- A high-density genetic map construction and sex-related loci identification in. - Chinese Giant salamander. - Results: In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. - Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively.. - Conclusion: We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. - Keywords: Chinese giant salamander, ddRAD, SNP, High-density linkage map, Sex-related loci mapping. - Previous studies reported that the Chinese giant sala- mander has a huge genome (about 50 Gb) which was a big challenge to assemble [12], and to this direction the construction of a genetic linkage map will be a valuable tool. - we also charac- terized sex related gene in the sex differentiation [34, 35]. - Studies on the genetic level are necessary to identify sex related regions and ascertain the sex determination mechanism. - davidianus full-sib family to construct a high- density linkage map based on the ddRAD sequencing.. - Using the constructed linkage map. - We identified three sex-related loci in different linkage groups. - High-density linkage map construction. - In the present study, Join-map and Lep-Map were used to construct the high-density genetics linkage map of A.. - The maternal map con- tained 4830 SNPs with a total genetic distance of 2580.04 cM., The length of LGs ranged from 0 cM (LG27) to 298.26 cM (LG1) with an average genetic length of 86.00 cM (Table 1). - The total length of the integrated map was 2643.10 cM. - Hu et al. - Sex-related loci. - Sex-related loci of A. - 96246 in the sex-related loci were correlated with phenotype by the single-marker analysis of the WinQTL cart 2.5 (Table 2, Fig. - Eight maternal SNPs were found in the sex-related loci qs-1 and qs-2. - amphibians possessed a large genome [38, 39], which ex- hibited a challenge in constructing a high-density genetic linkage map. - davidianus has been reported, but identified markers were not used to build a linkage map [40]. - Sessions et al. - Andrias davidianus possesses a genome of ~ 50 G [12], hampering genomic and genetic study because of lack of large genome assembly technology and linkage map. - The present study exhibited the first high-density genetic linkage map using SNPs of A. - Thirty linkage groups were constructed with the aver- age marker-interval of 0.24 cM, which was the highest density linkage map in amphibians. - The highest density linkage map of fish species was con- structed for channel catfish, with the average marker interval of 0.22 cM [21]. - davidianus SNP linkage map displays high density even compared to fish species with relatively small genomes. - The high-density linkage map provided the means of fine mapping A. - davidianus sex-related QTL. - The genetic distance of the QTL locus ranged from 0.1 cM to 3.5 cM suggested a narrow re- gions in the linkage group. - This may provide valuable in- formation for sex-related gene detection. - While the same method was used to identify the loci on the mater- nal and paternal maps, all observed sex-related loci were on the maternal map. - It is possible that some key sex- related markers were homozygous on the paternal map.. - Some sex-related QTLs have been de- tected in other species, seven in the half-smooth tongue. - We analyzed sex related markers in this region and found correlation coefficient which ranged from 57.81 to 68.18% between phenotype and genotype in eight maternal SNP marker. - Possibly due to low sequencing depth, some key SNPs in sex-related loci were not mapped on the linkage group. - This region was considered as sex-related loci. - Further research requires expanded knowledge of the A. - We constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data from one full-sib family. - 2 Sex-related loci of Andreas davidianus. - Table 3 Correlation of markers in sex-related loci with phenotype. - At last, we found three sex related loci on the maternal map LG6 (qs-1, qs-2) and LG11(qs-3).. - 297384, 99.nn_np nn_np_278109, and 90.hk_hk_96246) in the sex-related loci were signifi- cantly correlated with phenotype which indicated the four markers were sex-related markers. - We con- structed a High-density genetic linkage map and mapped 3 sex-related loci, which provides the linkage map is a useful tool for genomic study and provides a genetic basis for marker-assisted breeding of Chin- ese giant salamander.. - The high quality genomic DNA (250 ng) from each of the 97 individuals were used to construct libraries. - 39 genotyping-deletion rate) of the individuals.. - Linkage map construction. - The linkage map was constructed using joinmap and Lep- Map. - Sex-related loci mapping. - CIM method of WinQTL Cart 2.5 software was used to map the sex-related loci on the male and female linkage maps respectively [49]. - All maternal SNPs in the located sex-related region were analyzed to detect cor- relation with the phenotype to find sex-related SNPs.. - org/10.1186/s . - https://doi.org . - 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