Whole-genome sequencing of native Pekin and Cherry Valley Pekin ducks
Muscle growth and lipid deposition are co-ordinately regulated processes. Cherry Valley Pekin duck is a lean-type duck strain with high growth rate, whereas native Pekin duck of China has high lipid deposition. Phenotypic analysis demonstrated that native Pekin ducks had smaller fibre diameter and larger density in breasts muscle at 3-weeks of age, and higher content of intramuscular fat at 6-weeks of age compared to the values in Cherry Valley Pekin ducks.Here, wo performed Whole-genome sequencing from nine native and Cherry Valley Pekin duck individuals was extracted from breast samples. Paired-end sequencing profiles, with an insert size of 380 bp, were constructed according to the manufacturer’s instructions for TureSeq on Illumina Hiseq 4000 platform. Sequencing and base calling were performed according to the standard Illumina protocols.Adapter and low quality reads were removed from the raw data using an in-house perl script. The genomic reads were aligned to the duck reference genome (Anas_platyrhynchos.BGI_duck_1.0) using Burrows-Wheeler algorithm. The alignment outputs (BAM files) were sorted and the PCR duplicates generated during library construction were removed using SAMtools. Genomic variants including SNPs and indels were called using genome analysis toolkit. The genomic variants were annotated, with as much detail as possible, using Python HTseq and an in-house Python script.