Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken

• DOI: 10.3389/fgene.2022.830393
• Publication Date: 2022-03-28T16:00:55Z
• Authors: Xia Chen; Xue Bai; Huagui Liu; Binbin Zhao; Zhixun Yan; Yali Hou; Qin Chu
• Keywords: Phenotypic trait

Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication breed shaping, whole-genome CNVs were detected via multiple methods. Using sequencing data from 51 individuals, corresponding to six domestic breeds wild red jungle fowl (RJF), we determined 19,329 duplications 98,736 deletions, which covered 11,123 copy regions (CNVRs) 2,636 protein-coding genes. The principal component analysis (PCA) showed these individuals could be divided into four populations according their selection purpose. Seventy-two highly duplicated CNVRs across all revealing pivotal roles nervous system (NRG3, NCAM2), sensory (OR), follicle development (VTG2) in genome. When contrasting those RJFs, 235 harboring 255 genes, predominantly involved pathways nervous, immunity, reproductive development, discovered. In breed-specific CNVRs, some valuable genes identified, including HOXB7 for beard trait Beijing You chicken; EDN3, SLMO2, TUBB1, GFPT1 melanin deposition Silkie SORCS2 aggressiveness Luxi Game fowl. Moreover, CSMD1 NTRK3 with high found exclusively White Leghorn chicken, POLR3H, MCM9, DOCK3, AKR1B1L Recessive Rock may contribute egg production fast-growing traits, respectively. candidate characteristics are resources further studies artificial breeding chickens.