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Projects / Programmes source: ARIS

Endangered small-ruminant breeds of Slovenia as a genetic resource to study molecular consequences of animal breeding and evolution

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Research activity

Code Science Field Subfield
4.02.01  Biotechnical sciences  Animal production  Genetics and selection 

Code Science Field
B400  Biomedical sciences  Zootechny, animal husbandry, breeding 

Code Science Field
4.02  Agricultural and Veterinary Sciences  Animal and Dairy science 
Keywords
critically endangered Drežnica goat, genetic characterization, population history, hybridization with Alpine ibex, etnographic study
Evaluation (rules)
source: COBISS
Evaluation of bibliographic research performance indicators according to ARIS methodology
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (12)
no. Code Name and surname Research area Role Period No. of publications
1.  05098  PhD Peter Dovč  Biotechnology  Researcher  2019 - 2022  935 
2.  10412  PhD Simon Horvat  Biotechnical sciences  Head  2019 - 2022  561 
3.  28971  Ana Jakopič    Technical associate  2022  14 
4.  20790  MSc Jurij Krsnik  Animal production  Researcher  2021  171 
5.  51857  Neža Pogorevc  Animal production  Junior researcher  2019 - 2022  34 
6.  15795  PhD Bojana Rogelj Škafar  Ethnology  Researcher  2019 - 2022  357 
7.  28180  PhD Mojca Simčič  Animal production  Researcher  2019 - 2022  416 
8.  38858  Katja Skulj    Technical associate  2019 - 2022  14 
9.  15798  Barbara Sosič  Ethnology  Researcher  2019 - 2022  163 
10.  55504  Martin Šimon    Technical associate  2021 - 2022  39 
11.  32581  PhD Minja Zorc  Computer science and informatics  Researcher  2019 - 2022  182 
12.  21234  Metka Žan Lotrič  Animal production  Researcher  2019 - 2022  323 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  66,240 
2.  0622  Slovene Ethnographic Museum  Ljubljana  5052653000  3,690 
Abstract
Background. Genetic research in domestic animals has important scientific and socio-economic effects in the field of medicine, health, welfare of domestic animals and agriculture in general. Due to the thousands of years of artificial selection of breeders to certain traits and of parallel-acting natural selection, especially on survival traits, rare local breeds present a unique source of genetic and phenotypic variability and are important also for food production, geographical and cultural identity. This proposal will be focused on the only autohtonous Slovenian goat breed, Drežnica goat. According to FAO criteria, Drežnica goat has the highest degree of the risk before extinction, a so-called critically endangered status. This is due to a small population size and because it is now confined in a very small Alpine area of only 15 km radius. Therefore, research of such exceptional rare breeds is important from a scientific point of view and in preserving positive cultural and soci-economic effects in remote unpopulated areas. Problem and objectives. In Slovenia, breeders have a strong economic pressure to switch or to cross local breeds with commercial breeds. Traits that local Drežnica goat still possesses, such as resistance to local diseases, adaptation to poor forage, homing and gregarious behaviour represent key traits for the survival and farming in harsh Alpine environment. Genetic and ethnographic research proposed in here can help to characterize and preserve such traits as well as promote expansion of the breed. The aim of objective 1 is to provide a broader DNA-based characterization of Drežnica goat including genetic diversity (variability) and its relationships to other goat breeds, population history, maternal and paternal phylogeny. Drežnica goat has shared the East Alpine pastures for hundreds of years with another species, Alpine ibex. We have preliminary results (goat-ibex hybrid) and other supporting evidence that Drežnica goats occasionally still interbreeds with Alpine ibex. Objective 2 will check the hypothesis about the possibility and extent of the goat-ibex introgression. Methods. For objective 1 we will employ the most advanced genomic approaches such as sequence analyses of the whole mitochondrial genomes, parts of chromosome Y and the autosomal genome analyses by SNP chips. For objective 2 we will try to infer Drežnica goat haplotypes in the genomes of Alpine ibex using whole genome SNP genotyping, sequencing the entire mtDNA and parts of chromosome Y. As we also have an F1 goat-ibex hybrid available, we will characterize in detail its phenotype, reproductive traits including further backcrosses to goats. During the field work for objectives 1 and 2, the expert team from Slovene Ethnographic Museum (SEM) will join to complement the scientific part of this proposal with socio-ethnographic research. Expected results and significance: Genomic analyses under objective 1 should bring novel knowledge of Drežnica goat-specific genetic population structure, diversity, new insights of post‑domestication migration routes and in reconstructing admixture. So-called selective sweep analyses should uncover novel loci important for adaptation to harsh environments and to resist diseases. Climate change and the emergence of new and virulent animal diseases underline the need to retain this adaptive capacity. Objective 2 experiments should determine if there is genetic exchange between the Alpine ibex and Drežnica goat and potentially in all goat breeds throughout the Alps. This is important from the point of view of basic and evolutionary research as well as from the applicability in nature-protection programs for wildlife and breeders. The importance of complementing ethnographic study of Drežnica goat breeding practices is in preserving material and non-material (tangible and intangible) cultural heritage to save and help revive these practices in the future.
Significance for science
Genetic research of local breeds is important for the advancement of genomic research in general. Slovenian local Drežnica goat breed, which is the subject of this project, is not important only for Slovenia, but also globally for the wider Alpine and pre-Alpine areas and other similar geographical and climatic zones. This population is an important genetic resource that still carries adapted and selective alleles for such a habitat, which the cosmopolitan high productive commercial breeds have already lost, due to the intensive selection and adaptation to the intensive rearing conditions in the stables.   Within experiments and analyses of workpackage 1 genomic analyses should bring novel knowledge of Drežnica goat-specific genetic population structure and diversity. Additionally, mtDNA and chromosome Y analysis should bring new insights of post-domestication migration routes and in reconstructing admixture. A genome-wide investigation of the distinctiveness of selective sweep regions in Drežnica goat should uncover novel loci important for adaptation to harsh environments and to resist diseases. Climate change and the emergence of new and virulent animal diseases underline the need to retain this adaptive capacity. Studying, and protecting rare local breeds such as Drežnica goat breed is therefore of increasing significance.   We also envisage important results obtained within workpackage 2 to asses goat genome introgression into another species, Alpine ibex. Evaluation of the genome-wide magnitude of cross-species introgression has only recently become possible. As goats (especially Drežnica goat breed) have shared for hundreds of years the high altitude Alpine pastures with Alpine ibex, gene flow between these two species could be expected. Reports of hybrids in nature and captivity confirm that. Introgressed regions should identify candidate genes with a potentially important role in environmental adaptation, similar to what has been shown with incorporation of Neanderthal DNA into the genome of non-African humans and between cattle and Yaks. Analyses of a goat-ibex hybrid that will be examined should bring novel data on its sperm quality and other reproductive parameters as well as hybrid’s capacity to sire offspring when back crossed to goats.     In summary, the proposed research belongs to the propulsive and important field of genomics and evolutionary research of domestic and wild animals. The results of this project can also be extremely useful for animal husbandry applications, wildlife management and medicine, as some genes and phenotypes can be a model for further biomedical research. The identified genomic differences between goats and Alpine ibex should also help to illuminate which genes are related to important economical traits as a result of domestication-artificial selection and, on the other hand to adaptive/evolutionary traits as a result of natural selection.
Significance for the country
Genetic research of local breeds is important for the advancement of genomic research in general. Slovenian local Drežnica goat breed, which is the subject of this project, is not important only for Slovenia, but also globally for the wider Alpine and pre-Alpine areas and other similar geographical and climatic zones. This population is an important genetic resource that still carries adapted and selective alleles for such a habitat, which the cosmopolitan high productive commercial breeds have already lost, due to the intensive selection and adaptation to the intensive rearing conditions in the stables.   Within experiments and analyses of workpackage 1 genomic analyses should bring novel knowledge of Drežnica goat-specific genetic population structure and diversity. Additionally, mtDNA and chromosome Y analysis should bring new insights of post-domestication migration routes and in reconstructing admixture. A genome-wide investigation of the distinctiveness of selective sweep regions in Drežnica goat should uncover novel loci important for adaptation to harsh environments and to resist diseases. Climate change and the emergence of new and virulent animal diseases underline the need to retain this adaptive capacity. Studying, and protecting rare local breeds such as Drežnica goat breed is therefore of increasing significance.   We also envisage important results obtained within workpackage 2 to asses goat genome introgression into another species, Alpine ibex. Evaluation of the genome-wide magnitude of cross-species introgression has only recently become possible. As goats (especially Drežnica goat breed) have shared for hundreds of years the high altitude Alpine pastures with Alpine ibex, gene flow between these two species could be expected. Reports of hybrids in nature and captivity confirm that. Introgressed regions should identify candidate genes with a potentially important role in environmental adaptation, similar to what has been shown with incorporation of Neanderthal DNA into the genome of non-African humans and between cattle and Yaks. Analyses of a goat-ibex hybrid that will be examined should bring novel data on its sperm quality and other reproductive parameters as well as hybrid’s capacity to sire offspring when back crossed to goats.     In summary, the proposed research belongs to the propulsive and important field of genomics and evolutionary research of domestic and wild animals. The results of this project can also be extremely useful for animal husbandry applications, wildlife management and medicine, as some genes and phenotypes can be a model for further biomedical research. The identified genomic differences between goats and Alpine ibex should also help to illuminate which genes are related to important economical traits as a result of domestication-artificial selection and, on the other hand to adaptive/evolutionary traits as a result of natural selection.
Most important scientific results Interim report
Most important socioeconomically and culturally relevant results Interim report
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