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

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) widely distributes 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 8,487 SNP markers assigning on 50 linkage groups (LGs) and spanned 3,762.88 cM with an average marker interval of 0.44 cM and genome coverage of 98.8 %. The female map had 4,410 SNPs and spanned 3,500.42 cM (0.79 cM/marker), while the male map had 4,625 SNPs and spanned 3,346.33 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 an evidence that crucian carp had experienced the fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at two months after hatch were detected on five LGs, explaining 10.1-13.2% of the phenotypic variations. Potential candidate growth-related genes, such as EGF-like domain and TGF-beta, were identified within the QTL intervals. This high-density genetic map and QTL analysis supply a basis for genome evolutionary studies in cyprinid fishes, genome assembly and QTL fine mapping for complex traits in crucian carp.

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