Genetic status of lowland-type Racka sheep colour variants.

Lowland-type Racka is an indigenous sheep breed that beside Hungarian Grey cattle and Mangalitza pig is one of the national symbols of Hungary. However, the genetic description of Racka sheep has not yet been conducted based on whole-genome screening. By using the Geneseek Ovine SNP50 BeadChip, we have sampled the genome of 126 Black and 128 White Racka sheep. For comparative purposes, we used 134 Hungarian Merinos and further 3345 animals from 81 different breeds have been included from an available database. Performance of a multidimensional scaling plot showed that White and Black Rackas represent well-separated groups among other sheep breeds and clustered separately from each other. However, the number and total length of Runs of Homozygosity was similar to other sheep breeds, except Soay. The inbreeding coefficients (method-of-moments relatedness F coefficient) of Black and White Racka were 0.147 and 0.133, respectively. Based on multidimensional scaling and admixture analyses and on comparisons of genetic distances of the investigated 84 populations, we suggest considering the colour variants of Racka as genetically differentiated breeds. The most differentiated markers between Black and White Racka highlight several candidate genes including 5-Hydroxytryptamine Receptor 5A, Insulin Induced Gene 1, Cyclin Dependent Kinase 5 and Melanocortin 1 Receptor. The results of this study help the recognition of Racka as a unique genetic resource among sheep and pave the way of application of genome screens to guide the resolution of questions arising among breeders.

Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene.

The Mangalitza lard-type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow-Belly Mangalitza and Red Mangalitza. The Swallow-Belly line has a black coat combined with yellow-blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with HapFLK and BayeScan, and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18-20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.

Genetic position of Hungarian Grey among European cattle and identification of breed-specific markers.

Hungarian Grey is an indigenous cattle breed that is one of the national symbols of Hungary. However, genetic description of the Hungarian Grey cattle has not yet been conducted based on whole-genome screening. Using the GeneSeek high-density Bovine SNP (single nucleotide polymorphism) 150 K BeadChip, we sampled the genome of 36 Hungarian Grey, 12 Maremmana, 13 Hungarian Fleckvieh and 5 Holstein-Friesian cattle for population studies and used data of 139 other cattle from an additional dataset created on European cattle breeds (Upadhyay et al.2017. Heredity 118, 169-176). The performance of a multidimensional scaling plot showed that Hungarian Grey clustered independently from other European cattle. The number and total length of runs of homozygosity (ROH) is similar or slightly below the value of other European cattle; FROH coefficients (proportion of the autosomal genome covered by ROH) are similar to Maremmana and Maronesa. The frequency of ROH does not show increased values as it can be noticed in Heck and Maltese. These results indicate that the Hungarian Grey cattle have been successfully maintained avoiding negative genetic effects, and reflect the uniqueness among European cattle. The identification of breed-specific loci has been aimed at differentiating Hungarian Grey (n = 136 in this case) from other cattle breeds (n = 169). Ten loci (-log10P > 5) were identified as markers capable for differentiation of Hungarian Grey. These markers are located on chromosomes 6, 14, 15, 16, 20 and 24.

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs.

The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.

Mitochondrial D-loop analysis reveals low diversity in Mangalica pigs and their relationship to historical specimens.

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.

AluI polymorphism of the bovine growth hormone (GH) gene, resumption of ovarian cyclicity, milk production and loss of body condition at the onset of lactation in dairy cows.

Relationships among GH genotype (AluI polymorphism), parity, metritis and interval from calving to first ovulation, milk production and body condition score (BCS) loss were determined in dairy cows (n=307) on four large-scale farms in Hungary. Cows with systemic signs of puerperal metritis or mastitis were excluded. Time of the first postpartum (PP) ovulation was obtained from milk progesterone profiles. Based on GH genotype determination, groups of leucine homozygous cows (n=246) and valine allele carriers (n=61) were formed. All animals became cyclic during the study period. The average interval to first ovulation was 27.6+/-0.69-d PP (mean+/-S.D.). Genotype had no effect on the commencement of ovarian cyclicity. First ovulation occurred sooner after calving in pluriparous than in primiparous cows. The greater BCS loss cows had during the first 30-d PP, the longer they took to resume cyclic ovarian function. The interval from calving to first ovulation was substantially affected by farm, but not by mild cases of puerperal metritis. Genotype was not related to cumulative 30-d milk yield or BCS loss after calving. Primiparous cows had lower milk yield than pluriparous ones. Cows with metritis lost more body condition than healthy individuals in the first month postpartum. We concluded that, under field conditions, AluI polymorphism of the bovine GH gene had no effect on the interval from calving to first ovulation and could not be directly related to differences in milk yield and to the extent of BCS loss during the first month after calving in Holstein-Friesian cows.

Y-chromosome analysis of ancient Hungarian and two modern Hungarian-speaking populations from the Carpathian Basin.

The Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic family. The Tat C allele is an interesting marker in the Finno-Ugric context, distributed in all the Finno-Ugric-speaking populations, except for Hungarians. This question arises whether the ancestral Hungarians, who settled in the Carpathian Basin, harbored this polymorphism or not. 100 men from modern Hungary, 97 Szeklers (a Hungarian-speaking population from Transylvania), and 4 archaeologically Hungarian bone samples from the 10(th) century were studied for this polymorphism. Among the modern individuals, only one Szekler carries the Tat C allele, whereas out of the four skeletal remains, two possess the allele. The latter finding, even allowing for the low sample number, appears to indicate a Siberian lineage of the invading Hungarians, which later has largely disappeared. The two modern Hungarian-speaking populations, based on 22 Y-chromosomal binary markers, share similar components described for other Europeans, except for the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection, and high frequency of haplogroup J in both Szeklers and Hungarians. MDS analysis based on haplogroup frequency values, confirms that modern Hungarian and Szekler populations are genetically closely related, and similar to populations from Central Europe and the Balkans.

Effect of MYOG genotypes on growth rate and production traits in Hungarian large white pigs.

The effect of the porcine myogenin (Myog) 3' polymorphism on birth weight, growth rate, carcass weight, lean weight, lean meat percentage and back-fat thickness has been investigated in Hungarian Large White pigs. MYOG genotypes were determined by PCR-RFLP assay. The obtained MYOGA frequency value was 0.6275. Due to the small number of BB piglets the effect of the MYOG genotypes on birth weight was not significant; however, an increasing tendency was observed from genotype AA to BB. The growth rate difference between MYOG genotypes was significant: BB animals showed the highest growth rate values during the fattening period. Since few results are available on the possible use of MYOG gene polymorphism in selection to improve carcass and growth traits, by this study the authors hope to provide additional data on this particular subject.

Influence of porcine coat colour genotypes on haematological parameters, piglet birth weight and body weight gain until weaning.

Two F2 generations of an intercross between Hampshire boars and Hungarian Large White sows were produced to estimate the effects of the porcine KIT genotypes (II, Ii and ii) on quantitative and qualitative haematological indices, on piglet birth weight and growth performance until weaning. Piglets carrying the I allele had significantly fewer lymphocytes (p = 0.041) than the ii homozygotes, heterozygotes had measures between the two homozygotes. KIT genotypes did not influence white blood cells, red blood cells, haemoglobin and haematocrite. II genotype piglets were significantly lighter at birth than the ones carrying the recessive i allele, the effect of KIT genotypes on gain until weaning was not significant, but II piglets tended to gain less. The results of this study support the hypothesis of M. Johansson, H. Ellegren, L. Marklund, U. Gustavsson, E. Ringmar-Cederberg, K. Andersson, I. Edfors-Lilja and L. Andersson [(1992) Genomics, 14, 965] that the pleiotrophic effect of the porcine KIT mutations on haematopoietic cells must be mild.

Oestrogen receptor genotypes and litter size in Hungarian Large White pigs.

A total of 869 litter records of 226 Hungarian Large White sows have been analysed to investigate the possible use of the oestrogen receptor gene (ESR) as marker to improve litter size. First, second and later parities have been evaluated separately. Frequencies of A = 0.55 and B = 0.45 have been calculated for the two ESR alleles and the observed/ expected number of the three genotypes were as follows: AA: 71/69.1, AB: 108/111.8 and BB: 47/45.1. BB type first and later parity sows were superior to AB and AA sows for number born alive (NBA), total number of born (TNB) and the corrected number of weaned piglets (CNW), respectively.

Expression of the aromatase cytochrome P450 encoding gene in cattle and sheep.

During this report the tissue-specific expression and promoter usage of the aromatase cytochrome P450 encoding gene, Cyp19, are compared between cattle and sheep. In addition, data will be presented on the identification of cis-acting regulatory sequences located in the bovine placenta-specific promoter 1.1. In cattle and sheep Cyp19 is mainly expressed in the foetal placental layer and ovarian granulosa cells but also in other organs as brain or testis. Differently spliced transcripts of Cyp19 which include an invariable coding region but a variable 5'-untranslated region could be detected in tissues of both species. However, in contrast to ovary and brain which express homologous transcript variants, different transcripts are present in placentae suggesting that also different placenta-specific promoter regions are active in cattle and sheep. The analysis of the chromatin structure of the main placental promoter 1.1 in different bovine tissues revealed that hypomethylation and the occurrence of DNaseI hypersensitive sites (HS) within this region are associated with promoter activity. Active regulatory elements were identified in reporter gene studies in JEG-3 choriocarcinoma cells. The co-localisation of an E-box element within one of the placenta-specific HS suggests that this element is important for Cyp19 expression in the bovine placenta.

Placenta-specific transcripts of the aromatase encoding gene include different untranslated first exons in sheep and cattle.

The aim of the present study was the characterization of the ovine aromatase cytochrome P450 encoding gene (Cyp19) and the analysis of its tissue-specific expression. Two loci with considerable sequence identity were found (Cyp19 and Cyp19b). From Cyp19, tissue-specific transcript variants with different untranslated first exons but identical coding regions could be identified. Cyp19b transcripts were not detected. In the sheep brain and ovarian granulosa cells transcript variants, starting with the untranslated exons 1.4 and 2, respectively, were preferentially found. Exons 1.2 and 1.3 which had been described in bovines could not be detected in sheep and the major 5' untranslated region of the bovine placental transcript, exon 1.1, was also not found to predominate in the sheep placenta. However this exon frequently was combined with a new untranslated exon (exon 1.1a) thus generating an alternative splice variant. The main placental transcripts in sheep had a different first exon (exon 1.5). Two alternatively spliced variants of this transcript were found with tissue-specific preference. From the present data it can be concluded: (a) that the ovine genome contains two copies of Cyp19 of which only one is transcribed and may encode a functional protein; and (b) that in spite of being closely related species, sheep and cattle have remarkable differences concerning tissue-specific transcript distribution and presumable promoter usage.

Accelerated separation of random complex DNA patterns in gels: comparing the performance of discontinuous and continuous buffers.

Complex DNA fragment patterns produced by random amplified polymorphic DNA (RAPD) assays were separated in agarose as well as polyacrylamide gels using a continuous buffer and two discontinuous buffer systems, with and without urea, respectively. The effect of very high field strength/current levels on the duration of separation, the relative mobilities of the selected bands, and the appearance of the pattern was tested. The use of discontinuous buffer systems resulted in sharper bands and better resolution at 30 min duration of separation for DNA fragments in the size range of 200-2000 base pairs. These observations could help researchers in the rapid separation of band patterns produced by polymerase chain reaction (PCR)-based methods utilized in small- to mid-scale genome searches.

Simultaneous analysis of bovine kappa-casein and BLAD alleles by multiplex PCR followed by parallel digestion with two restriction enzymes.

An improved and simplified method allowing simultaneous genetic typing of kappa-casein and CD 18 (bovine leucocyte adhesion deficiency; BLAD) loci has been developed. The method is based on the simultaneous amplification of fragments of the two groups of alleles by multiplex PCR, and on a concurrent, parallel digestion of the products by two restriction enzymes (PstI and HaeIII) in the same incubation buffer. Digestion with PstI distinguishes kappa-casein A and B alleles and does not cut within any of the BLAD alleles, while digestion with HaeIII allows the differentiation between normal and mutant allele variants of the CD18 locus. All combinations of the known mutants of the two alleles, characterized to the regions amplified and resulting in phenotypic effect, could be detected by electrophoretic separation performed on the same agarose gel owing to the vast differences in the length of the restriction fragments.

Agarose electrophoresis of DNA in discontinuous buffers, using a horizontal slab apparatus and a buffer system with improved properties.

Using a horizontal slab apparatus with a buffer in the reservoirs at the level of the gel ("sea-level electrophoresis"), the retrograde discontinuous buffer system reported by Wiltfang et al. for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of proteins was applied to DNA electrophoresis. This application yielded the advantages of an increased displacement rate of the moving boundary front and a decrease in the concentration of the counterion base in the resolving phase, which yielded reduced relative mobility values at equivalent gel concentrations and practicable low buffer concentrations. The change of relative mobilities (Rf) with a variation of field strength is decreased compared to that of the migration rate in the continuous Tris-boric-acid-EDTA (TBE) buffer and thus the robustness of the system is improved, as well as the efficiency of separation. The system of Wiltfang et al. has in common with previously described discontinuous DNA system, that it is able to stack DNA from dilute samples and is insensitive to sample components with lower net mobilities than DNA, such as acetate. However, the variance of Rf at constant current density in the discontinuous buffer system is not improved over that of the migration rate at constant field strength in the continuous TBE buffer.