Linkage Disequilibrium Decay in Selected Cattle Breeds

Area of Science:

• Genomics and Bioinformatics
• Animal Genetics
• Population Genetics

Background:

• Linkage disequilibrium (LD) mapping is crucial for understanding the genetic basis of traits in various species.
• Modern sequencing technologies provide extensive SNP data for quantifying LD in cattle breeds.
• Understanding LD patterns aids in genetic resource management and trait association studies in cattle.

Purpose of the Study:

• To determine and compare linkage disequilibrium (LD) levels across different genomic distances in Sistani cattle.
• To compare LD patterns of Sistani cattle with Bos taurus and Bos indicus subspecies.
• To investigate potential genetic or historical relationships influencing LD in Sistani cattle.

Main Methods:

• Genotyping of 60 cattle samples (Sistani, Bos indicus: Sahiwal, Nellore; Bos taurus: Hereford, Holstein) using Illumina Bovine HD 770k chip.
• Evaluation of LD at various genomic distances: 1-50 Kb, 50-100 Kb, 100-500 Kb, and 0.5-1 Mb.
• Calculation of average r² values for all autosomes within defined distance classes to quantify LD.

Main Results:

• Average r² values exceeded 0.2 at distances <100 Kb for all breeds. Sistani, Nellore, and Sahiwal showed average r² > 0.2 between 100-500 Kb.
• Average r² > 0.3 was observed <50 Kb for all breeds, while Holstein and Hereford showed this at 50-100 Kb.
• Sistani cattle exhibited LD decay patterns similar to indicine breeds (Nellore, Sahiwal), with significant changes observed at <10 Kb.

Conclusions:

• The Sistani breed's LD patterns are comparable to indicine cattle, potentially due to geographic proximity to Pakistan or historical genetic ties.
• SNP ascertainment bias on the used chip may also contribute to the observed LD patterns in Sistani cattle.
• These findings provide insights into the genetic structure and evolutionary history of Sistani cattle in relation to other major cattle subspecies.