Genomic Variability in Mexican Chicken Population Using Copy Number Variation

Copy number variations are polymorphisms, which influence phenotypic variation and are an important source of genetic variation in populations. In Mexico, the backyard poultry population is not divided into breeds, but it is the widespread Creole chicken (Gallus gallus domesticus), an undefined cross among different breeds brought to Mexico from Europe and under natural selection for almost 500 years. The aim of this study was to investigate genomic variation in the Mexican chicken population using CNVs.

A total of 256 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array were used in the analyses. After stringent quality control the individual-based CNV calling, based on log-R ratio (LRR) and B-allele frequency (BAF) values, was performed by the Hidden Markov Model (HMM) of PennCNV software on autosomes. CNV were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools.

The HMM detected a total of 1924 CNVs in the genome of 256 samples, which comprised 1538 gains and 386 losses and resulting at population level in 1216 CNV regions, of which 959 gains, 226 losses and 31 complex CNVRs (i.e. containing both losses and gains), covering a total of 47 Mb of sequence length corresponding to 5,12 % of the chicken galGal4 assembly autosome. A comparison among CNV lengths was performed. The highest number of gain CNVRs are those with a length of 10–100 Kb, while the loss CNVRs have generally a length of 1–10 and the complex CNVR have mainly a length of 10-100 Kb.