In the Carpathian Basin the wild boar (Sus scrofa) belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different (p < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an F_st value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations’ genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces’ having been preserved from both the last ice age and the period before the Hungarian water regulation.

The golden jackal (Canis aureus) is a reoccurring species in the centre of the Carpathian basin, in Hungary. In total, 31 golden jackal tissue samples were collected, from 8 white-coated, 2 black-coated and one mottled animal across Hungary. Sequences and fragment length polymorphisms were studied for white colour (MC1R), and for black coat colouration (CBD103). In each white animal, the most widespread mutation causing white fur colour in dogs in homozygous form was detected. Three animals were found to carry the mutation in heterozygous form. The two black golden jackals were heterozygous for the 3 bp deletion in CBD103 that mutation for black coat colouration in dogs, and one of them also carried the mutation causing white fur. None of the white animals showed signs of hybridization, but both the black and the mottled coloured individuals were found to be hybrids based on genetic testing. Kinship was found three times, twice between white animals, and once between a white animal and an agouti animal carrying the mutation of white coat. Our results confirm the findings that golden jackal–dog hybrids may occur without human intervention, and the detected mutation causing white fur colour in golden jackals could possibly be due to an early hybridization event.

A global genome database of all of Earth's species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ~1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 34 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

In the food supply chain, quality control has a very important role in maintaining customer confidence. In the EU, food safety aspects are strictly regulated; however, composition requirements and standard control methods are generally undefined. The rapidly increasing wild boar population has a growing market share in venison or game meat production. Several methods have been described for species identification and control of composition in food products, but only some of these are suitable for routine measurements. The aim of our research was to design a rapid, reliable and simple PCR insertion/deletion (InDel)-based genetic tool suitable for species identification in food quality control laboratories. In total, 59 different swine (Sus scrofa) whole genomes were tested with bioinformatic tools to identify wild boar-specific insertions or deletions. Three independent InDels were suitable for marker development, multiplex PCR amplification and separation in agarose gel. Altogether, 209 samples of wild boar and ten other domestic pig breeds were taken for DNA extraction and validation of the three multiplexed InDel markers. Statistical analysis showed a very high combined predictive value (0.996), indicating the capability of the newly developed markers to detect wild boars with a probability over 99%. Breed assignment tests confirm that the InDel markers developed are suitable for rapid, sensitive and reliable identification of the wild boar meat content of food products. The use of the reported method in food quality control can mean a simple and cost-effective way to maintain consumer confidence and to support the competitiveness of fair producers.

Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

After the last glacial, the Carpathian Basin was repopulated from either eastward or northward colonisation routes for various species; one of these was the emblematic member of the European megafauna, the red deer, Cervus elaphus. We analysed 303 red deer individuals from the middle of the region, in seven Hungarian game reserves, at ten microsatellite loci (C01, C229, T26, T108, T123, T156, T172, T193, T501, T507), to investigate the genetic diversity of these subpopulations. We discovered high levels of genetic diversity of red deer subpopulations; allelic richness values ranging 4.99–7.01, observed heterozygosity 0.729–0.800, polymorphic information content 0.722–0.806, and Shannon’s information index 1.668–2.064. Multi-locus analyses indicated population admixtures of various degrees that corresponded to geographical location, and complex genetic structures were shown by clustering. Populations in the south-western and the north-eastern parts of the region formed two highly separated groups, and the red deer from populations in between them were highly admixed (in western Pannonia/Transdanubia, where the Danube flows into the Carpathian Basin). This pattern corresponds to the distribution of mitochondrial as well as Y-chromosome lineages. Assignment tests showed that a large fraction of individuals (29.4%) are found outside of their population of origin, indicating that the dispersal of red deer is rather common, which could be expected considering the life course of the species.