DOI: 10.5061/dryad.tx95x6b26
title: Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

description: 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.
description: A total of 63 blood samples were collected from four commercial
 breeds of <em>taurus</em> and <em>indicus</em>
 cattle (Brahman, Braunvieh, Gyr, and Fleckvieh). According to their
 pedigree, up to grandfathers, genetic origins for Brahman and Gyr were
 predominantly from Brasil; for Braunvieh, Switzerland and Colombia; while
 for Fleckvieh was Germany (Supplementary material 1). Blood sampling was
 performed from a government herd (EEA Donoso) located in Huaral, Lima (128
 masl; 11º31’18’’ S and 77º14’06’’ W). Precautions were taken to avoid
 sampling from related individuals. Blood samples were collected from the
 epidural vein using a vacutainer containing EDTA as an anticoagulant and
 were immediately transferred to the laboratory for DNA extraction.
 Additionally, hair samples were collected from the tail of Arequipa
 fighting bull (AFB) bovines from the Andagua district, Castilla province,
 in Arequipa (3574 masl; −15.499548◦, −72.359927◦). These individuals were
 selected as they possessed most of the morphological characteristics of a
 PCC. In addition, the owners indicated its parents were also creole.
 Genomic DNA was extracted from whole blood and hair samples using
 protocols elaborated in-house. The concentration and purity of isolated
 DNA were measured by the Nanodrop spectrophotometer (Model ND2000, Thermo
 Fisher Scientific, Wilmington, DE, USA) prior to genotyping. After, DNA
 samples were genotyped using Illumina Bovine HD Genotyping BeadChip and
 Illumina GGP Bovine 100K BeadChip with the help of the commercial
 genotyping service provider (Neogen, Geneseek, NL, USA). The Bovine HD and
 100K chips possess 777,962 and 95,256 SNPs, respectively, uniformly
 spanning over the entire bovine genome. A total of 81,975 common markers
 between both SNP panels were used for the following analysis. 
description: PLINK v1.9p program