During 2018–2019 Ukraine took part in the project of Food and Agriculture Organization (FAO) «Conservation and development of double-purpose cattle breeds in Eastern Europe» (TCP/RER/3604). The project covered Brown Carpathian and Brown Caucasian breeds of Armenia, Georgia and Ukraine. On the results of the project, experts from the FAO Regional Office for Europe and Central Asia, international experts prepared reports on gender, social and economic characteristics of the studied regions, genomic analysis of samples and provided recommendations for breeding in the regions with the breeds. It was considered expedient to present these results to the general scientific community.
At each country FAO have chosen service-provider (organization), which should make survey on productive environment of targeted breed (in Ukraine – Brown Carpathian), conclude the general state of the breed, visit at least 100 farms where Caucasian/Carpathian Brown cattle breed was kept, collect information from 300 cows and 20 bulls, and genetic samples from at least 100 cows and 20 bulls kept for breeding. Service-provider in Ukraine was M.V.Zubets Institute of Animal Breeding and Genetics, NAAS.
Scientists of M.V.Zubets Institute of Animal Breeding and Genetics and other sub-contracting organizations during February-June, 2019 investigated 265 heads of cattle in 31 villages 5 districts of the Transcarpathian region, phenotypically classified as Brown Carpathian breed, including 6 breeding bulls of mating age (1.5–2 years). Each animal was photographed, linearly descriptive features of the exterior were evaluated, the necessary body measurements were taken with the help of appropriate tools, live weight and constitutional features were determined, and samples were taken for genetic testing.
A total of 554 hair samples were taken from the project (123 – from Armenia, 141 – from Georgia and 290 – from Ukraine).
The basis for classifying the animals as Brown Carpathian was phenotypic examination and strict compliance with the main characteristics of the breed: uniform grey or brown colour with different shades of it, general conformation typical for the breed, lighter belt along the back, black muzzle with lighter hair around it, black hooves and horn tips, lighter "glasses" around the eyes, thick light hair inside outer ears.
To form the genetic passport of the population, hair was selected from the tail switch of selected animals using equipment provided by FAO, sent to the laboratories of the International Atomic Energy Agency, Austria. In the laboratory in the district of Siebersdorf, DNA was isolated from the obtained samples, the genetic diversity of populations, the degree of inbreeding and their effective number, kinship between populations were assessed and the genetic structure and level of influence of other breeds were analysed.
DNA was extracted from each hair follicle using a MasterPure kit (Biozym, Illumina, USA) according to the protocol of the Association of Public Health Laboratories (APHL). The isolated DNA was subjected to a two-step quality control procedure before preparation for wide-genome typing. DNA samples were measured using a Nanodrop spectrophotometer to obtain a concentration with a ratio of 260/280 and 260/230. According to the results obtained using a spectrophotometer, DNA samples were diluted to measure high-quality double-stranded DNA (dsDNA) by PicoGreen Assay. The final working DNA was prepared based on PicoGreen measurements and stored at – 20°C for further processing.
Sample genotyping was performed using a third-generation 384-cell matrix to assess Bovine individuals on the Affymetrix-Axiom platform (Axiom Bovine Genotyping v3 array). Within the project, 48 individuals of Austrian Simmental and 18 – Ayrshire breeds were also genotyped for comparison. The matrix included 64.000 SNPs, providing a high probability of covering genomic variations of the Bos taurus and Bos indicus breeds.
Intra-breed genetic diversity was assessed using PLINK v1.09 to calculate actual heterozygosity (H0) and inbreeding coefficient (FIS).
Analysis of genetic parameters of population diversity evidenced a rather low inbreeding rate of Brown Carpathian breed and a fairly high effective population size compared to European breeds, which can indicate a very limited practice of artificial insemination and lack of selection among bulls.
Analysis of genetic differentiation and relationship between populations, principal components analysis and determination of admixtures of other breeds proved the uniqueness of the Brown Carpathian breed from a genetic point of view.
Based on the conducted genomic analysis of populations, consultations with project participants, reports of service providers of each country, an international consultant on animal genetic resources, chairman of the ICAR working group on functional traits, formed a breeding program for the studied populations. The breeding program included proposals for further selection work, calculation of basic selection-genetic parameters, selection effect, number of bulls and heifers for selection nucleus, number of doses to maintain genetic diversity of the population, cost of population restoration, breeding work of breeding centre and work plan by years to implement a breeding program.
Gender analysis of service providers' reports showed some gender differentiation in livestock care, processing and everyday life of owners of Brown Carpathian cattle.
384 Genetic and Genomic Analysis in Livestock with Increasing Datasets
