Diversidad genética entre subpoblaciones raciales bovinas de Costa Rica

Martínez, Manuel A.; Vargas, Bernardo; Cordero, Juan M.; Chacón, I S Maria; León, Bernal

doi:10.15517/rac.v39i2.21772

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“…Creole breeds are primarily used in the Peruvian livestock systems to establish crosses with other species of B. taurus, particularly Brown Swiss and Simmental in high Andean areas (Primo, 1992;Quispe, 2016). Considering AFB, the mean value of Ho (0.42) obtained in this study is lower than that (0.77) reported by Martínez et al (2015) in Costa Rica, (0.75) Lirón et al (2006) in Argentine and Bolivian Creole Breeds, (0.68) Egito et al (2007), in Brazil, (0.67) Ginja et al (2010) in Portuguese Native Cattle, (0.70) Acosta et al (2012) in Cuban cattle breeds. However, most of these studies are also in creole cattle from Latin America where the values greatly differ from ours.…”

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confidence: 69%

Genetic diversity and population structure of a Peruvian cattle herd using SNP data

et al. 2023

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New-generation sequencing technologies, among them SNP chips for massive genotyping, are useful for the effective management of genetic resources. To date, molecular studies in Peruvian cattle are still scarce. For the first time, the genetic diversity and population structure of a reproductive nucleus cattle herd of four commercial breeds from a Peruvian institution were determined. This nucleus comprises Brahman (N = 9), Braunvieh (N = 9), Gyr (N = 5), and Simmental (N = 15) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N = 9), were incorporated. Female individuals were genotyped with the GGPBovine100K and males with the BovineHD. Quality control, and the proportion of polymorphic SNPs, minor allele frequency, expected heterozygosity, observed heterozygosity, and inbreeding coefficient were estimated for the five breeds. Admixture, principal component analysis (PCA), and discriminant analysis of principal components (DAPC) were performed. Also, a dendrogram was constructed using the Neighbor-Joining clustering algorithm. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 51.42% in Gyr to 97.58% in AFB. Also, AFB showed the highest expected heterozygosity estimate (0.41 ± 0.01), while Brahman the lowest (0.33 ± 0.01). Besides, Braunvieh possessed the highest observed heterozygosity (0.43 ± 0.01), while Brahman the lowest (0.37 ± 0.02), indicating that Brahman was less diverse. According to the molecular variance analysis, 75.71% of the variance occurs within individuals, whereas 24.29% occurs among populations. The pairwise genetic differentiation estimates (FST) between breeds showed values that ranged from 0.08 (Braunvieh vs. AFB) to 0.37 (Brahman vs. Braunvieh). Similarly, pairwise Reynold’s distance ranged from 0.09 (Braunvieh vs. AFB) to 0.46 (Brahman vs. Braunvieh). The dendrogram, similar to the PCA, identified two groups, showing a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh, Simmental, and AFB). Simmental and Braunvieh grouped closely with the AFB cattle. Similar results were obtained for the population structure analysis with K = 2. The results from this study would contribute to the appropriate management, avoiding loss of genetic variability in these breeds and for future improvements in this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

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