A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus) Using 2b-RAD Sequencing

Abstract

A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus) is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs) and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker), while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker). The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1-13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp.

Keywords: QTL; SNP; candidate growth gene; comparative genomics; crucian carp; genetic linkage map.

Figure 1

Genetic distances and marker distribution of 50 linkage groups in the consensus linkage map of crucian carp. Within each linkage group, blue, green, and red lines represent maternal heterozygous SNPs, paternal heterozygous SNPs, and SNPs heterozygous in both parents, respectively.

Figure 2

Circos diagram representing syntenic relationships between crucian carp and zebrafish (A and B), grass carp (C and D), and common carp (E and F). (B, D, and F) show only 1:2, 1:4 or 1:1 perfect orthologous pairs.

Figure 3

Genomic synteny visualized using Oxford grids between crucian carp linkage groups and zebrafish chromosomes. The numbers in each cell represent number of homologous loci between crucian carp consensus linkage groups and zebrafish chromosomes. Homologous linkage groups and chromosomes are highlighted in yellow.

Figure 4

Genomic synteny between crucian carp linkage groups and grass carp linkage groups visualized using Oxford grids. The numbers in each cell represent number of homologous loci between crucian carp consensus linkage groups and grass carp linkage groups. Homologous linkage groups are highlighted in yellow.

Figure 5

Genomic synteny between crucian carp linkage groups and common carp chromosomes visualized using Oxford grids. The numbers in each cell represent number of homologous loci between crucian carp consensus linkage groups and common carp chromosomes. Homologous linkage groups and chromosomes are highlighted in yellow.

Figure 6

A genome scan of LOD profiles for body weight. The solid lines indicate the chromosome-wide significance thresholds.

Figure 7

The distribution of eight QTL for body weight on five genetic linkage groups of crucian carp.