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

• Published in: Scientific reports Vol. 5; no. 1; p. 16358
• Main Authors: Wang, Le, Wan, Zi Yi, Bai, Bin, Huang, Shu Qing, Chua, Elaine, Lee, May, Pang, Hong Yan, Wen, Yan Fei, Liu, Peng, Liu, Feng, Sun, Fei, Lin, Grace, Ye, Bao Qing, Yue, Gen Hua
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.11.2015; Nature Publishing Group
• Subjects: 45/22; 45/43; 631/1647/2217/2138; 631/208/1348; Animals; Bass - genetics; Bass - growth & development; Chromosome Mapping; Computational Biology - methods; Female; Fish; Gene mapping; Genetic Linkage; Genomes; Genomics - methods; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; Lod Score; Male; Molecular Sequence Annotation; multidisciplinary; Nucleotide sequence; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Quantitative Trait, Heritable; Recombination, Genetic; Science; Single-nucleotide polymorphism; Synteny
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep16358

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 F 2 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.