High-throughput genotype-based population structure analysis of selected buffalo breeds

Area of Science:

• Animal Genetics
• Livestock Genomics
• Population Genetics

Background:

• India is a major center for diverse buffalo breeds, but their genetic makeup remains largely uncharacterized.
• Understanding buffalo genetic structure is vital for effective breeding programs and conservation efforts.

Purpose of the Study:

• To analyze genetic variability and population structure in seven Indian buffalo breeds.
• To identify genetic markers for differentiating breeds and inform breeding strategies.

Main Methods:

• Utilized the Axiom Buffalo Genotyping Array for genetic analysis.
• Employed Principal Component Analysis (PCA) and STRUCTURE analysis to assess population structure.
• Analyzed linkage disequilibrium (LD) decay and concordance with quantitative trait loci (QTLs).

Main Results:

• Observed genetic diversity ranging from 0.364 (Surti) to 0.384 (Murrah).
• Identified significant genetic differentiation for Surti, Pandharpuri, and Jaffarabadi breeds.
• Found early LD decay in Murrah and Mehsana, and late decay in Surti.
• Highlighted 4,090 markers from LD blocks associated with various traits, with 4.65% concordance to QTLs.

Conclusions:

• Single-nucleotide polymorphism (SNP) markers can differentiate phenotypically distinct buffalo breeds.
• Further development of SNP chips using local breed sequence data is recommended.
• The findings provide a foundation for targeted breeding and genetic improvement in Indian buffalo populations.