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Exploratory analysis of genomic prediction profiles in Arequipa fighting cattle using commercial SNP panels

Year: 2026

Type: article

Abstract: Genomic technologies based on single nucleotide polymorphisms (SNPs) have become powerful tools for improving genetic evaluation in cattle populations lacking comprehensive phenotypic and pedigree records. The present study aimed to assess the genomic potential for meat and milk production traits in Arequipa fighting cattle, a culturally significant but poorly characterized bovine biotype in Peru. A total of 95 adult animals were sampled, of which 60 and 22 individuals passed quality control for the Igenity Beef and Igenity Basic panels, respectively. Genomic scores were analyzed using descriptive statistics and multivariate approaches to evaluate genetic variability and population structure. The results revealed substantial genomic heterogeneity within the population, enabling the identification of individuals with superior genetic merit for growth performance, carcass yield, meat quality, and maternal traits. Genomic ranking distinguished groups associated with maternal and terminal production objectives, suggesting the presence of differentiated genetic profiles within the herd. Analysis of milk protein markers showed a high frequency of favorable β-casein genotypes associated with improved digestibility and potential value in A2 milk markets, whereas alleles linked to enhanced cheese-making properties were less frequent. Hierarchical clustering further revealed the presence of genetically structured subpopulations, indicating the maintenance of genetic diversity. hese findings provide the first genomic assessment of productive traits in Arequipa fighting cattle using SNP-based commercial panels. They highlight the potential of genomic tools to identify animals with desirable productive and maternal characteristics and support the development of selection, conservation, and breeding strategies adapted to regional production systems.

Source: Scientific Reports