Comparative analysis of marker selection approaches for population stratification in Garole and Deccani sheep
DOI:
https://doi.org/10.59317/7jtj2052Keywords:
Genomic breed clustering, Low-density panel, MAF, Ovine50KSNP positionAbstract
The present study was undertaken to identify ancestry-informative single nucleotide polymorphism (SNP) markers from medium-density Ovine50K genotyping data for the development of low-density SNP panels in Deccani and Garole sheep breeds of India. These panels can be used for efficient and cost-effective genetic analysis and breed identification. Genotyping data from 49 individuals (25 Garole, and 24 Deccani) was analyzed using the OvineSNP50 BeadChip array. Quality control measures were applied to ensure data accuracy and improve reliability and reproducibility of results. Admixture analysis was performed to assess genetic structure and identify potential marker sets for low-density panels. Three different methods (distance, frequency, and index) were used to select markers based on their distribution and allele frequencies. The low-density panels were designed at pre-set sizes of 500, 1000, 2000, 3000, and 5000. The results revealed that low-density panels, particularly with 3K and 5K markers, can effectively differentiate between Deccani and Garole sheep. In conclusion, the 0.5K dense SNP panel developed via index method (followed by frequency method) can be recommended for better genomic clustering (~90%) for both the breeds. The developed SNP panels provide a valuable resource for genetic analysis and breed identification in these sheep populations, potentially facilitating conservation efforts and genetic improvement programs.
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