First high-resolution genetic linkage map of taimen (Hucho taimen) and its application in QTL analysis of growth-related traits

Abstract Taimen (Hucho taimen) is an excellent aquaculture species. Currently, no selective breeding program has been conducted. To promote molecular breeding for taimen, we used genotype-by-sequencing technology to construct a high-resolution linkage map and performed QTL studies of growth-related traits. We sequenced 177 individuals of two full-sib families and obtained 58,016 SNPs. Among them, 30,535 SNPs were assigned to 42 linkage groups. The linkage map contained 6734 unique loci and spanned 4253.484 cM in total, with an average interval distance of 0.657 cM. The length for each linkage group ranged from 66.257 cM to 135.533 cM, with an average interval distance of 0.468 cM to 1.110 cM. This SNP linkage map integrated 65.1% scaffolds of the Hucho hucho genome to form 42 pseudo-chromosomes, with a mean correlation coefficiency of 0.893 between the linkage map and the genome. Based on this high-resolution linkage map, we performed QTL analyses of four growth-related traits of taimen aged 6–7 months. The analyses discovered 27 QTLs, including 18 QTLs for bodyweight, 5 QTLs for standard length, 3 QTLs for body thickness, and 1 QTL for body height. Based on Hucho hucho genome annotation, 487 genes within QTL regions were enriched in metabolism-related pathways; these genes could serve as candidate genes associated with the growth of taimen. The linkage map and QTLs obtained in this study provide useful tools for genetic studies and molecular breeding of taimen.