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An experiment, carried out in the Middle Adriatic in late May 2017, documented the existence of a dense water dome in the area between the island of Blitvenica (close to the east coast) and the island of Jabuka (in the open sea). The yo-yo CTD measurements showed that the dome center was located at a distance of about 20 km from the coast while the vmADCP measurements revealed that the surface circulation around the dome was cyclonic. The temperature above the dome was slightly lower than farther off, as documented by in situ and remotely-sensed data. At the same time, a decrease of temperature close to the east coast was documented by bottom probes and satellite images. The meteorological data and modeling results showed that during the May 2017 experiment the northern winds prevailed, implying that the observations could be interpreted in terms of simultaneous occurrence of open-sea and coastal upwelling. With the aim of verifying the interpretation, a number of schematized numerical experiments were conducted. To begin with, the modelled wind fields were decomposed into the curl and curl-free components by using the Helmholtz-Hodge decomposition. Subsequently, the components were used to impose the forcing on the Adriatic model, assuming flat bottom and realistic bathymetry. The simulations showed that the wind curl was responsible for the occurrence of open-sea upwelling whereas the curl-free wind component supported the development of coastal upwelling., The 28th IUGG General Assembly (IUGG2023) (Berlin 2023)

Five oceanographic cruises were organized from 2017 to 2021 to explore occurrence of upwelling and downwelling in the eastern part of Middle Adriatic. Four cruises took place in late May or early June whereas the 2020 cruise was in August. High-resolution, yo-yo CTD profiling together with ship-borne ADCP measurements were performed along a vertical cross-section over the Middle Adriatic Pit. Wind fields were obtained from operational meteorological model ALADIN. The strongest upwelling, both coastal and open-sea, was observed in 2017 after several days of strong, upwelling favorable NNW winds, also characterized by a significant positive curl. In 2018, under mild, nearly curl-free NW winds, the pycnocline was almost flat, slightly rising in the vicinity of coast, whereas in 2019 moderate sirocco with negative curl produced strong downwelling in the area stretching about ~30 km from the coast. Measurements in 2020 were performed twice, one day apart; in a strongly stratified sea with no offshore wind-curl, only coastal upwelling was observed as an almost linear rise of the pycnocline. First measurement in 2021 was done after two days of strong NW wind turning to strong sirocco, the second followed two days later. The two passes revealed a complex wave-like structure of the pycnocline (variability of ~15 m in the vertical and ~35 km in the horizontal direction). Hydrodynamic model ROMS is used to reproduce and interpret the empirical findings. The open-sea upwelling in the eastern Middle Adriatic occurs when a significant positive-curl wind blows for several days over moderately stratified sea., The 28th IUGG General Assembly (IUGG2023) (Berlin 2023)

BackgroundDocking the tails of young lambs in long-tailed sheep breeds is a common practice worldwide. This practice is associated with pain, suffering and damage to the affected animals. Breeding for a shorter tail in long-tailed sheep breeds could offer one of the alternatives. This study aimed to analyze the natural tail length variation in the most common German Merino variety, and to identify possible causal alleles for the short tail phenotype segregating within a typical long-tailed breed.ResultsHaplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs resulted in a genome-wide significant mapping at position 37,111,462 bp on sheep chromosome 11 and on chromosome 2 at position 94,538,115 bp (Oar_v4.0). Targeted capture sequencing of these regions in 48 selected sheep and comparative analyses of WGS data of various long and short-tailed sheep breeds as well as wild sheep subspecies identified a SNP and a SINE element as the promising candidates. The PCR genotyping of these candidates revealed complete linkage of both the candidate variants. The SINE element is located in the promotor region of HOXB13, while the SNP was located in the first exon of HOXB13 and predicted to result in a nonsynonymous mutation.ConclusionsOur approach successfully identified HOXB13 as candidate genes and the likely causal variants for tail length segregating within a typical long-tailed Merino breed. This would enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development.

The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in Southeast Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity. We found 1725 polymorphic sites (810 singletons, 853 parsimony-informative sites and 57 indels), 701 unique haplotypes, a haplotype diversity of 0.9995 and a nucleotide diversity of 0.0015. In addition to the dominant T-3 and several rare haplogroups (Q, T-5, T-4, T-2 and T-1), we have identified maternal line in Austrian Murbodner cattle that possess surviving aurochs' mitochondria haplotype P-1 that diverged prior to the Neolithization process. This is convincing evidence for rare female-mediated adaptive introgression of wild aurochs into domesticated cattle in Europe. We revalidated the existing haplogroup classification and provided Bayesian phylogenetic inference with a more precise estimated divergence time than previously available. Occasionally, classification based on partial mitogenomes was not reliable; for example, some individuals with haplogroups P and T-5 were not recognized based on D-loop information. Bayesian skyline plot estimates (median) show that the earliest population growth began before domestication in cattle with haplogroup T-2, followed by Q (-10.0-9.5 kyBP), whereas cattle with T-3 (similar to 7.5 kyBP) and T-1 (similar to 3.0-2.5 kyBP) expanded later. Overall, our results support the existence of interactions between aurochs and cattle during domestication and dispersal of cattle in the past, contribute to the conservation of maternal cattle diversity and enable functional analyses of the surviving aurochs P-1 mitogenome.

Extensive, but short oceanographic measurements were conducted in the spring seasons from 2017 to 2021 with an aim to investigate the middle Adriatic upwelling. The exception was cruise in 2020, when measurements were performed in August. As cruises have been conducted under different meteorological and hydrological conditions, high resolution CTD and shipborne ADCP measurements revealed strong variability in the upwelling strength and occurrence. The strongest upwelling, both in the coastal and open sea area, was recorded in May 2017 and it was related to strong NNW winds that had been blowing for several days before and during the 2017 cruise. Field measurements in June 2018, although conducted under upwelling-favourable winds from NW direction, revealed a rather flat pycnocline due to the low wind intensity, except in the first 5 km close to the coast where the pycnocline was rising onshore. Coastal upwelling was also recorded during the following cruises in June 2019, August 2020 and May 2021, whereas rising of thermocline through Ekman pumping in the open sea was detected only in May 2021. To overcome limitations of the measurements and to shed more light on the upwelling dynamics and its occurrence, realistic and idealised ROMS model simulations are conducted. Realistic simulations are performed by Adriatic scale ROMS model forced by surface momentum, heat and water fluxes calculated using results of operational numerical weather prediction model ALADIN-HR. In addition to atmospheric forcings, river discharges, tides and water mass exchange through the Strait of Otranto are also implemented in the realistic simulations. Reliable results of the realistic baseline experiments, assessed with available in situ and satellite data, allowed us to define sensitivity studies. Sensitivity experiments focus on the influence of both local and remote processes, particularly on the Adriatic river discharges and their parameterization in the ROMS simulations, as well as on the external dynamics and its parameterization at the model open boundary. Strength and character of the middle Adriatic upwelling simulated in the experiments with two available Adriatic river climatologies show no significant distinctions. Moreover, sensitivity of the model results to horizontal grid spacing of atmospheric forcing and oceanographic model grid is investigated. To further elucidate upwelling mechanism, additional idealised simulations with homogeneous upwelling-favourable wind for the eastern Adriatic coast from NW direction are set up and run.

Large animal models for Duchenne muscular dystrophy (DMD) are crucial for preclinical evaluation of novel diagnostic procedures and treatment strategies. Pigs cloned from male cells lackingDMDexon 52 (DMDΔ52) resemble molecular, clinical and pathological hallmarks of DMD, but cannot be propagated by breeding due to death before sexual maturity. Therefore, femaleDMD+/-carriers were generated. A single founder animal had 11 litters with 29DMDY/-, 34DMD+/-as well as 36 male and 29 female wild-type (WT) offspring. Breeding with F1 and F2DMD+/-carriers resulted in additional 114DMDY/-piglets. The majority of them survived for 3-4 months, providing large cohorts for experimental studies. Pathological investigations and proteome studies of skeletal muscles and myocardium confirmed the resemblance of human disease mechanisms. Importantly,DMDY/-pigs reveal progressive fibrosis of myocardium and increased expression of connexin-43, associated with significantly reduced left ventricular fractional shortening and ejection fraction already at age 3 months. Furthermore, behavioral tests provided evidence for impaired cognitive ability ofDMDY/-pigs. Our breeding cohort ofDMDΔ52 pigs and standardized tissue repositories fromDMDY/-pigs,DMD+/-carriers, and WT littermate controls provide important resources for studying DMD disease mechanisms and for testing novel diagnostic procedures and treatment strategies.

Tail docking in young lambs of long-tailed breeds has become a regular practice worldwide, but nowadays animal welfare also plays an increasingly important role in society. Consequently, a genetic solution to breed for a shorter tail is needed, especially in long-tailed breeds like Merino, one of the most important and most numerous sheep breeds worldwide. A serious genetic analysis of the natural diversity in tail length should consider the autocorrelation of tail length and individual body size. This study aimed to compare different morphometric measurements and their suitability as a correction factor for individual body size and to identify an optimal time point for phenotyping of the main and correlated traits. For this purpose, a total of 88 Merinolandschaf lambs, the most common German Merino variety, were measured weekly during their first eight weeks of life. Besides absolute tail length itself, the following morphometric traits where phenotyped: body weight, withers height, back height, length of the body measured with a rule, length of the body measured with a measuring tape, length of the metacarpus, length of the femur and length from the anus to the hock. Additionally, the length of the tail was scored according to the Ovicap scoring scheme, gender and litter were identified and the tail wound in lambs that had to be docked due to injuries was examined. A high correlation (0.854) between initial tail length and the length at weaning confirmed that predictions about the development of tail length from data at birth should be possible. For correcting tail length for individual body size, withers height and body weight in five-week-old lambs proved most suitable. Withers height and body weight were selected for their high coefficient of determination in the linear model, their high correlation with tail length and the good retest reliability. The advantages of phenotyping and genotyping five-week-old lambs are easier handling compared to adult sheep, the ability to detect phenocopies produced by docking in case of tail injuries, a high coefficient of determination in the linear regression model and a good retest reliability at this time point.

Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.

Additional file 6: Figure S3. Graph of Principal Component Analysis (PCA) performed with SNP alleles of goat breeds from the Euro2Step dataset, where admixed and related animals were excluded. Besides first and second principal components (A), the third principal component was also analyzed (B).

Additional file 5: Figure S2. Phylogenetic neighbor net of global goat breeds from the two-step (excluding admixed and related animals) optimized dataset constructed with Nei’s DA distances (scale in the upper left corner) calculated with the 4-SNP blocks.

Additional file 4: Figure S1. Phylogenetic neighbor net of European goat breeds from the two-step (excluding admixed and related animals) optimized dataset constructed with Nei’s DA distances (scale in the upper left corner) calculated with the 4-SNP blocks.

Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.

To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.

In the course of evolution, pecorans (i.e. higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as ‘headgear’, which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats, are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

In a previous study, genome-wide mapping of quantitative trait loci (QTL) for five body composition traits, three bone mineral traits and live weight was performed using whole-body dual-energy X-ray absorptiometry (DXA) data. Since QTL for bone mineral traits were rare, the current study aimed to clarify whether the mapping results were influenced by the analysed body regions. Thus, the same material (551 pigs) and methods as in the whole-body QTL mapping study were used. However, for evaluation of the DXA scans, we manually defined two body regions: (i) from the last ribs to the pelvis (A) and (ii) including the pelvis and the hind limbs (P). Since live weight was not affected by the regional analysis, it was omitted from the QTL mapping design. Our results show an overall high consistency of mapping results especially for body composition traits. Two thirds of the initial whole-body QTL are significant for both A and P. Possible causes for the still low number of bone mineral QTL and the lower consistency found for these traits are discussed. For body composition traits, the data presented here show high genome-wide Pearson correlations between mapping results that are based on DXA scans with the time-saving whole-body standard setting and mapping results for DXA data that were obtained by time-consuming manual definition of the regions of interest. However, our results also suggest that whole-body or regional DXA scans might generally be less suitable for mapping of bone mineral traits in pigs. An analysis of single reference bones could be more useful.

Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A.

Additional file 7: Figure S4. Phylogenetic tree. Neighbor-joining tree based on Nei’s genetic distance DA using multi-allelic SNP blocks. Mongolian yak (YAK) was used as a root. Dotted lines indicate the reduced length of YAK and GIR to improve visibility. Special square marks represent the influence of East-Podolian (grey), Alpine (green) and North-West (olive green) group.

Additional file 2: Table S1. Phenotypic variance explained by all SNPs for all phenotype codings. Table S2. Genome-wide significance thresholds for LRT values of cLDLA for different phenotype codings detected by permutation testing. Table S3. Power to detect a QTL for the four different codings (Table 1) of 232 high-density genotyped animals. Table S4. Gene content of the respective intervals used for the gene set enrichment analysis.

Additional file 6: Figure S3. Tessellated projection. Spatial geographic presentation of the estimated allele sharing distance matrix (DPS) among breeds using multi-allelic SNP-blocks.

Additional file 6: Figure S3. Tessellated projection. Spatial geographic presentation of the estimated allele sharing distance matrix (DPS) among breeds using multi-allelic SNP-blocks.

Additional file 2. Detailed description of the indigenous Greek and Cypriot cattle. Compilation of information on Greek indigenous cattle breeds from diverse sources [16, 33, 71–87]. This includes also information from records in Greek, which were formerly not accessible to the international scientific community due to language barriers.

Additional file 3: Figure S2. Results of the cLDLA for scurs of BC1 phenotype coding with sw40. LRT-values are shown on the y-axis, bovine chromosomes on the x-axis. The red horizontal line marks the genome-wide significance threshold (α = 0.00005) derived from permutation testing.

Additional file 7: Figure S4. Phylogenetic tree. Neighbor-joining tree based on Nei’s genetic distance DA using multi-allelic SNP blocks. Mongolian yak (YAK) was used as a root. Dotted lines indicate the reduced length of YAK and GIR to improve visibility. Special square marks represent the influence of East-Podolian (grey), Alpine (green) and North-West (olive green) group.

Additional file 4: Figure S2. Tessellated projection. Spatial geographic presentation of the estimated effective population number (Ne5, Ne50, Ne2000).

Additional file 3: Figure S1. Tessellated projection. Spatial geographic presentation of the herein estimated diversity parameters (mA, AR, HE, HE(SNP), npA, nspA).

Additional file 8: Figure S5. Admixture analysis. Population structure of the 114 studied breeds/populations presented for each of K inferred ancestral population value, using a genome‐wide set of bi-allelic SNPs. All the analyzed individuals are presented as colored vertical bars, divided at most K segments and with proportional heights, according to their genotype membership. In the depicted plots (K = 2 to K = 26), a different color is presented for each cluster. From left to right within each group the presented breeds are as follows: Minor Asia: ATER, ATBC, ATSR, ATSY, TRG; Greece and Cyprus: CYP, AGT, CRT, NSY, GRB, KAS, KEA, PRG, ROG, SYK, KTR; South East Europe: RHS, MKB, SRB, PRE, RMB, SHB, DGB, DBB, MAB, LKB, SKB, MNB, BHB, HRB; East Podolian: HRI, HRP, UKP; Tyrrhenian: PODO, CINI, MOSI, RSIC, MOSA, SARD, SBRU, CORS, AGER, MARE, CHI, MPIS, CALV, MCH, RMG, GARF, PONT, MODE, CABA, REGG, PMT, BURL; Alpine: PRDO, OVAR, REND, BPUS, PUST, SIC, PIN, TGV, MWF, OBV, BBV, DFV, FGV, VOG, ABO, MON, TAR; France: RDBI, SAL, AUB, LIM, CHR, PAR, BAQ, GAS; Iberian: MNRQ, MALL, NGAN, CANA, MARI, ALEN, BAR, MARO, SYG; North West Europe: BPN, NOR, MAN, BBB, LKF, HF, GNS, JSY, HER, SHR, KRY, DXT, GLW, AAN, HGL, NRC, SERC, FJL, FIAY, FINE, FINW, FINN, YARO.

Additional file 1: Table S1. Sample description, group allocation, RGB (color) code assigned to the pre-defined groups within this paper, breed names, breed code, number of sampled and genotyped individuals (N), number of genotyped and unrelated individuals used to estimate the diversity parameters (Nd), current breeding purposes as well as sporadic or recent past breeding purposes in parenthesis, breed origin, and source of the samples or genotypes used in this study or from previous studies [17, 25, 28, 30, 34, 35, 67–70]. Table S2. Phenotypic, productive and reproductive traits. Description of phenotype, productive and reproductive traits of the 11 Greek and Cypriot analyzed breeds. Table S3. Evolution of bovine population sizes on the islands during the last 60 years. Statistical information regarding the evolution of cattle population on the Greek island based on [62].

Objective To analyze the change in prevalence and incidence of hereditary eye diseases (HED) in dachshunds due to breeding regulations based on biennial examinations performed by the German panel of veterinary ophthalmologists (DOK) from 1998 to 2011. Animals included A total of 12 242 dachshunds examined by the DOK and pedigree data of 318 852 dachshunds provided by the German Dachshund Club (DTK). Procedures The prevalence of congenital cataract (CC), distichiasis (DIST), hereditary cataract (HC), persistent pupillary membranes (PPMs), persistent hyperplastic tunica vasculosa lentis / persistent hyperplastic primary vitreous (PHTVL/PHPV), progressive retinal atrophy (PRA), retinal dysplasia (RD), and findings such as fiberglass-like cataract (FGC) and prominent suture lines (PSLs) was analyzed. The significance (P), confidence interval (CI), odds ratio (OR), relative risk (RR) and inbreeding coefficients (F) were calculated and P < 0.05 was considered significant. The incidence was evaluated based on affected dogs within birth cohorts from 1993 to 2006. Results The prevalent conditions studied were as follows: CC 0.5%, DIST 6.7%, HC 3.9%, PPMs 8.4%, PHTVL/PHPV 0.4%, PRA 1.5%, RD 0.2%, FGC 2.2%, and PSL 1.5%. The incidence of PRA decreased significantly from 6.0% to 0.6% for dogs born from 1993 to 2006, while HC showed a decreasing trend from 8.7% to 3.1%. More males than females were diagnosed with HC and PRA. Dachshunds with HEDs had an F that was not significantly higher than that of healthy dachshunds. Conclusions The decreasing incidence of PRA and HC in dachshunds supports the use of frequent HED examinations in combination with breeding control.

The phylogenetic layout of the genotyped (30 microsatellite) 18 sheep breeds in this study demands and provides the opportunity to evaluate both neutral and adaptive components of genetic diversity in a naturally and artificially selected and subdivided sheep population. Seven Pramenka strains from Bosnia and Herzegovina and Croatia characterized by a very low intensity of artificial selection, preserved the highest neutral genetic variability. Eight central and north-western European breeds under considerable artificial isolation and selection preserved the lowest genetic variability. Only combinations of various phylogenetic parameters offer a reasonable explanation for underlying evolutionary forces working in the investigated island and mainland sheep breeds under variable natural and artificial selection. More than 60% of total genetic, diversity was allocated to virtually unselected Pramenka strains, and an additional 25% to native moderately selected Graue Gehoernte Heidschnucke and intensively selected Ostfriesische Milchschafe. Some economically very important breeds and strains did not contribute to a pool with maximal genetic diversity, while they play an important role in the cultural heritage of respective countries.

Additional file 4. Alignment of the repetitive elements at the beginning and end of the 6-kb candidate segment. Pairwise alignment of the reference sequences (BosTaurus8) of LINE BovB at the beginning of the 6-kb candidate segment and LINE BovB at the end of the segment. This file shows the huge level of similarity between the start and end of the candidate segment as is also obvious in Fig. 2d.

Additional file 6. Alignment of the repetitive elements at the beginning of the 6-kb candidate segment according to bosTaurus6 and bosTaurus8. The pairwise alignment of the reference sequence of the SINE element ART2A (bosTau6) and the LINE element BovB (bosTau8) at the beginning of the 6-kb candidate segment shows that ART2A is part of BovB.

Additional file 2: Table S2 The joint dataset used in the study. Description: This table provides information on the joint dataset, which includes the Russian sheep breeds and sheep breeds from across the world. The breeds are grouped according to their ancestral geographic origin (Russia, the British Isles, Northern Europe, Central Europe, Southwestern Europe, Asia, Southwestern Asia, Africa and the Americas). The table presents the information concerning the breedsâ abbreviation and color representation for the geographical group of breeds, the sample size, country (region) of sample collection, and the references where the genotyping data were previously published.

Additional file 5. Nanopore sequencing results. (a) Nanopore reads mapped (minimap2) to the belted candidate region are shown. The shaded parts of the reads highlight unmapped portions of the read that were mapped as a secondary alignment in a separate read. These secondary alignments are highlighted by blue borders. (b) Split-alignment of breakpoint-spanning read visualized by Ribbon [52]. The highlighted read (bold blue line) is shown as a zoom in the lower panel, showing that the beginning of the read is found at the end of the repeated region and the end is found at the beginning, thus illustrating the concatenation of the repeat units found in belted cattle. (c) Exact breakpoints were identified by inspection of the partially mapped reads. The right breakpoint at 118,614,132Â bp shows that the unmapped portion of the split-aligned reads starts with a sequence that is located at 118,608,362Â bp, which thus defines the left breakpoint.

Additional file 7. Gene interaction network. This figure illustrates the interactions between KIT (causal for the belt in pigs), ADAMTS20 (causal for the belt in mice) and TWIST2 (most likely causal for the belt in cattle) in mice. Interaction line colors are as follows: orange: predicted functional relationship, red: physical interactions, purple: co-expression; grey: phenotype (based on mouse genome informatics) and blue: participation in the same reaction within a pathway.

Additional file 3. TLA results. The genomic region chr3:118,590,000â 118,632,000 (bosTau8) is displayed. The arrows indicate the position of the primer sets used for TLA. For the belted animal (GLW54-2), an increased copy number (3 to 4.5 times) was detected in the region indicated by the red rectangle. The y-axis is limited to max. 1000X.

Additional file 3: Table S3 Genetic differentiation of 25 Russian sheep breeds based on Weir and Cockerhamâ s fixation index (FST). This table provides information about FST values between the Russian breeds under study. The breedsâ groups of the same wool type are framed in blue (for coarse wool breeds), red (for semi-fine wool breeds) and green (for fine wool breeds). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2).

Additional file 1: Table S1 Short description of the Russian sheep breeds under study.

In this study, we present the first complete mitochondrial genomes of two species of the genus Ovis – snow sheep (Ovis nivicola) and thinhorn sheep (Ovis dalli). The mitochondrial genomes h...

Quantitative trait loci (QTL) mapping projects have been implemented mainly in the Holstein dairy cattle breed for several traits. The aim of this study is to map QTL for milk yield (MY) and milk protein percent (PP) in the Brown Swiss cattle populations of Austria, Germany, and Italy, considered in this study as a single population. A selective DNA pooling approach using milk samples was applied to map QTL in 10 paternal half-sib daughter families with offspring spanning from 1,000 to 3,600 individuals per family. Three families were sampled in Germany, 3 in Italy, 1 in Austria and 3 jointly in Austria and Italy. The pools comprised the 200 highest and 200 lowest performing daughters, ranked by dam-corrected estimated breeding value for each sire-trait combination. For each tail, 2 independent pools, each of 100 randomly chosen daughters, were constructed. Sire marker allele frequencies were obtained by densitometry and shadow correction analyses of 172 genome-wide allocated autosomal markers. Particular emphasis was placed on Bos taurus chromosomes 3, 6, 14, and 20. Marker association for MY and PP with a 10% false discovery rate resulted in nominal P-values of 0.071 and 0.073 for MY and PP, respectively. Sire marker association tested at a 20% false discovery rate (within significant markers) yielded nominal P-values of 0.031 and 0.036 for MY and PP, respectively. There were a total of 36 significant markers for MY, 33 for PP, and 24 for both traits; 75 markers were not significant for any of the traits. Of the 43 QTL regions found in the present study, 10 affected PP only, 8 affected MY only, and 25 affected MY and PP. Remarkably, all 8 QTL regions that affected only MY in the Brown Swiss, also affected MY in research reported in 3 Web-based QTL maps used for comparison with the findings of this study (http://www.vetsci.usyd.edu.au/reprogen/QTL_Map/; http://www.animalgenome.org/QTLdb/cattle.html; http://bovineqtl.tamu.edu/). Similarly, all 10 QTL regions in the Brown Swiss that affected PP only, affected only PP in the databases. Thus, many QTL appear to be common to Brown Swiss and other breeds in the databases (mainly Holstein), and an appreciable fraction of QTL appears to affect MY or PP primarily or exclusively, with little or no effect on the other trait. Although QTL information available today in the Brown Swiss population can be utilized only in a within family marker-assisted selection approach, knowledge of QTL segregating in the whole population should boost gene identification and ultimately the implementation and efficiency of an individual genomic program.

Additional file 1: Fig. S1. Pedigree of the albino calves. As the red highlighted paths show, both albinos and all carriers of the SNPs g.39829806G>A and g.39864148C>T can be traced back to a single natural service sire (B1). Symbols are as follows: squares = males, circles = females, filled symbols = albinos (homozygous for both SNPs), symbols with dot inside = heterozygous individuals, symbols with question mark inside = genotype unknown, crossed out symbols = no material available. For bull S2, 50K genotype data was available from previous studies; however, no material for targeted genotyping was available.

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1, 828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome‐ assisted cross‐border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.

Summary Bovine arachnomelia is an inherited congenital disorder with malformation mainly of the limbs, the vertebral column and the skull, following a monogenic autosomal recessive heredity. Despite almost identical pathological findings, arachnomelia has previously been mapped to bovine chromosome 23 and 5 in Fleckvieh and Braunvieh respectively. Therefore, this disorder may be an example of locus heterogeneity in cattle. This study aimed to refine the candidate region to allow positional cloning and sequence analyses of candidate genes in Fleckvieh cattle. For that purpose, a case-control association mapping design was set up with a case group of 16 pre-selected affected individuals and a control group of 50 unrelated animals. The subset of affected animals was selected from a total of 129 pathologically confirmed cases due to the occurrence of recombination(s) within a 14.5 cM candidate interval previously mapped to chromosome 23. Six linked microsatellites currently used for indirect gene testing in Fleckvieh were analysed for this purpose. In all selected cases, a genome-wide scan using 44 473 informative SNPs revealed shared segments of homozygosity at 15 adjacent SNPs on chromosome 23. Additional haplotype analysis of 37 carrier bulls confirmed the localization of the arachnomelia locus to a region of 927 kb (13.622–14.549 Mb) containing molybdenum cofactor biosynthesis protein 1 gene, the most likely candidate gene for arachnomelia in Fleckvieh. The number of recombinant haplotypes observed in cases was more than doubled compared with the number of expected recombinations. This remarkably increased mapping resolution and thus illustrates the benefit of pre-selection in association studies.