Fodor E.,Eotvos Lorand University |
Zsigmond A.,Eotvos Lorand University |
Horvath B.,Hungarian Academy of Sciences |
Molnar J.,BIOMI Ltd. |
And 6 more authors.
PLoS ONE | Year: 2013
Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be complete. In order to identify new genes involved in the establishment of the dorsoventral (DV) axis during early stages of zebrafish embryonic development, we employed next generation sequencing for full transcriptome analysis of normal embryos and embryos lacking overt DV pattern. A combination of different statistical approaches yielded 41 differentially expressed candidate genes and we confirmed by in situ hybridization the early dorsal expression of 32 genes that are transcribed shortly after the onset of zygotic transcription. Although promoter analysis of the validated genes suggests no general enrichment for the binding sites of early acting transcription factors, most of these genes carry "bivalent" epigenetic histone modifications at the time when zygotic transcription is initiated, suggesting a "poised" transcriptional status. Our results reveal some new candidates of the dorsal gene regulatory network and suggest that a plurality of the earliest upregulated genes on the dorsal side have a role in the modulation of the canonical Wnt pathway. © 2013 Fodor et al. Source
Molnar J.,BIOMI Ltd. |
Molnar J.,Hungarian Academy of Sciences |
Nagy T.,Agricultural Biotechnology Institute |
Steger V.,Agricultural Biotechnology Institute |
And 4 more authors.
BMC Genomics | Year: 2014
Background: Mangalicas are fatty type local/rare pig breeds with an increasing presence in the niche pork market in Hungary and in other countries. To explore their genetic resources, we have analysed data from next-generation sequencing of an individual male from each of three Mangalica breeds along with a local male Duroc pig. Structural variations, such as SNPs, INDELs and CNVs, were identified and particular genes with SNP variations were analysed with special emphasis on functions related to fat metabolism in pigs.Results: More than 60 Gb of sequence data were generated for each of the sequenced individuals, resulting in 11× to 19× autosomal median coverage. After stringent filtering, around six million SNPs, of which approximately 10% are novel compared to the dbSNP138 database, were identified in each animal. Several hundred thousands of INDELs and about 1,000 CNV gains were also identified. The functional annotation of genes with exonic, non-synonymous SNPs, which are common in all three Mangalicas but are absent in either the reference genome or the sequenced Duroc of this study, highlighted 52 genes in lipid metabolism processes. Further analysis revealed that 41 of these genes are associated with lipid metabolic or regulatory pathways, 49 are in fat-metabolism and fatness-phenotype QTLs and, with the exception of ACACA, ANKRD23, GM2A, KIT, MOGAT2, MTTP, FASN, SGMS1, SLC27A6 and RETSAT, have not previously been associated with fat-related phenotypes.Conclusions: Genome analysis of Mangalica breeds revealed that local/rare breeds could be a rich source of sequence variations not present in cosmopolitan/industrial breeds. The identified Mangalica variations may, therefore, be a very useful resource for future studies of agronomically important traits in pigs. © 2014 Molnár et al.; licensee BioMed Central Ltd. Source
Molnar J.,BIOMI Ltd. |
Toth G.,Agricultural Genomics and Bioinformatics Group |
Steger V.,Agricultural Genomics and Bioinformatics Group |
Zsolnai A.,Research Institute for Animal Breeding and Nutrition |
And 7 more authors.
Journal of Animal Breeding and Genetics | Year: 2013
The genetic relationship between 195 Mangalica and 79 non-Mangalica pigs was studied using mitochondrial D-loop SNP genotyping. Altogether, 35 polymorphic sites and 27 haplotypes were identified. Of the haplotypes, eight and 16 are Mangalica and non-Mangalica specific, respectively, while three contain both Mangalica and non-Mangalica individuals. Genetic distance values and phylogenetic analysis indicate that Mangalica individuals are very closely related, and five haplotypes represent approximately 92% of the Mangalica pigs involved in the study, thus determining the major maternal lineages. In contrast to previous microsatellite studies, individuals of Mangalica could not be distinguished as three separate breeds using mtDNA genotyping. Comparing modern and archaeological mtDNA sequences revealed that present day Mangalica is related to pigs that lived in the Carpathian basin where postulated ancestors of Mangalica also lived. This is the first DNA-based genetic evidence to support the described breeding history of Mangalica. © 2012 Blackwell Verlag GmbH. Source
Steger V.,Eotvos Lorand University |
Steger V.,Institute of Genetics |
Molnar A.,Eotvos Lorand University |
Molnar A.,Institute of Genetics |
And 22 more authors.
Molecular Genetics and Genomics | Year: 2010
Antlers of deer display the fastest and most robust bone development in the animal kingdom. Deposition of the minerals in the cartilage preceding ossification is a specific feature of the developing antler. We have cloned 28 genes which are upregulated in the cartilaginous section (called mineralized cartilage) of the developing ("velvet") antler of red deer stags, compared to their levels in the fetal cartilage. Fifteen of these genes were further characterized by their expression pattern along the tissue zones (i.e., antler mesenchyme, precartilage, cartilage, bone), and by in situ hybridization of the gene activities at the cellular level. Expression dynamics of genes col1A1, col1A2, col3A1, ibsp, mgp, sparc, runx2, and osteocalcin were monitored and compared in the ossified part of the velvet antler and in the skeleton (in ribs and vertebrae). Expression levels of these genes in the ossified part of the velvet antler exceeded the skeletal levels 10-30-fold or more. Gene expression and comparative sequence analyses of cDNAs and the cognate 5′ cis-regulatory regions in deer, cattle, and human suggested that the genes runx2 and osx have a master regulatory role. GC-MS metabolite analyses of glucose, phosphate, ethanolamine-phosphate, and hydroxyproline utilizations confirmed the high activity of mineralization genes in governing the flow of the minerals from the skeleton to the antler bone. Gene expression patterns and quantitative metabolite data for the robust bone development in the antler are discussed in an integrated manner. We also discuss the potential implication of our findings on the deer genes in human osteoporosis research. © Springer-Verlag 2010. Source
Szanto-Egesz R.,BIOMI Ltd. |
Janosi A.,NARIC Food Science Research Institute |
Mohr A.,BIOMI Ltd. |
Szalai G.,University of South Carolina |
And 6 more authors.
Food Analytical Methods | Year: 2016
A fast and reliable diagnostic system has been developed for the detection of Mangalica meat in foods. This qualitative test is based on a recombinase polymerase amplification which can be performed on the field, in situ, where it may be necessary to determine Mangalica content in food products at once. The required equipments for the procedure are pipettes, a portable homogenizer and a portable thermostat. DNA amplification is carried out at a constant temperature, and the detection is based on antibody reaction. The detection limit is one copy of the target sequence in 1 μl reaction volume. The test can be used for uncovering falsification of local brands on the spot within a very short (25–45 min) period of time. The present approach can be adopted for the detection of other food ingredients, if the species-specific target DNA sequence is known, e.g. in case of chicken, turkey, horse, and cattle. © 2015, Springer Science+Business Media New York. Source