Conservation & local programs

Evaluation of Population Structure in Cattle: Comparison between Single Nucleotide Polymorphism and Microsatellite Marker Performance

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Abstract

Population structure is the composition of individuals within a population, characterized by age, sex, fertility and migration patterns. Single Nucleotide Polymorphisms (SNPs) and Microsatellites (MSAT) are both DNA markers used in genetic studies, but differ significantly in their nature, informativeness, and application. However, the shift from traditional, lower throughput MSAT genotyping to high throughput, cost effective SNP arrays, requires an empirical comparison to guide marker choice. Hence, the aim was to assess differences in performance between the two marker types for characterizing population structure of South African cattle populations. Ethical approval was obtained (APIEC21/17, APAEC24/08). For the microsatellite analysis, MSAT data of 467 animals from 6 populations (Lesedi A, Lesedi B, COJ, Tshwane, Merafong and Randfontein) was used, while for SNP analysis, 96 animals were randomly selected across the same population and underwent SNP genotyping using Bovine 50K SNP bead chip. SNP quality control was performed using PLINK v1.9. Observed heterozygosity (Ho), expected heterozygosity (He), and inbreeding coefficients (Fis) were calculated per population per marker using the 'adegenet' and 'hierfstat' R packages. Population genetic analysis was conducted separately for SNP and MSAT markers using Discriminant Analysis of Principal Components (DAPC) implemented in 'adegenet' R package. Spearmen correlations were used to compare the SNP and MSAT between their DAPC population assignment probabilities. High level of genetic diversity was found across all populations, with an average heterozygosity of 75% with MSAT, whereas SNPs revealed a mean He of 28%. MSAT exhibit high He due to their high mutation rates and multi-allelic nature, whereas individual SNPs possess low per-locus heterozygosity due to low mutation rates and being bi-allelic. The average Fis varied from 0.023 detected with MSAT to -0.001 with SNPs, overall indicating low inbreeding within the populations. SNPs provide a more genome-wide precise Fis estimate, whereas MSAT overestimates Fis at the individual loci. The DAPC identified six genetically distinct clusters within the cattle population. The SNP dataset revealed more distinct and tightly defined genetic clusters, while the MSAT produced more overlapping clusters. Both SNP and microsatellite markers reveal similar population structure across the six cattle populations. The correlation matrix showed high positive correlations for COJ, Randfontein and Tshwane across SNP and MSAT analysis, confirming strong congruence in these groups. While the Lesedi A, Lesedi B and Merafong populations showed weaker or negative cross-marker correlations, highlighting specific populations where the two marker systems differed. Together, these tests show that both marker types capture a similar population structure. In conclusion, MSAT provide a picture of the overall genetic structure, even though less accurate than SNP, it is still relevant especially when background information is limited. However, the SNP results were able to further interrogate the population structure, with increased accuracy and definition.

Keywords: 2026

How to Cite:

Soma, P. & Kooverjee, B., (2026) “Evaluation of Population Structure in Cattle: Comparison between Single Nucleotide Polymorphism and Microsatellite Marker Performance”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286799. doi: https://doi.org/10.31274/wcgalp.24123

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