Effects of a feeding strategy to increase intramuscular fat content of pork under the conditions of organic farming

In an ongoing study, the effect of the implementation of a specific feeding strategy using a high portion of home-grown grain legumes on the intramuscular fat (IMF) content of pork, is assessed under different conditions on organic farms in Germany and Austria. Preliminary results indicate that variation in the IMF content seems to be higher between farms than between treatments within each farm

Untersuchung zukunftsorientierter Fütterungskonzepte für laktierende Zuchtsauen in der Biologischen Landwirtschaft

Im vorliegenden Projekt wurden mittels partizipativen Ansatzes Lösungsmöglichkeiten für die Problematik der „100% Biofütterung“ von laktierenden Zuchtsauen entwickelt. Dazu wurden 2 Rationen im Exaktversuch über 2 Jahre getestet: eine Ration wies einen niedrigen Proteingehalt und eine unausgewogene Aminosäurenzusammensetzung auf. Die zweite Ration wurde diesbezüglich weitgehend optimiert. Etwa zu Mitte des Exaktversuchs wurden die gewonnenen Erkenntnisse auf 4 Praxisbetrieben umgesetzt. Aus den nach diesen Untersuchungen vorliegenden Daten lassen sich für Beratung und Praxis folgende Erkenntnisse ableiten: Sauen können Minderversorgungen durch Rationen, die unter den empfohlenen Gehalten für die Protein- und insbesondere die Aminosäurenausstattung liegen, weitgehend kompensieren. Dies setzt allerdings eine hohe Futteraufnahme voraus. Eine negative Beeinflussung der Fruchtbarkeit der Sauen und der Ferkelverluste in der Säugezeit durch eine Unterversorgung mit essentiellen Aminosäuren während der Laktation ist unter Verhältnissen, wie sie in den vorliegenden Versuchen bestanden, nicht zu erwarten. Die tendenzielle Verschlechterung der Fruchtbarkeit in der unbalancierten Gruppe des Exaktversuchs lässt aber doch vermuten, dass hier die Untergrenze für eine gerade noch akzeptable Versorgungssituation erreicht wurde. Für Beratung und Praxis lässt sich daraus die Empfehlung ableiten, dass Betriebe, die ihre laktierenden Sauen in Hinkunft (nach Auslaufen der Übergangsfrist laut EG-Verordnung Ende 2011) bewusst mit diesen knapp formulierten Rationen füttern wollen, unbedingt ein professionelles Fütterungsmanagement sicherstellen müssen. Dazu gehören insbesondere regelmäßige Futtermittelanalysen, da die Schwankungen des Nährstoffgehalts in den Futtermitteln relativ groß sein können, wie auch in der vorliegenden Untersuchung dokumentiert wurde. Die bei niedriger bzw. unbalancierter Aminosäurenversorgung der Sauen nicht auszuschließende verminderte Lebendmasse-Entwicklung der Ferkel ist aus der Sicht der Praxis von großer Bedeutung. Dies ist deshalb besonders relevant, da die Formulierung geeigneter Saugferkel-Beifutter und Ferkelaufzuchtfutter unter den Bedingungen einer 100 % Bio-Fütterung von den Betriebsleitern als besondere Herausforderung angesehen wird

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (ρ) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination

Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping

A Critical Analysis of Atoh7 (Math5) mRNA Splicing in the Developing Mouse Retina

The Math5 (Atoh7) gene is transiently expressed during retinogenesis by progenitors exiting mitosis, and is essential for ganglion cell (RGC) development. Math5 contains a single exon, and its 1.7 kb mRNA encodes a 149-aa polypeptide. Mouse Math5 mutants have essentially no RGCs or optic nerves. Given the importance of this gene in retinal development, we thoroughly investigated the possibility of Math5 mRNA splicing by Northern blot, 3′RACE, RNase protection assays, and RT-PCR, using RNAs extracted from embryonic eyes and adult cerebellum, or transcribed in vitro from cDNA clones. Because Math5 mRNA contains an elevated G+C content, we used graded concentrations of betaine, an isostabilizing agent that disrupts secondary structure. Although ∼10% of cerebellar Math5 RNAs are spliced, truncating the polypeptide, our results show few, if any, spliced Math5 transcripts exist in the developing retina (<1%). Rare deleted cDNAs do arise via RT-mediated RNA template switching in vitro, and are selectively amplified during PCR. These data differ starkly from a recent study (Kanadia and Cepko 2010), which concluded that the vast majority of Math5 and other bHLH transcripts are spliced to generate noncoding RNAs. Our findings clarify the architecture of the Math5 gene and its mechanism of action. These results have implications for all members of the bHLH gene family, for any gene that is alternatively spliced, and for the interpretation of all RT-PCR experiments

The Beaker phenomenon and the genomic transformation of northwest Europe

From around 2750 to 2500 bc, Bell Beaker pottery became widespread across western and central Europe, before it disappeared between 2200 and 1800 bc. The forces that propelled its expansion are a matter of long-standing debate, and there is support for both cultural diffusion and migration having a role in this process. Here we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries

Population genomics of speciation and admixture

The application of population genomics to the understanding of speciation has led to the emerging field of speciation genomics. This has brought new insight into how divergence builds up within the genome during speciation and is also revealing the extent to which species can continue to exchange genetic material despite reproductive barriers. It is also providing powerful new approaches for linking genotype to phenotype in admixed populations. In this chapter, we give an overview of some of the methods that have been used and some of the novel insights gained. We also outline some of the pitfalls of the most commonly used methods and possible problems with interpretation of the results

Random orthogonal matrix simulation with exact means, covariances, and multivariate skewness

© 2017 Elsevier B.V. We develop a simulation algorithm that generates multivariate samples with exact means, covariances, and multivariate skewness. If required for financial applications, absence of arbitrage can be ensured. Potential applications include the simulation of risk factors for the risk management of financial institutions. We use the Kollo measure of multivariate skewness, which is more informative for these applications than the Mardia skewness previously used in this context