High-density genetic linkage mapping in turbot (Scophthalmus maximus L.) based on SNP markers and major sex- and growth-related regions detection

• Published in: PloS one 2015-03, Vol.10 (3), p.e0120410-e0120410
• Main Authors: Wang, Weiji, Hu, Yulong, Ma, Yu, Xu, Liyong, Guan, Jiantao, Kong, Jie
• Format: Article
• Language: English
• Subjects: Animals; Aquaculture; Biochemistry; Body length; Body Size - genetics; Body weight; Chromosomes; Commercial fishing; Deoxyribonucleic acid; DNA; DNA sequencing; Enzymes; Farming; Feasibility studies; Female; Females; Fish; Fishery sciences; Fishes; Fishing; Flatfishes - genetics; Flatfishes - growth & development; Gender differences; Gene mapping; Gene sequencing; Genetic aspects; Genetic Linkage; Genetic research; Genomes; Genomics; Growth; Homology; Laboratories; Male; Mapping; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Researchers; Scophthalmus maximus; Sex; Sex determination; Sex Determination Processes - genetics; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Sustainable development
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0120410

This paper describes the development of a high density consensus genetic linkage map of a turbot (Scophthalmus maximus L.) family composed of 149 mapping individuals using Single Nucleotide Polymorphisms (SNP) developed using the restriction-site associated DNA (RAD) sequencing technique with the restriction enzyme, PstI. A total of 6,647 SNPs were assigned to 22 linkage groups, which is equal to the number of chromosome pairs in turbot. For the first time, the average marker interval reached 0.3958 cM, which is equal to approximately 0.1203 Mb of the turbot genome. The observed 99.34% genome coverage indicates that the linkage map was genome-wide. A total of 220 Quantitative Traits Locus (QTLs) associated with two body length traits, two body weight traits in different growth periods and sex determination were detected with an LOD > 5.0 in 12 linkage groups (LGs), which explained the corresponding phenotypic variance (R2), ranging from 14.4-100%. Among them, 175 overlapped with linked SNPs, and the remaining 45 were located in regions between contiguous SNPs. According to the QTLs related to growth trait distribution and the changing of LGs during different growth periods, the growth traits are likely controlled by multi-SNPs distributed on several LGs; the effect of these SNPs changed during different growth periods. Most sex-related QTLs were detected at LG 21 with a linkage span of 70.882 cM. Additionally, a small number of QTLs with high feasibility and a narrow R2 distribution were also observed on LG7 and LG14, suggesting that multi LGs or chromosomes might be involved in sex determination. High homology was recorded between LG21 in Cynoglossus semilaevis and turbot. This high-saturated turbot RAD-Seq linkage map is undoubtedly a promising platform for marker assisted selection (MAS) and flatfish genomics research.