Genome-wide SNP genotyping in common carp

Genomic DNA was extracted from whole blood using a DNeasy 96 Blood & Tissue Kit (Qiagen, Shanghai, China) following the manufacturer’s protocol. The extracted DNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, United States). The integrity of DNA was examined on a 1.5% agarose gel by electrophoresis. The final DNA concentration was diluted to 50 ng/μL for genotyping. The total amount of qualified genomic DNA for whole genome sequencing was 2 μg per sample. The common carp 250K SNP array was developed in a previous study using the Affymetrix Axiom genotyping technology (Xu J. et al., 2014 (link)). Genotyping was performed by GeneSeek (Lincoln, Nebraska, United States). After genotyping, PLINK v1.9³ was used for quality control (Chang et al., 2015 (link)). SNPs with low call rate (<95%) or low minor allele frequency (MAF < 5%) were excluded, and samples with <90% genotyping rates were filtered out.