Verification of isogenic clonal lines in the Atlantic salmon (Salmo salar) through ddRADseq. Verification of isogenic clonal lines in the Atlantic salmon

The aim of the study is the verification of isogenic nature of clonal lines in the Atlantic salmon. Starting from outbred founders, 6 G1 fish (doubled haploid-meiotic gynogenetics) and 5 G2 fish - putative clonal lines - from each of the G1 fish (one of the G1 fish failed to have progeny) have been used to construct double digest restriction associated DNA library (ddRAD lib) with a haploid family. In total, 35,862,448 raw reads (162 bases long) were produced in one sequencing lane in Miseq (Illumina). After removing low quality sequences (quality score under 30), ambiguous barcodes and orphaned paired end reads, 86.3% of the raw reads were retained (30,958,609 reads). The Stacks package (Catchen et al., 2011) with likelihood-based SNP-calling algorism (Hohenlohe et al., 2011) was then used to make the de novo assembly of the sampled loci from each individual: 257,358 unique RAD-tags were retrieved. No convincing evidence of any sire contribution has been detected to the progeny after further investigation of the segregation pattern on the potential sire contributor RAD alleles as well as all female contributor RAD alleles as control.