Construction of a high-density linkage map and QTL detection of growth and sex in blotched snakehead (Channa maculata)

High-density genetic linkage maps are comprehensively used in quantitative trait loci (QTLs) mapping, traitrelated genes identification, marker-assisted selection, genome assembly and comparative genomic analysis in domestic species. The blotched snakehead (Channa maculata) is an important aquaculture species in China and Southeast Asia, but the genetic improvement was lagged by lacking of genomic information. In this study, the first high-density genetic linkage map was constructed for blotched snakehead using 2b-RAD sequencing technology. The consensus map consists of 6352 single nucleotide polymorphism (SNP) markers that are assigned to 21 linkage groups (LGs) and spanning 2143.7 cM with an average marker interval of 0.34 cM. Comparative genomic analysis revealed 1:1 and/or 1:2 syntenic relationships between blotched snakehead LGs and chromosomes of medaka, European seabass and northern snakehead separately. Nine chromosome-wide QTLs associated with body weight were identified in three LGs, explaining 9.8?11.9% of the phenotypic variation. Putative candidate genes for growth rate, such as bone morphogenetic protein 6 (BMP 6), were identified adjacent to the QTLs. A single major locus tightly linked to sex was identified in LG2 that explained 98.8?100% of the phenotypic variation.Four markers within the sex-linked locus were found to be heterogametic in males and homogametic in females. One sex-specific SNP marker located in the sex QTL region was validated for practical verification of sex in blotched snakehead. Those results suggest that the LG2 may be a sex-related chromosome in blotched snakehead and an XX/XY chromosomal sex determination system in this species. The high-density linkage map and QTLs supply a basis for genome evolutionary studies, QTL fine mapping of economic traits and sex-control breeding in blotched snakehead.

Automated summary

The high-density genetic linkage map for blotched snakehead was constructed and revealed genomic information for the aquaculture species. The map identified chromosome-wide QTLs for body weight and a sex-related chromosome with a potential XX/XY sex determination system. The results provide important insights for genome evolutionary studies, QTL fine mapping, and sex-control breeding in blotched snakehead.