Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.)

Abstract

In order to identify candidate genes or loci associated with growth performance of the newly established common carp strain, Xinlong, we conducted a genome-wide association analysis using 2b-RAD technology on 123 individuals. We constructed two sets of libraries associated with growth-related parameters (weight, length, width and depth) measured at two different grow-out stages. Among the 413,059 SNPs identified using SOAP SNP calling, 147,131 were tested for GWAS after quality filtering. Finally, 39 overlapping SNPs, assigned to four genomic locations, were associated with growth traits in two stages. These loci were assigned to functional classes related to immune response, response to stress, neurogenesis, cholesterol metabolism and development, and proliferation and differentiation of cells. By overlapping results of Plink and EMMAX analyses, we identified three genes: TOX, PLK2 and CD163 (both methods P < 0.05). Our study results could be used for marker-assisted selection to further improve the growth of the Xinlong strain, and illustrate that largely different sets of genes drive the growth of carp in the early and late grow-out stages.

Figure 1

Comparison of mean growth rates of two carp populations at harvest. Con; Control group; Sel: selection group; hBwt: body weight (g); hBlen: body length (cm); hBwid: body width (cm); hBdep: body depth (cm). Data are expressed as the mean ± SD.

Figure 2

Effect of PLK2 genotype observed by GWAS on four growth parameters of the Xinlong carp strain after 8 months of grow-out culture. (a) Bwt5m (body weight, g), Blen5m (body length, mm), Bdep5m (body depth, mm) and BWid5m (body width, mm). Different characters represent significant differences between two genotypes. (b) DNA sequencing electropherograms of the AG and GG genotypes. The targeted SNP sites are indicated by black arrows.