Andrej Razpet

Database of cattle candidate genes and genetic markers for milk production and mastitis.

A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3′UTRs of candidate genes.

Resolving taxonomic uncertainties using molecular systematics: Salmo dentex and the Balkan trout community

The genetic structure of Salmo dentex and its phylogenetic relations to sympatric salmonids in the Neretva and Skadar River basins were evaluated using mitochondrial DNA (mtDNA) control region, eight microsatellites, and somatolactin (SL) gene. In the Neretva River basin of Bosnia–Herzegovina, the results based on mtDNA analysis showed extensive haplotype sharing between S. marmoratus, S. dentex, and S. trutta, and were therefore not conclusive; however, F-statistics and assignment testing based on nuclear DNA markers indicated that S. dentex of the Neretva basin were grouped in a genetically unified cluster with S. marmoratus in the Neretva basin. Using the same analytical approach, S. dentex from the Skadar basin in Montenegro appeared to be genetically distinct from S. marmoratus in the same basin and indistinct from local S. trutta. Molecular data also indicated that S. dentex of the Neretva basin in Bosnia–Herzegovina are not closely related to S. dentex of the Skadar basin in Montenegro. Based on these results, we hypothesize S. dentex to be a particular life history form of S. marmoratus in the Neretva basin and of S. trutta in the Skadar basin. These results clearly demonstrate that S. dentex does not represent a monophyletic lineage and should not be considered a distinct species.

Re‐evaluation of Salmo data by Gridelli (1936)—description of stocking, hybridization and repopulation in the River Soča basin

History of stocking in Salmo marmoratus habitat in the Adriatic region and its effects are poorly known due to data deficiency. Well‐documented research from 1936 based on trout external morphological characters was compared with research of extant trout populations based on genetic markers in an attempt to clarify the impact of stocking in the River Soča basin. Application of multivariate statistical methods reveals a similar pattern of native and non‐native trout distribution in 1936 and after a recently started S. marmoratus repopulation project. Remnants of initial stocking from 1906 were detected in one stream in the upper Soča basin. Gridellis samples of S. dentex, one of the least researched trout species of the Adriatic region, were also re‐analysed and were found to differ from all other trout populations used in the study.

Genetic composition of the Jadro softmouth trout following translocation into a new habitat

Genetic founder effects of a historical translocation (1965; app. 12 generations ago) of endangered softmouth trout from the only remaining indigenous population to an adjacent uninhabited river were investigated.A comparison of 15 microsatellites from contemporary samples in both the source and re-established populations indicated a very low level of genetic diversity within the two populations. Furthermore, considerable differences in estimates of variability and effective population sizes were detected between populations, but no recent bottlenecks were evident. Our data suggest that the re-established population has lost variation due to genetic drift associated with founder effects following the translocation. Accordingly, in relation to management, we suggest that the re-established population could serve as a secondary source of individuals to buffer possible extinction due to demographic events. Finally, conservation initiatives to enhance the census population size and increase levels of variability in the re-established population are proposed.

Genetic variation of European grayling (Thymallus thymallus) populations in the Western Balkans

In order to elucidate genetic composition of European grayling (Thymallus thymallus) populations in the Western Balkans, the partial mitochondrial DNA (mtDNA) control region was sequenced and 12 microsatellite loci genotyped in 14 populations originating from tributaries of the Adriatic and Danube drainages. Eleven mtDNA haplotypes were found, one confined to the Adriatic clade, one to the Alpine group and the rest to the ‘Balkan’ grayling phylogenetic clade. Haplotypes from the Balkan clade were confined to the Danube drainage and constituted two groups: northern group with haplotypes found in the Slovenian part of the Danube drainage, and southern group, consisting from Bosnia–Herzegovina and Montenegro. Substantial genetic distance between northern and southern groups of haplotypes (0.75–1.8%) and well supported divisions within the northern group indicate very structured grayling population within the studied Danube basin that most probably did not evolve due to vicariance but rather as a consequence of multiple colonization waves that might have occurred during the Pleistocene. Furthermore, genetic distance of ~4% between Adriatic and Danube populations’ haplotypes, suggest that their separation occurred in mid-Pliocene. These findings imply a complex colonization pattern of the Western Balkans drainages. Microsatellite data also confirm high genetic diversity in Western Balkans populations of grayling (on average 7.5 alleles per microsatellite locus and Hexp 0.58). Limited stocking activities were detected based on microsatellites and mtDNA data. Regarding current knowledge of grayling phylogeography appropriate management strategies were proposed to preserve unique, autochthonous grayling populations in Western Balkan.

Analysis of genetic structure of huchen (Hucho hucho) in Serbia inferred from mitochondrial and nuclear DNA.

Abstract The purpose of this study was to assess the genetic diversity of Serbian huchen and provide guidelines for conservation and management. Fourteen huchen individuals were collected from six localities. For all individuals the mitochondrial DNA control region and the NADH1 gene were sequenced, and two microsatellite loci were genotyped. Sequencing of two mtDNA loci showed the presence of the same haplotypes (Hh_CR_1 and Hh_ND1_1) in all investigated specimens and the complete absence of genetic variability at inter- and intra-populational level. However, analyzed individuals from Serbia have the largest number of control region repeats (average 8.7) compared to all other huchen populations from the Danube basin. Microsatellite data show that the most of Serbian huchens were placed in the “eastern” cluster except one individual from the Drina River which clustered with “western” samples, most likely a consequence of stocking. In spite of only two loci used, four unique alleles found in the studied Serbian and Drina basin population indicate that the Danube basin may possess more region specific alleles than previously thought, which could be of great importance for efficient species management in the future. Abstract Cilj ovoga rada je bio da se izvrši procena genetičkog diverziteta mladice u Srbiji, i da se na osnovu dobijenih rezultata daju preporuke za buduće očuvanje i upravljanje fondom mladice. Za ovu svrhu sakupljeno je 14 jedinki sa šest lokaliteta. Za sve sakupljene jedinke sekvencirana je kontrolna regija, NADH1 gen mitohondijske DNK i genotipizirana su dva mikrosatelitska lokusa. Sekvenciranjem dva mtDNK lokusa utvrđeno je prisustvo istih haplotipova (Hh_CR_1 i Hh_ND1_1) kod svih ispitanih jedinki, odnosno, potpuno odsustvo genetičke varijabilnosti na inter- i intra-populacionom nivou. Međutim, analizirane jedinke iz Srbije karakterišu se najvećim brojem ponovaka kontrolne regije (prosečno 8,7), u poređenju sa svim ostalim populacijama mladice iz dunavskog sliva. Analizom mikrosatelitskih podataka, utvrđeno je da se gotovo sve jedinke iz Srbije svrstavaju u “istočnu” grupu, izuzev jedne jedinke iz Drine, koja je svrstana sa “zapadnim” uzorcima, što je najverovatnije posledica poribljavanja. Kod analiziranih jedinki sa teritorije Srbije i iz celokupnog sliva Drine pronađena su četiri jedinstvena alela, uprkos analizi samo dva mikrosatelitska lokusa. Dobijeni rezultati ukazuju da dunavski sliv može posedovati više regionalno specifičnih alela nego što se ranije smatralo, što bi moglo biti od velikog značaja za uspešno upravljanje fondom mladice u budućnosti.