A Genome-Wide Association Study Reveals Loci Influencing Height and Other Conformation Traits in Horses

The molecular analysis of genes influencing human height has been notoriously difficult. Genome-wide association studies (GWAS) for height in humans based on tens of thousands to hundreds of thousands of samples so far revealed ∼200 loci for human height explaining only 20% of the heritability. In domestic animals isolated populations with a greatly reduced genetic heterogeneity facilitate a more efficient analysis of complex traits. We performed a genome-wide association study on 1,077 Franches-Montagnes (FM) horses using ∼40,000 SNPs. Our study revealed two QTL for height at withers on chromosomes 3 and 9. The association signal on chromosome 3 is close to the LCORL/NCAPG genes. The association signal on chromosome 9 is close to the ZFAT gene. Both loci have already been shown to influence height in humans. Interestingly, there are very large intergenic regions at the association signals. The two detected QTL together explain ∼18.2% of the heritable variation of height in horses. However, another large fraction of the variance for height in horses results from ECA 1 (11.0%), although the association analysis did not reveal significantly associated SNPs on this chromosome. The QTL region on ECA 3 associated with height at withers was also significantly associated with wither height, conformation of legs, ventral border of mandible, correctness of gaits, and expression of the head. The region on ECA 9 associated with height at withers was also associated with wither height, length of croup and length of back. In addition to these two QTL regions on ECA 3 and ECA 9 we detected another QTL on ECA 6 for correctness of gaits. Our study highlights the value of domestic animal populations for the genetic analysis of complex traits.

Late Quaternary history of the Vakinankaratra volcanic field (central Madagascar): insights from luminescence dating of phreatomagmatic eruption deposits

The Quaternary Vakinankaratra volcanic field in the central Madagascar highlands consists of scoria cones, lava flows, tuff rings, and maars. These volcanic landforms are the result of processes triggered by intracontinental rifting and overlie Precambrian basement or Neogene volcanic rocks. Infrared-stimulated luminescence (IRSL) dating was applied to 13 samples taken from phreatomagmatic eruption deposits in the Antsirabe–Betafo region with the aim of constraining the chronology of the volcanic activity. Establishing such a chronology is important for evaluating volcanic hazards in this densely populated area. Stratigraphic correlations of eruption deposits and IRSL ages suggest at least five phreatomagmatic eruption events in Late Pleistocene times. In the Lake Andraikiba region, two such eruption layers can be clearly distinguished. The older one yields ages between 109 ± 15 and 90 ± 11 ka and is possibly related to an eruption at the Amboniloha volcanic complex to the north. The younger one gives ages between 58 ± 4 and 47 ± 7 ka and is clearly related to the phreatomagmatic eruption that formed Lake Andraikiba. IRSL ages of a similar eruption deposit directly overlying basement laterite in the vicinity of the Fizinana and Ampasamihaiky volcanic complexes yield coherent ages of 68 ± 7 and 65 ± 8 ka. These ages provide the upper age limit for the subsequently developed Iavoko, Antsifotra, and Fizinana scoria cones and their associated lava flows. Two phreatomagmatic deposits, identified near Lake Tritrivakely, yield the youngest IRSL ages in the region, with respective ages of 32 ± 3 and 19 ± 2 ka. The reported K-feldspar IRSL ages are the first recorded numerical ages of phreatomagmatic eruption deposits in Madagascar, and our results confirm the huge potential of this dating approach for reconstructing the volcanic activity of Late Pleistocene to Holocene volcanic provinces.

Quaternary uplift rates of the Central Anatolian Plateau, Turkey: insights from cosmogenic isochron-burial nuclide dating of the Kızılırmak River terraces

The Central Anatolian Plateau (CAP) in Turkey is a relatively small plateau (300 × 400 km) with moderate average elevations of ∼1 km situated between the Pontide and Tauride orogenic mountain belts. Kızılırmak, which is the longest river (1355 km) within the borders of Turkey, flows within the CAP and slowly incises into lacustrine and volcaniclastic units before finally reaching the Black Sea. We dated the Cappadocia section of the Kızılırmak terraces in the CAP by using cosmogenic burial and isochron-burial dating methods with 10Be and 26Al as their absolute dating can provide insight into long-term incision rates, uplift and climatic changes. Terraces at 13, 20, 75 and 100 m above the current river indicate an average incision rate of 0.051 ± 0.01 mm/yr (51 ± 1 m/Ma) since ∼1.9 Ma. Using the base of a basalt fill above the modern course of the Kızılırmak, we also calculated 0.05–0.06 mm/yr mean incision and hence rock uplift rate for the last 2 Ma. Although this rate might be underestimated due to normal faulting along the valley sides, it perfectly matches our results obtained from the Kızılırmak terraces. Although up to 5–10 times slower, the Quaternary uplift of the CAP is closely related to the uplift of the northern and southern plateau margins respectively.

Late Quaternary history of North Eurasian Norway spruce ( Picea abies ) and Siberian spruce ( Picea obovata ) inferred from macrofossils, pollen and cytoplasmic DNA variation

Aim We used combined palaeobotanical and genetic data to assess whether Norway spruce (Picea abies) and Siberian spruce (Picea obovata), two major components of the Eurasian boreal forests, occupied separate glacial refugia, and to test previous hypotheses on their distinction, geographical delimitation and introgression. Location The range of Norway spruce in northern Europe and Siberian spruce in northern Asia. Methods Pollen data and recently compiled macrofossil records were summarized for the Last Glacial Maximum (LGM), late glacial and Holocene. Genetic variation was assessed in 50 populations using one maternally (mitochondrial nad1) and one paternally (chloroplast trnT–trnL) inherited marker and analysed using spatial analyses of molecular variance (SAMOVA). Results Macrofossils showed that spruce was present in both northern Europe and Siberia at the LGM. Congruent macrofossil and pollen data from the late glacial suggested widespread expansions of spruce in the East European Plain, West Siberian Plain, southern Siberian mountains and the Baikal region. Colonization was largely completed during the early Holocene, except in the formerly glaciated area of northern Europe. Both DNA markers distinguished two highly differentiated groups that correspond to Norway spruce and Siberian spruce and coincide spatially with separate LGM spruce occurrences. The division of the mtDNA variation was geographically well defined and occurred to the east of the Ural Mountains along the Ob River, whereas the cpDNA variation showed widespread admixture. Genetic diversity of both DNA markers was higher in western than in eastern populations. Main conclusions North Eurasian Norway spruce and Siberian spruce are genetically distinct and occupied separate LGM refugia, Norway spruce on the East European Plain and Siberian spruce in southern Siberia, where they were already widespread during the late glacial. They came into contact in the basin of the Ob River and probably hybridized. The lower genetic diversity in the eastern populations may indicate that Siberian spruce suffered more from past climatic fluctuations than Norway spruce.

Gas-phase fragmentation and conformation of the sugar-modified antisense oligonucleotide tcDNA

Tricyclo-DNA (tcDNA) is a sugar- and backbone-modified analogue of DNA that is currently tested as antisense oligonucleotide for the treatment of Duchenne muscular dystrophy. The name tricyclo-DNA is derived from the modified sugar-moiety: the deoxyribose is extended to a three-membered ring system. This modification is designed to limit the flexibility of the structure, thus giving rise to entropically stabilized hybrid duplexes formed between tcDNA and complementary DNA or RNA oligonucleotides. While the structural modifications increase the biostability of the therapeutic agent, they also render the oligonucleotide inaccessible to enzyme-based sequencing methods. Tandem mass spectrometry constitutes an alternative sequencing technique for partially and fully modified oligonucleotides. For reliable sequencing, the fragmentation mechanism of the structure in question must be understood. Therefore, the presented work evaluates the effect of the modified sugar-moiety on the gas-phase dissociation of single stranded tcDNA. Moreover, our experiments reflect the exceptional gas-phase stability of hybrid duplexes that is most noticeable in the formation of truncated duplex ions upon collision-induced dissociation. The stability of the duplex arises from the modified sugar-moiety, as the rigid structure of the tcDNA single strand minimizes the change of the entropy for the annealing. Moreover, the tc-modification gives rise to extended conformations of the nucleic acids in the gas-phase, which was studied by ion mobility spectrometry-mass spectrometry.

Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed

To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation traits and one performance trait. Therefore, our results suggest that the application of sequence-derived genotypes increases the power to identify novel QTL which were not identified previously based on 50K SNP chip data.

Towards mapping the late Quaternary vegetation change of Europe

The number of well-dated pollen diagrams in Europe has increased considerably over the last 30 years and many of them have been submitted to the European Pollen Database (EPD). This allows for the construction of increasingly precise maps of Holocene vegetation change across the continent. Chronological information in the EPD has been expressed in uncalibrated radiocarbon years, and most chronologies to date are based on this time scale. Here we present new chronologies for most of the datasets stored in the EPD based on calibrated radiocarbon years. Age information associated with pollen diagrams is often derived from the pollen stratigraphy itself or from other sedimentological information. We reviewed these chronological tie points and assigned uncertainties to them. The steps taken to generate the new chronologies are described and the rationale for a new classification system for age uncertainties is introduced. The resulting chronologies are fit for most continental-scale questions. They may not provide the best age model for particular sites, but may be viewed as general purpose chronologies. Taxonomic particularities of the data stored in the EPD are explained. An example is given of how the database can be queried to select samples with appropriate age control as well as the suitable taxonomic level to answer a specific research question.

Mineral-magnetic record of Late Quaternary climatic changes in a high Alpine lake

The magnetic properties of a sediment core from a high altitude lake in the Swiss Alps were compared with palynological and geochemical data to link climatic and mineral magnetic variations. According to pollen data, the sediments extend from the present to the Younger Dryas, i.e., they cover more than 10,000 years of environmental change in the Alps. The major change in magnetic properties corresponds to the climatic warming of the early Holocene. High-coercivity magnetic minerals that characterize the Late Glacial period almost disappeared during the Holocene and the concentration of ferrimagnetic minerals increased sharply. The contribution of superparamagnetic grains also decreased in the Holocene sediments. Similar variations in {SP} content and coercivity, of smaller magnitude, are found in the Holocene and are interpreted to represent minor climatic variations. Comparison with the historical record of the last 1000 years confirms this interpretation. The magnetic mineralogy, the superparamagnetic contents, and the {IRM} intensity in the coarse-grained, Late Glacial sediments are similar to those measured in the catchment bedrock. This indicates a detrital origin. The different properties and the higher concentration of magnetic minerals in the Holocene sediments are due to authigenic phases. Magnetic properties provide a high resolution record of climatic change. They are sensitive even to small variations that are not recorded in the pollen or {LOI} data. Magnetic parameters show fine-scale variation and constitute a valuable supplement to conventional climatic indicators.