Analysis of copy number variations and selection signatures using whole-genome sequencing data from 16 Chinese duck breeds

1. Copy number variation (CNV) is an important source for identifying genetic differences. This study compared the genome-wide CNV and their regions (CNVR) across 16 Chinese local duck breeds and detected key genes and pathways involved in growth and reproduction-related traits using this dataset.2. Breakdancer, Pindel and CNVnator were used to detect reliable CNV, and HandyCNV was used to obtain CNVR. Selection signatures were analysed in meat (MD) and egg-laying ducks (ED) compared to wild ducks (WD) using fixation and differentiation index DIsv methods. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was carried out to identify key pathways and related genes.3. Principal component analysis (PCA) using CNV data clustered 127 ducks into 4 populations: WD, MD, ED and meat+egg-type ducks (MED). In total, 237,630 CNV and 6,176 CNVR were detected across these samples. Intersection analysis identified 1,384 common CNVR and 2,105 unique CNVR. The KEGG analysis showed that common CNVR were enriched in 7 basic life activity pathways, while unique CNVR were enriched in 9 population-specific pathways. Compared to WD, MD selection signatures were found in 4 enriched pathways and 8 genes (LRP2, NID1, ATP1B3, PDGFD, MAGI2, FLT1, DMD, RALGAPB) related to growth and meat traits. The ED signatures revealed three key pathways and eight genes (PRKN, CTNNA2, DLG2, PDGFD, PRKD1, RAPGEF4, EIF2S1, CRB2) linked to reproduction.4. Using this dataset comprising 16 duck breeds, CNVR patterns were compared among WD, MD, ED and MED birds to identify common and unique CNVR. The study investigated selection signatures in MD and ED ducks and revealed key pathways and candidate genes related to growth and reproduction.