Dataset Information

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora).

ABSTRACT: A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24?cM and covered nearly the whole genome (99.4%) with a resolution of 0.47?cM. 1,457 scaffolds spanning 435.15?Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

SUBMITTER: Qiu C

PROVIDER: S-EPMC6250659 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora).

Qiu Changliang C Han Zhaofang Z Li Wanbo W Ye Kun K Xie Yangjie Y Wang Zhiyong Z

Scientific reports 20181122 1

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of th ...[more]

PMID: 30467365

Similar Datasets

Project description:Most of fish species exhibit striking sexual dimorphism, particularly during growth. There are also sexual dimorphisms of internal organs and biological functions, including those of intestinal microbiota, which likely plays a key role in growth. In this study, the growth and intestinal microbiota of the female, male, and all-female Nibea albiflora (yellow drums) were comprehensively analyzed. The caged culture female and all-female yellow drums showed higher growth rates than males. A further analysis of the intestinal microbiota showed a significant difference in diversity between females and males in the summer, whereas there were no significant differences in the diversity and richness between females and males in the winter. In contrast, a significant difference in richness was observed between all-female and male fish, regardless of the season. Although the main composition of the intestinal microbiota showed no significant sex differences, the community structure of the intestinal microbiota of yellow drums did. Furthermore, the correlations between intestinal microbial communities are likely to be influenced by sex. The ecological processes of the intestinal microbial communities of the yellow drums showed clear sexual dimorphism. Further network analysis revealed that, although the main components of the network in the intestinal microbiota of female, male, and all-female fish were similar, the network structures showed significant sex differences. The negative interactions among microbial species were the dominant relationships in the intestinal ecosystem, and Bacteroidetes, Firmicutes, and Proteobacteria were identified as the functional keystone microbes. In addition, the functional pathways in the intestinal microbiota of yellow drums showed no significant sexual or seasonal differences. Based on the findings of this study, we gain a comprehensive understanding of the interactions between sex, growth, and intestinal microbiota in yellow drums.

Dataset Information

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora).

Publications

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets