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Projects / Programmes source: ARIS

IDENTIFICATION AND CHARACTERIZATION OF GENES INVOLVED IN SALMO PIGMENTATION

Research activity

Code Science Field Subfield
4.06.00  Biotechnical sciences  Biotechnology   

Code Science Field
B220  Biomedical sciences  Genetics, cytogenetics 
Keywords
Salmo, brown trout, marble trout, pigmentation, comparative genomics
Evaluation (rules)
source: COBISS
Researchers (7)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  05098  PhD Peter Dovč  Biotechnology  Researcher  2007 - 2009  935 
2.  24769  PhD Gregor Gorjanc  Animal production  Junior researcher  2007 - 2009  497 
3.  22445  PhD Andrej Razpet  Biotechnology  Researcher  2007 - 2009  64 
4.  28506  PhD Urška Sivka  Biochemistry and molecular biology  Junior researcher  2007 - 2009  19 
5.  11906  PhD Aleš Snoj  Animal production  Researcher  2007 - 2009  219 
6.  15658  PhD Simona Sušnik Bajec  Biochemistry and molecular biology  Head  2007 - 2009  194 
7.  17513  Vida Štuhec    Technical associate  2007 - 2009  10 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  66,306 
Abstract
Gene annotation in vertebrate genome represents one of the major goals of genomic analyses. During the last decade genetic model organisms enhanced studies of functional genomics and allowed considerable advances to take place in this field especially by applying comparative genomics approach with non-model organisms. Despite a great number of studies performed so far, the genes underlying differences of the adult phenotype still remain largely unknown, particularly among the vertebrates. Adult pigment patterns in fish are model examples for genetic and developmental analyses because these patterns can differ dramatically across closely related species. Among fish - zebrafish (Danio rerio) represents a genetic model organism and is one of the most studied fish for demonstrating genetic mechanisms of pigment pattern diversification. Up to date many genes have been described of being potentially involved in pigment pattern formation in zebrafish. Therefore available data could in combination with comparative genomics approach enable genomic studies and “pigment” gene identification in other non-model fish species, e.g. Salmo. The proposed project aims to find genomic regions associated with specific diagnostic features of marble trout, i. e. marble colour pigmentation, in order to gain new insights into genetic mechanisms influencing complex pigmentation pattern traits in Salmo sp. Marble trout (S. trutta marmoratus), one of the most phenotypically distinct evolutionary lineages of S. trutta, has been chosen as a model organism for the proposed study due to, (i) it’s highly distinct morphological characteristics (marbled colour pattern, growth) and (ii) due to the availability of the samples from F1 and F2 generations of the cross between the marble and the brown trout. The results of this study will be among the first in assessing the genetic base for pigment pattern diversity in the genus Salmo and will for the first time aim to describe the genetic diversity leading to marble pigmentation pattern, characteristic for marble trout.
Significance for science
Functional genomic approach has played an important role in model and farm animal research during the last decade and has since then advanced in methodology used and in availability of genomic databases. However, direct applications of molecular evidences in the field of QTL and candidate gene detection remain scarce at the population’s level, mainly due to complex genetic background which complicates the estimation of the direct phenotypic effect of targeted loci. Nevertheless, the same approach is beginning to emerge also in studies of wild animals, where it is expected to offer a functional upgrade of phylogenetic and population genetic studies performed to date. Recently, large genomic libraries became available also for some economically important Salmonidae species (Salmo salar and Oncorhynchus mykiss) that using comparative approach, promise to promote research in functional genomic studies also in closely related species, such as S. trutta. A number of studies already showed that using comparative genomic information to develop SNP markers in candidate genes is very efficient in non-model organisms, but to our knowledge this approach has not been applied to study adaptive gene evolution in genus Salmo, yet. The research work was of fundamental nature and it is anticipated that it will promote the genomic research in salmonid fishes, particularly in a non-model and commercially less interesting Salmo trutta. Atlantic (Salmo salar) and pacific salmon (Onchorhynchus mykiss) represent model organisms for studies of functional genomics in Salmonid fishes. Preliminary studies have already shown that some of the pigment genes, previously described in other model species, are involved in pigmentation process also in these two salmonid species, but none of the gene was directly linked to a specific pigmentation pattern. Brown trout (Salmo trutta), one of the phenotypically most diverse vertebrate species, was not a subject of similar studies, yet. This project therefore represents one of the first studies of functional genomics in trout. Project results thus contribute to knowledge about genetic mechanisms affecting complex pigmentation pattern in trout. We believe that knowledge about the individual gene evolution will give new dimensions not only to our understanding of evolutionary pathways of the species and adaptation to the environment, but also to identification of genetic resources of high importance in a sense of adaptive potential.
Significance for the country
The research work included marble trout, Soča river endemic species, as the main subject of interest. Due to its highly distinct and prominent marbled colour pattern and growth potential, marble trout is known and appreciated worldwide for sport-fishing activities. Despite its peculiarity, marble trout is considered as an endangered taxon due to its limited habitat and hybridization with introduced brown trout. Its management is a necessity and it has been successfully carried on during the last decade by our collaborators and partner research team of the proposed project, the Angling club of Tolmin, particularly Dušan Jesenšek, the manager of Tolmin hatchery. Durability management, marble trout reasonable exploitation and preservation rely heavily on knowledge of the species biology, ecology and genetics. The results of the proposed project first time try to characterize by genetic means the most prominent feature of the marble trout. We anticipate that genotyping of the SNPs co-segregating with the marbling pattern will be implemented in the program of marble trout restoration and management, and will thus play an important role in marble trout preservation.
Most important scientific results Annual report 2008, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2008, final report, complete report on dLib.si
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