Genome-wide investigation to assess copy number variants in the Italian local chicken population

Abstract Background Copy number variation (CNV) holds significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local chicken breeds and investigate their distribution within the genome. Results The distribution of CNV was more prominent in the first six chromosomes and primarily associated with loss types. Most CNV among breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, chromosome 16 had a high proportion of its length covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the identified genes within CNVR, only those present in at least three animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTLs associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. Conclusions Genomic phenomena that can cause changes in the distribution of CNV within the genome over time and the comparison of the differences among the CNVR of the local chicken breeds reported in the present study could help in their conservation.