Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization

Area of Science:

• Genomics
• Animal Genetics
• Molecular Biology

Background:

• Copy number variants (CNVs) are structural variations in chromosomes, such as deletions or duplications.
• CNVs significantly influence traits and genetic diversity in various species, including chickens.
• Previous CNV studies in chickens utilized array comparative genomic hybridizations or SNP chip assays on diverse breeds.

Purpose of the Study:

• To discover novel copy number variants (CNVs) in two highly inbred chicken lines: Leghorn G-B2 and Fayoumi M15.2.
• To perform the first global assessment of CNVs in the Fayoumi breed.
• To identify CNVs that may underlie quantitative trait loci for disease resistance and other important traits.

Main Methods:

• Genomic DNA from Leghorn G-B2 and Fayoumi M15.2 chickens was analyzed using the Agilent chicken 244 K comparative genomic hybridization array.
• Quantitative PCR (qPCR) was employed to validate a subset of array data.
• Bioinformatic pipelines and Gene Ontology analysis were used to identify and analyze CNVs and associated genes.

Main Results:

• A total of 273 CNVs were identified, with 112 being novel.
• Enrichment analysis revealed significant pathways related to the major histocompatibility complex and immune responsiveness.
• Comparison between the two inbred lines identified 40 regions with significant copy number differences (deletions or duplications).

Conclusions:

• This study provides a comprehensive catalog of novel CNVs in chickens, particularly in the Fayoumi breed.
• The identified CNVs and regions with inter-line differences offer valuable resources for future genetic and functional genomics studies.
• These findings contribute to understanding the genetic basis of traits like disease resistance in chickens.