Insights into Copy Number Variation Architecture in Black Bengal Goat Genome
Sonali Sonejita Nayak1, Shikha Mittal2, Manjit Panigrahi1
1Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
International Journal of Molecular Sciences
|May 13, 2026
Summary
Copy number variations (CNVs) in Black Bengal goats reveal genetic changes enhancing reproduction and skin quality. This study maps these structural genomic variations for improved breeding and conservation efforts.
Area of Science:
- Genomics
- Animal Genetics
- Livestock Breeding
Background:
- Copy number variations (CNVs) are key drivers of genomic diversity in livestock, impacting traits like adaptation and reproduction.
- The Black Bengal goat is an economically vital Indian breed, recognized for high fecundity, superior skin, and climate resilience.
Purpose of the Study:
- To comprehensively map the structural genomic landscape of the Black Bengal goat through whole-genome CNV analysis.
- To identify CNVs and CNVRs and their associated genes influencing key production and adaptive traits.
Main Methods:
- Whole-genome sequencing (10× depth) was performed on eight Black Bengal goats.
- Identification and annotation of copy number variants (CNVs) and copy number variation regions (CNVRs) across the genome.
Main Results:
- A total of 31,816 CNVs, primarily duplications, were identified, forming 8910 CNVRs covering 5.3% of the autosomal genome.
- CNVR hotspots were concentrated on chromosome 1, with affected genes involved in immunity, reproduction, metabolism, and extracellular matrix (ECM) organization.
- CNVs in GDF9 and BMPR1B are linked to high reproductive capacity, while duplications in ECM genes like COL6A1 explain superior hide quality.
Conclusions:
- This study provides a detailed map of CNVs and CNVRs in the Black Bengal goat genome.
- Identified structural variations contribute significantly to the breed's reproductive performance and skin resilience.
- Findings support marker-assisted selection, comparative genomics, and conservation strategies for indigenous goat populations.
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