A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

Xiu Feng,Xiaomu Yu,Meixia Pang,Haiyang Liu,Xinhua Wang,Beide Fu,Jingou Tong

doi:10.1186/s12864-018-4613-1

Xiu Feng, Xiaomu Yu + Show 5 more

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https://doi.org/10.1186/s12864-018-4613-1

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Abstract

BackgroundA high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain.ResultsA high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin.ConclusionsWe mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Highlights

A high-density genetic linkage map is essential for quantitative trait loci (QTL) fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species
We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a highdensity genetic linkage map using single nucleotide polymorphism (SNP) and microsatellite markers for Yangtze River common carp
This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp

Summary

Introduction

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. RADrelated sequencing technologies have been successfully used for constructing high-resolution linkage maps in several aquaculture species, such as Atlantic salmon (Salmo salar) [13], Japanese flounder (Paralichthys olivaceus) [14], tilapia (Oreochromis niloticus L.) [15], Zhikong Scallop (Chlamys farreri) [5], pearl oyster (Pinctada fucata martensii) [16], Chinese mitten crab (Eriocheir sinensis) [17] and Asian seabass (Lates calcarifer) [18] Among those RAD-related methods, 2b-RAD strategy may have the simplest protocol for library preparation without any extra procedures for fragment selection and purification, and has been used for map construction in aquaculture species [5, 19, 20]. 2b-RAD produces uniform fragments for sequencing, providing more effective utilization of sequencing data among all individuals investigated

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