Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00027014%3A_____%2F22%3AN0000010" target="_blank" >RIV/00027014:_____/22:N0000010 - isvavai.cz</a>
Result on the web
<a href="https://vuzv.cz/_privat/22010.pdf" target="_blank" >https://vuzv.cz/_privat/22010.pdf</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.livsci.2022.104825" target="_blank" >10.1016/j.livsci.2022.104825</a>
Alternative languages
Result language
angličtina
Original language name
Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis
Original language description
Preserving genetic diversity and preventing its loss in livestock populations is essential for further sustainable development and breeding. The main purposes of this study were to estimate the current status of genetic diversity of the approved genetic resources (GRs) in indigenous Czech Red (CR) and Czech Spotted (CS) cattle and assess the impact of diversifying selection on two CR subpopulations based on genome-wide single-nucleotide polymorphism (SNP) analysis. The main within-breed genetic diversity indicators of CR and CS (share of polymorphic SNPs, observed heterozygosity, and minor allele frequency) are intermediate or high, and the inbreeding coefficients are below zero. The small degree of genetic differentiation (maximum FST = 0.088) suggests a low divergence between the breeds and populations. Principal component analysis (PCA) shows a less genetic variation in CS and, in contrast, larger variability within and genetic similarity between the two analysed CR subpopulations. Putative selection signatures based on FST revealed that the ten most differentiated genomic regions between the two CR subpopulations were located on chromosomes 1, 3, 11, 12, 18, and 22, encompassing only 7 Mb of sequence and 69 protein-coding genes. Selection differences are low and probably attributed to the influence of the CS genome exploited in CR cattle revitalization. The majority of the candidate genes are involved in the immune system response, fertility, and neuronal and brain function. Gene Ontology enrichment and quantitative trait loci database analyses show that the genes act in milk and meat production and reproductive performance. These findings expand our knowledge about the genomic diversity of endangered Czech indigenous cattle and provide helpful information to organize their breeding programmes and preservation.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
40203 - Husbandry
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Livestock Science
ISSN
1871-1413
e-ISSN
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Volume of the periodical
256
Issue of the periodical within the volume
February
Country of publishing house
NL - THE KINGDOM OF THE NETHERLANDS
Number of pages
8
Pages from-to
Article number: 104825
UT code for WoS article
000800445300008
EID of the result in the Scopus database
2-s2.0-85123262344