A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

A high-resolution genetic linkage map was constructed by using 5059 ddRAD markers in P. vachelli. The length of the map was 4047.01 cM with an average marker interval of 0.11 cM. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate gene for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation.Conclusions: We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map using SNP markers for P. fulvidraco. Our results provided a valuable tool towards more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.