Genome-Wide Analysis of Copy Number Variation in Vietnamese Local Chickens.

Area of Science:

• Genomics
• Animal Genetics
• Livestock Science

Background:

• Copy number variants (CNVs) are significant drivers of genetic diversity and phenotypic variation in livestock.
• Understanding CNVs in indigenous chicken breeds is crucial for conservation and trait improvement.

Purpose of the Study:

• To comprehensively characterize the genome-wide copy number variant (CNV) landscape in three Vietnamese indigenous chicken breeds.
• To identify genes within CNVs associated with breed-specific adaptations and traits.

Main Methods:

• Whole-genome sequencing (3-5× coverage) of 24 individuals from Dong Tao (DT), Cay Cum (CC), and Ri (RI) breeds.
• Detection and analysis of copy number variation regions (CNVRs) across the chicken genome.
• Identification and functional enrichment analysis of genes located within CNVRs.

Main Results:

• A total of 1743 CNVs were identified, forming 315 CNVRs, with most being rare.
• Losses were the most frequent CNV type (45.9%).
• 3633 genes were found within CNVRs, with specific genes in DT and RI breeds linked to adaptation, development, skeletal, and physiological traits.

Conclusions:

• This study presents the first genome-wide CNV map for Vietnamese indigenous chickens.
• The identified CNVs and associated genes provide a valuable resource for understanding breed-specific adaptations and genetic improvement in chickens.