Abstract
Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key production traits. In the current study, a population of 1,425 carp juveniles, originating from a partial factorial cross between 40 sires and 20 dams, was used for investigating the potential of genomic selection (GS) for juvenile growth, an exemplar polygenic production trait. RAD sequencing was used to identify and genotype SNP markers for subsequent parentage assignment, construction of a medium density genetic map (12,311 SNPs), genome-wide association study (GWAS), and testing of GS. A moderate heritability was estimated for body length of carp at 120 days (as a proxy of juvenile growth) of 0.33 (s.e. 0.05). No genome-wide significant QTL was identified using a single marker GWAS approach. Genomic prediction of breeding values outperformed pedigree-based prediction, resulting in 18% improvement in prediction accuracy. The impact of reduced SNP densities on prediction accuracy was tested by varying minor allele frequency (MAF) thresholds, with no drop in prediction accuracy until the MAF threshold is set <0.3 (2,744 SNPs). These results point to the potential for GS to improve economically important traits in common carp breeding programs.
Highlights
Carps have the highest global production volume of all aquaculture fish (FAO, 2015) and are farmed in a wide variety of environments and production systems (Balon, 1995)
In common with most aquaculture species, only a minority of farmed common carp are derived from family-based selective breeding programs, and crossbreeding of partially inbred strains is commonly applied to benefit from heterosis (Hulata, 1995; Vandeputte, 2003; Janssen et al, 2017)
Genomic Prediction in Juvenile Carp was to investigate the potential of genomic prediction of an exemplar polygenic trait in common carp using genome-wide SNP markers generated by Restriction-site-associated DNA sequencing (RAD-seq)
Summary
Carps have the highest global production volume of all aquaculture fish (FAO, 2015) and are farmed in a wide variety of environments and production systems (Balon, 1995). In common with most aquaculture species, only a minority of farmed common carp are derived from family-based selective breeding programs, and crossbreeding of partially inbred strains is commonly applied to benefit from heterosis (Hulata, 1995; Vandeputte, 2003; Janssen et al, 2017). Empirical data relating to selective breeding of family-based programs in several fish species show an increase in genetic gain of up to 15% per generation (Gjedrem, 2000). Genomic Prediction in Juvenile Carp was to investigate the potential of genomic prediction of an exemplar polygenic trait in common carp (juvenile growth) using genome-wide SNP markers generated by RAD-seq. RAD-seq was used to genotype genome-wide SNP markers, parentage assignment was performed, and heritability (of body weight and length) was estimated. GS was tested to evaluate the potential of incorporating genomic data for selective breeding compared to pedigree-based selection using this exemplar polygenic trait
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