Whole-genome sequencing reveals copy number variations and their associations with body weight and size traits at slaughter in Lion-head geese

Copy number variation (CNV) is an important type of genetic variations contributing to phenotypic differences in animals and may serve as an alternative molecular marker to single nucleotide polymorphism (SNP) for molecular breeding. We used whole-genome sequencing data to investigate the characteristic of CNVs and their associations with body weight and size traits for 504 120-day Lion-head geese. We detected 1,184,695 CNVs which consisted of 1,148,401 deletions and 36,294 duplications. Based on these CNVs, we obtained 8,043 CNV regions (CNVRs) including 7,578 deletions, 228 duplications and 237 mixeds, which covered 7.76% of the reference genome. The 81.03% of CNVRs had the length ranging from 50bp to1000bp. We filtered 8,767 high-quality genotyped CNVs (7,960 deletions and 807 duplications) to conduct the association analysis of the body weight and 11 body size traits with these CNVs. We found 42 chromosome-wide significant CNVs, among which 40 were novel, and 2 CNVs had the high linkage disequilibrium (r²>0.20) with adjacent SNPs with chromosome-wide significance. According to these significant CNVs, we annotated 47 genes. Among these genes, CEP112, TOM1L1 and STX8 simultaneously influenced body weight and other body size traits, which was worthy of further study.