Genomic variability in Mexican chicken population using copy number variants

Area of Science:

• Genomics
• Population Genetics
• Animal Breeding

Background:

• Copy number variations (CNVs) are key genome polymorphisms influencing phenotypic and genetic variation.
• Understanding structural variations is crucial for characterizing livestock populations.
• The Mexican Creole chicken population, known for morphological diversity, lacked genetic characterization.

Purpose of the Study:

• To investigate the genetic variability within the Mexican Creole chicken population using CNVs.
• To create a comprehensive CNV map for this native chicken breed.
• To assess the population structure based on genomic data.

Main Methods:

• Utilized the PennCNV software with a Hidden Markov Model to detect CNVs.
• Analyzed 256 Mexican Creole chicken genomes using the Axiom® Genome-Wide Chicken Genotyping Array.
• Mapped 1924 CNVs, identifying 1538 gains and 386 losses, forming 1216 CNV regions (CNVRs).

Main Results:

• Detected 1924 CNVs across 256 individuals, with 1538 gains and 386 losses.
• Identified 1216 CNV regions (CNVRs), covering 47 Mb (5.12%) of the chicken genome.
• The study revealed no distinct genetic subpopulations despite significant morphological variation.

Conclusions:

• Provides deep insight into the structural variation of an unselected Mexican chicken population.
• The Mexican Creole chicken population, despite morphological diversity, is genetically homogeneous.
• Generated a valuable chicken CNV map and genome-wide copy number estimates for a native, unselected breed.