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

Abstract

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

Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province

“…EDN3 is a gene that encodes endothelins (EDNs), which participate in the regulation of some physiological processes, such as cardiovascular development and function, pigmentation, and plumage in birds [ 39 ]. Embryonic development is regulated by EDN3–EDNRB2 signals, which are closely related to melanin deposition in duck epidermis [ 40 ] and feather patterns [ 41 ], consistent with the results of our previous study [ 42 ]. Coincidentally, the gene was also selected in the Guangxi chicken population [ 43 ].…”

Fourth Report on Chicken Genes and Chromosomes 2022

“…Like in all previous SNP-array-based studies, the vast majority of the CNVRs were singletons, with only 152 CNVRs common to all 51 birds. Around 600 CNVRs, including 90 protein-coding genes, were breed specific, suggesting their functional importance in driving chicken phenotypic and adaptive evolution [Chen X et al, 2022]. These two analyses clearly demonstrated the power of the WGS data in CNV identification and functional annotation.…”

“…For instance, 12,955 CNVs in 5,467 CNVRs, accounting for 9.42% of the genome, were found in two Iranian indigenous and commercial chicken breeds, with 34% of these CNVRs overlapping with those identified in SNP-array-based analyses [Sohrabi et al, 2018]. Across 51 WGS datasets of Chinese indigenous breeds (Xinghua, Luxi Game, Beijing-You, and Silkie), commercial lines (Recessive White Rock and White Leghorn), and red junglefowls, 19,329 duplications and 98,736 deletions in 11,123 CNVRs, accounting for 7% of the total autosomal size, and overlapping with 2,636 protein-coding genes were identified [Chen X et al, 2022]. Like in all previous SNP-array-based studies, the vast majority of the CNVRs were singletons, with only 152 CNVRs common to all 51 birds.…”

“…Considering the constraints of SNP arrays and the reduction of DNA sequencing costs, NGS-based WGS approach is now the most popular tool to infer the evolutionary history of chicken genomes, to assess the genetic diversity and population genetic structure at regional, continental, and global scales, to identify the genetic controls of specific traits of interest, and to screen for the signatures of selection for productive traits and environmental adaptation [Rubin et al, 2010;Mugal et al, 2013;Wang MS et al, 2015, 2016a, 2016bGuo X, , 2022Guo Y et al, , 2021Zhang et al, 2016Zhang et al, , 2022Li D et al, , 2019Boschiero et al, 2018;Derks et al, 2018;Lawal et al, 2018Lawal et al, , 2020Sohrabi et al, 2018;Almeida et al, 2019;Talebi et al, 2020;Tiley et al, 2020;Wang Q et al, 2020;Gheyas et al, 2021Gheyas et al, , 2022Li YD et al, 2021;Mariadassou et al, 2021;Rostamzadeh Mahdabi et al, 2021;Tan et al, 2021;Yang Z et al, 2021;Asadollahpour Nanaei et al, 2022;Chen X et al, 2022;Gao et al, 2022;Geibel et al, 2022;Li Y et al, 2022;Sun et al, 2022;Wang S et al, 2022;Xu et al, 2022;Yuan J et al, 2022;Zeng et al, 2022].…”

Population Structure and Selection Signatures of Domestication in Geese

“…This gene has been proposed to relate to reproduction; Csmd1 knockout in mice reduced fertility through altered regulation of spermatozoa production [ 40 ]. In the chicken, CSMD1 is considered potentially related to egg production [ 41 ]. Interestingly, we found an intronic mutation (NW_013185662.1: 9881517, A < C) in CSMD1 that displayed perfect genotype segregation with broodiness behavior.…”