Acronym
V4-2364
Department:
Department of Animal Science
Type of project
ARIS projects
Type of project
CRP projects
Role
Lead
Duration
01.10.2023 - 30.09.2024
Total
0,43 FTE
Project manager at BF
Gorjanc GregorAbstract
The small size of the population is a major constraint in the selection of indigenous breeds, with the Lipizzan horse being the most attractive. As a result, selection is not primarily aimed at improving the phenotype, but at maintaining genetic diversity or, as we often say, preserving breed characteristics. Thus, phenotype or productivity is only the second priority. In the case of the Lipizzan horse, maintaining genetic diversity is particularly challenging because the effective population size is small due to historical events such as herd movements due to war conditions. If we limit ourselves to the parent herd at Kobilarna Lipica (KL), where we are legally obliged to maintain 18 mare lines and 6 stallion lines, the challenges in selection are even more demanding. The current breeding program and the Law on livestock farming define the implementation of measures to prevent inbreeding with the aim of maintaining genetic diversity based on pedigree data. The estimation of relatedness based on pedigree data gives the expected relatedness between animals, which is often underestimated in relation to the actual genomic coefficient of relatedness, since pedigree analysis is limited by the depth and accuracy of the pedigree. In contrast, the estimate of relatedness based on genomic information represents the realized relatedness, which takes into account relatedness beyond the limits of the pedigree and reflects the actual result of the process of inheritance of DNA molecules (meiosis) from ancestors to animals living today. Technological advances and the reduction in the cost of genotyping have increased the availability of genomic information also in horses.
In our study, we will use medium-density SNP chips for genotyping, and genotype around 300 horses in KL. In order to capture more genetic variability, we will also obtain genomic information for some horses outside KL that has been collected within other projects. This approach will give us insight into the actual genetic diversity of the breed, develop mating plans based on actual relatedness, and develop a sustainable long-term management strategy for the KL Lipizzan herd, with the aim of conserving and managing the genetic diversity in the long term.
The aim of our research is to use pedigree and genomic data to (i) assess the current genetic variability and genetic structure of the Lipizzan population, (ii) analyze inbreeding and effective population size, (iii) analyze the contribution of individual animals, stallion line and mare line to the current population, (iv) test and implement a methodology to optimize matings in order to achieve a desired breeding goal and minimize inbreeding;(v) develop a mating plan to minimize relatedness in the next generation.
Researchers
The phases of the project and their realization
The work on the project will be divided into 3 main work packages:
WP1: Collection of samples for genotyping and collection of phenotypic data
October 2023 - December 2023
WP2: Sample preparation and genotyping
December 2023 – February 2024
WP3: Data management and methodology testing, statistical analysis of the collected data and interpretation of the results (points A-G)
December 2023 – October 2024
A. Quality control of genotypic data and linking of pedigree data
December 2023 – March 2024
B. Analysis of kinship coefficients and degree of relatedness based on pedigree data
April 2024 – August 2024
C. Analysis of kinship coefficients and degree of relatedness based on genomic data
April 2024 – August 2024
D. Analysis of population structure and estimation of genetic variability and effective population/breed size
April 2024 – August 2024
E. Estimation of the genetic contributions of individual stallion and mare lines to the current population
April 2024 – August 2024
F. Implementation of optimum contribution selection to manage genetic variability
April 2024 – August 2024
G. Development of a mating plan to minimize the inbreeding rate
April 2024 – August 2024
Citations for bibliographic records