Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass

Abstract

A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5-16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis.

Figure 1. Genetic lengths and marker distribution of 24 linkage groups in the sex-averagedlinkage map of Asian seabass.

Figure 2

Genomic synteny as shown by Circos diagram for each pair of alignments between Asian seabass and (a) European seabass, (b) Nile tilapia and (c) stickleback.

Figure 3. Whole genome scan of QTL for growth-related traits in Asian seabass, where chromosome-wide LOD (3.0) threshold is denoted with dashed line.

Significance for each QTL region is denoted with *(chromosome-wide P < 0.05) and ***(genome-wide P < 0.01).

Figure 4

The expression pattern of ACOX1 gene in (a) 10 tissues and (b) between two fish groups of different body weight of Asian seabass. *and **denote significance level of P < 0.05 and 0.01, respectively.