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Published on: July 11, 2025
Deciphering genetic diversity and selection footprints in Rathi cattle through ddRAD-based genome-wide analysis.
Nishu Bharia1, Anal Bose1, Sonali Sonejita Nayak1
1Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
Summary
Genomic analysis of Rathi cattle reveals moderate diversity and distinct genetic makeup, crucial for conservation. Declining effective population size highlights the urgent need for strategic breeding and management to preserve this valuable indigenous breed.
Area of Science:
- Animal Genomics
- Population Genetics
- Conservation Genetics
Background:
- Rathi cattle, an indigenous Bos indicus breed from north-western India, possess valuable traits like heat tolerance and dairy potential.
- Limited genomic information exists for Rathi cattle, hindering conservation and breeding efforts.
- Understanding the genetic diversity and demographic history is crucial for preserving this unique breed.
Purpose of the Study:
- To conduct the first genome-wide assessment of Rathi cattle using double-digest restriction-site associated DNA sequencing (ddRAD).
- To evaluate genetic diversity, population structure, demographic history, and identify selection signatures.
- To provide genomic resources for conservation and genetic improvement programs.
Main Methods:
- Genotyping of 96 Rathi cattle using ddRAD sequencing.
- Genome-wide SNP identification and alignment to the Bos taurus reference genome.
- Analyses included genetic diversity metrics, runs of homozygosity (ROH), effective population size (Ne), population structure (PCA, ADMIXTURE, STRUCTURE), and selection signatures (Tajima's D, CLR, ROH islands, iHS).
Main Results:
- Generated 78,193 high-quality SNPs, showing moderate genetic diversity (π = 0.33 ± 0.09) and heterozygosity.
- Low recent inbreeding (FROH = 0.0512) indicated by short ROH segments; significant decline in effective population size (Ne) from 1454 to 94.
- Population structure analysis confirmed Rathi cattle's genetic distinctness; identified candidate genes related to immunity, reproduction, lactation, and stress adaptation.
Conclusions:
- Rathi cattle exhibit unique genetic characteristics and adaptive potential, necessitating targeted conservation strategies.
- The declining effective population size poses a risk of genetic erosion, emphasizing the need for proactive management.
- Genomic insights provide a foundation for sustainable utilization and genetic improvement programs for Rathi cattle.
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