Genome-wide copy number profiling using high-density SNP array in chickens

Area of Science:

• Genomics
• Animal Genetics
• Molecular Biology

Background:

• Phenotypic diversity is driven by genetic variation.
• Copy number variation (CNV) is increasingly recognized as a key factor in phenotypic variability and disease susceptibility.
• Understanding CNVs in chickens is crucial for trait improvement and disease management.

Purpose of the Study:

• To conduct a genome-wide scan for copy number variations (CNVs) in diverse chicken breeds.
• To characterize the identified CNVs and their genomic distribution.
• To investigate the potential role of CNVs in chicken traits, particularly immune responses.

Main Methods:

• Genome-wide CNV scan using high-density Affymetrix 600K SNP arrays in 96 chickens across 12 breeds.
• Identification and characterization of autosomal CNV regions (CNVRs).
• Validation of novel CNVRs using qPCR assays.

Main Results:

• Identified 231 autosomal CNVRs covering 5.41 Mb (0.59% of the autosomal genome).
• CNVRs varied in size, with deletions showing lower GC content and enrichment in gene deserts.
• 102 CNVRs contained 128 chicken genes, predominantly involved in immune responses; 153 CNVRs were novel.
• qPCR validated 72.73% of 11 tested novel CNVRs.

Conclusions:

• High-density SNP arrays are effective for efficient and accurate CNV detection in chickens.
• CNVs, particularly deletions, represent a significant source of genetic variation in the chicken genome.
• These findings enhance the understanding of chicken genetic architecture and aid in identifying CNVs linked to important traits.