A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

Qiaomu Hu,Xiangshan Ji,Jiajie Zhu,Xiaolin Liao,Yang Liu,Haifeng Tian,Hanbing Xiao

doi:10.1186/s12864-021-07550-0

Abstract

BackgroundThe Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci.ResultsIn 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. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively.ConclusionWe constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

Highlights

The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal
A panel of 10,896 highfidelity single nucleotide polymorphisms (SNP) in both parents was identified, and alleles for each marker were assigned to their respective parent donor
The genetic length of linkage groups (LG) ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26)

Summary

Introduction

The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci. The Chinese giant salamander Andrias davidianus, historically widely distributed in China, is the world’s largest extant amphibian. Previous studies reported that the Chinese giant salamander 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. With the development of biotechnology, single nucleotide polymorphisms (SNP) has become the most popular tools to construct the highdensity linkage maps, because of their widely distribution in the genome and development of genomic sequence technology. High-density genetics maps are not yet available in amphibians

Methods

Results

Discussion

Conclusion