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

New-generation sequencing technologies, among them SNP chips for massive
genotyping, have proven to be useful for the effective management of
genetic resources. Also, developing nucleus herds is an effective method
for genetic improvement work. To date, molecular studies in Peruvian
cattle are still in their infancy. To close this gap, we here employed two
SNP panels (BovineHD and Bovine100K) to determine for the first time the
Peruvian nucleus herd’s genetic diversity and population structure that
belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14),
Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a
locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12),
were incorporated into the study. The genetic diversity indices in all
breeds showed a high proportion of polymorphic SNPs, varying from 69.37%
in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest
observed heterozygosity (0.53±0.17), while Brahman possessed the lowest
(0.44±0.10), indicating that the former is more diverse compared to the
other cattle breed groups. According to the molecular variance analysis,
83.92% of the variance occurs within individuals, whereas 16.0% occurs
between populations. The pairwise FST estimates between breeds showed
values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs
AFB). Pairwise Reynold’s distance showed a pattern similar to the one
obtained with the FST statistics, with values ranging from 0.058 to 0.309.
A dendrogram was constructed using the Neighbor-Joining clustering
algorithm, and similar to the principal coordinate analysis, three groups
were identified. Results showed a clear separation between Bos indicus
(Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For
Fleckvieh and Braunvieh, there were two subgroups each one of them
grouping with the AFB group. Similar results were obtained with ADMIXTURE
analysis with K= 3 as the most optimal number for the inferred genetic
structure of the populations. The results from the current study would
contribute to the appropriate management avoiding loss of genetic
variability in these breeds and to future improvements for this nucleus.
Additional work is needed to speed up the breeding process in the Peruvian
cattle system.