. Six markers with a sex-determining locus were found to be heterogametic in males and homogametic in females. A sex-specific SNP marker located in the sex QTL region was validated for practical verification of sex in snakehead. All of the results suggest an XX/XY sex determination system in this species. This high-density genetic map and QTL analysis supply a basis for genome evolutionary studies, genome assembly and QTL fine mapping of complex traits in snakehead.