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Genome-wide association study for tail alterations in German Holstein dairy cows

Kremer-Rücker, P.; Schubert, K.; Meier, S. (2022)

Proceedings of the 31. World Buiatric Congress, September 4th-8th, Madrid, 2022, GB-P02 (2), S. 89-90.

 

Objectives
Tail injuries and pathological alterations have been reported in many species. In cattle, they were investigated
mainly in fattening bulls and feedlot cattle. In dairy cows high prevalences for different tail alterations were
found. However, aetiology and pathogenesis of this health trait are still unclear and need further investigation.
Out of 4443 phenotypes of different tail alterations we assorted seven groups common in dairy cows: 1. very
tip of the tail , 2. ring-like, 3. scurf, 4. swelling, 5. thinning, 6. axis anomaly, and 7. verruca-like mass. The
objective of this study was to identify genomic regions that may influence the occurrence of different tail
alterations in dairy cows, which could be useful for a potential implementation of a genomic selection tool for
more robust and healthy cows in the future.
Material and methods
Occurrence data of each tail alteration group were collected monthly from 167 German Holstein cows. The
cows originated from a German 1300 cows dairy herd. Data collection was performed from May to December
2021, since calving of all included cows was from April to May. The cows were in their first to seventh lactation.
The phenotype was encoded binary, where 0 means the absence and 1 the presence of a tail alteration group
within the whole timespan.
For 118 cows, Illumina EuroG10k genotypes were available and imputed up to 45k (FImpute). The remaining
cows were genotyped with the Illumina EuroG MD (V1, V1.1, V2) with 45613 SNPs. After quality check (only
segregating SNPs, at least two groups with a minimum of 10 observations, no duplicated markers, a minor
allele frequency of 1%, and within Hardy-Weinberg-Equilibrium P>0.01), 41062 SNPs remained.
A genome-wide association study was performed using the software GEMMA and the univariate linear mixed
model. Each tail alteration group was treated as a separate phenotype. A standardized relatedness matrix was
included in the model and calculated on SNP chip data to consider the population stratification, since many
half-sib groups were present. The lactation (1st, 2nd, ≥3rd) was included as covariate. The genotype matrix was
included in the model and the effect size per marker was estimated and tested for significance using a Wald
test.
For positional candidate gene analysis, genomic regions around top markers (P < 0.0001) of 325kbp wereconsidered,since the linkage disequilibrium decay analysis gave a mean r² of >0.61 within this distance. The
marker positions are given on the ARS-UCD 1.2 Bos taurus genome assembly.
Results
In total 51 top markers resulted for all seven tail alteration groups, whereof one marker reached Bonferronicorrected
genome-wide significance threshold for tail alteration group “thinning” (BTA1: rs42577957, −log10(P)
= 9.22). The markers were found on 18 different chromosomes. Close to these markers, 65 positional
candidate genes reside. Among them CCDC122 (rs42421906, −log10(P) = 5.46), which was associated with
the phenotype “scurf” in our analysis. CCDC122 is one of the top differentially expressed genes in liver
metabolism in pigs showing swine inflammation and necrosis syndrome (Ringseis et al., 2021). This syndrome
results in severe tail alterations in pigs as well.
Conclusions
This first genetic investigation of tail alterations in dairy cows showed the potential of finding genetic markers
for this novel health trait. Nonetheless, it is recommended to increase the sample size of cows and to further
investigate the cause of tail alterations, to substantiate the reported phenotypes.

Literature

Ringseis, R., Gessner, D. K., Loewenstein, F., Kuehling, J., Becker, S., Willems, H., et al. (2021). Swine inflammation and necrosis syndrome is associated with plasma metabolites and liver transcriptome in affected piglets. Animals 11, 1–14. doi:10.3390/ani11030772

Sargolzaei, M., Chesnais, J. P., and Schenkel, F. S. (2014). A new approach for efficient genotype imputation using information from relatives. BMC Genomics 15. doi:10.1186/1471-2164-15-478

Zhou, X., and Stephens, M. (2014). Efficient Algorithms for Multivariate Linear Mixed Models in Genome-wide Association Studies. Nat Methods 11, 407–409. doi:10.1038/nmeth.2848

Acknowledgement
We thank the MASTERRIND GmbH, Verden, Germany, for providing the genotypes from the investigated
cows.
Funding
Part of the data results from the project TINCa Dairy, which is funded by the Tönnies Forschung, Rheda,
Germany.

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Dynamically Self-Adjusting Gaussian Processes for Data Stream Modelling

Hüwel, J.; Haselbeck, F.; Grimm, D.; Beecks, C. (2022)

KI 2021: Advances in Artificial Intelligence 2022.
DOI: 10.1007/978-3-031-15791-2_10


Open Access
 

One of the major challenges in time series analysis are changing data distributions, especially when processing data streams. To ensure an up-to-date model delivering useful predictions at all times, model reconfigurations are required to adapt to such evolving streams. For Gaussian processes, this might require the adaptation of the internal kernel expression. In this paper, we present dynamically self-adjusting Gaussian processes by introducing Event Triggered Kernel Adjustments in Gaussian process modelling (ETKA), a novel data stream modelling algorithm that can handle evolving and changing data distributions. To this end, we enhance the recently introduced Adjusting Kernel Search with a novel online change point detection method. Our experiments on simulated data with varying change point patterns suggest a broad applicability of ETKA. On real-world data, ETKA outperforms comparison partners that differ regarding the model adjustment and its refitting trigger in nine respective ten out of 14 cases. These results confirm ETKA's ability to enable a more accurate and, in some settings, also more efficient data stream processing via Gaussian processes.


Code availability: https://github.com/JanHuewel/ETKA

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Für die Streuobstwiesen

Honecker, R.; Wölfl, S.; Gruber, P. (2022)

LandInForm-Magazin für Ländliche Räume (3.22), S. 40-41.

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Hochwasser- und Naturschutz: Der Polder Holter Hammrich in Niedersachsen

König, C.; Moning, C.; Weiß, F. (2022)

Der Falke 2022 (9), S. 57-61.

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Wärmeströme im Gewächshaus optimieren

Born, S.; Haas, H.; Stiele, V.; Hauser, B.; Hannus, T. (2022)

DEGA Gartenbau 2022 (09), S. 28-30.

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Herrscher der Lüfte: Raubvögel vor dem Aussterben?

Medienbeitrag, .; Zahner, V. (2022)

Planet Wissen (eine Sendung des ARD alpha), ausgestrahlt am 31.08.2022, Dauer: 59 Min., Verfügbar bis 31.08.2027.

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TerZ live - Ergebnisse aus der substratanalytischen Begleitung

Fritzsche, R. (2022)


An approximation algorithm for a general class of multi-parametric optimization problems

Helfrich, S.; Herzel, A.; Ruzika, S.; Thielen, C. (2022)

Journal of Combinatorial Optimization 44 (3).
DOI: 10.1007/s10878-022-00902-w


Open Access
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Robin Who? Bird Species Knowledge of German Adults

Enzensberger, P.; Schmid, B.; Gerl, T.; Zahner, V. (2022)

Animals 12, 2213 (17), S. 1-14.
DOI: 10.3390/ani12172213


Open Access
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Recent extreme drought events in the Amazon rainforest: assessment of different precipitation and evapotranspiration datasets and drought indicators

Papastefanou, P.; Zang, C.; Angelov, Z.; Anderson de Castro, A.; Jimenez, J....

Biogeosciences 19, S. 3843–3861.
DOI: 10.5194/bg-19-3843-2022


Open Access
 

Over the last decades, the Amazon rainforest has been hit by multiple severe drought events. Here, we assess the severity and spatial extent of the extreme drought years 2005, 2010 and 2015/16 in the Amazon region and their impacts on the regional carbon cycle. As an indicator of drought stress in the Amazon rainforest, we use the widely applied maximum cumulative water deficit (MCWD). Evaluating nine state-of-the-art precipitation datasets for the Amazon region, we find that the spatial extent of the drought in 2005 ranges from 2.2 to 3.0 (mean =2.7) ×106 km2 (37 %–51 % of the Amazon basin, mean =45 %), where MCWD indicates at least moderate drought conditions (relative MCWD anomaly ). In 2010, the affected area was about 16 % larger, ranging from 3.0 up to 4.4 (mean =3.6) ×106 km2 (51 %–74 %, mean =61 %). In 2016, the mean area affected by drought stress was between 2005 and 2010 (mean  km2; 55 % of the Amazon basin), but the general disagreement between datasets was larger, ranging from 2.4 up to 4.1×106 km2 (40 %–69 %). In addition, we compare differences and similarities among datasets using the self-calibrating Palmer Drought Severity Index (scPDSI) and a dry-season rainfall anomaly index (RAI). We find that scPDSI shows a stronger and RAI a much weaker drought impact in terms of extent and severity for the year 2016 compared to MCWD. We further investigate the impact of varying evapotranspiration on the drought indicators using two state-of-the-art evapotranspiration datasets. Generally, the variability in drought stress is most dependent on the drought indicator (60 %), followed by the choice of the precipitation dataset (20 %) and the evapotranspiration dataset (20 %). Using a fixed, constant evapotranspiration rate instead of variable evapotranspiration can lead to an overestimation of drought stress in the parts of Amazon basin that have a more pronounced dry season (for example in 2010). We highlight that even for well-known drought events the spatial extent and intensity can strongly depend upon the drought indicator and the data sources it is calculated with. Using only one data source and drought indicator has the potential danger of under- or overestimating drought stress in regions with high measurement uncertainty, such as the Amazon basin.

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New approaches to assess stability of wood fiber

Beuth, E.; Schreiner, M.; Lohr, D.; Meinken, E. (2022)

31. International Horticultural Congress (IHC2022); International symposium on innovative technologies and production strategies for sustainable controlled environment horticulture.

 

In the wake of the decarbonisation of the entire economy, the use of peat in horticulture is under increasing pressure. In Germany, wood fibre is by far the most important substitute in growing media for professional horticulture. However, due to readily microbial degradability and a wide C:N ratio, nitrogen immobilization is a major problem of wood fibre products and considerably limits their use. Concurrently, stability of wood fibre is assessed by incubation experiments in which the change of mineral nitrogen is measured. However, these experiments have three shortcomings: First, they are quite labour and time-consuming as incubation period is up to 21 days. Second, if long-term fertilizers – especially urea-aldehyde condensation products – are applied by the manufacturer, the experiments only provide information about the stability of the N balance, but not about the stability of the material itself. Third, comparability and repeatability of the incubation experiments are rather poor. To overcome these shortcomings new approaches to evaluate stability of wood fibre were tested.

The setup of the first approach is similar to the currently used incubation experiments. However, the incubation period is only five days and additionally to change in mineral nitrogen from the beginning to the end of the experiment, carbon mineralization is analysed continuously by Oxitop®-C measuring heads. The second approach focusses on the characterization of readily decomposable nitrogen and carbon fractions in the wood fibre. On the one hand, hydrolysable nitrogen and carbon is measured and on the other hand, a stepwise thermal fractionation of carbon under pyrolytic conditions is done.

The results of the two approaches are compared to nitrogen immobilization measured in common incubation experiments and further validated by nitrogen balances deduced form short-term pot experiments with Chinese cabbage.

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Development of an adaptive and sensor-based water management for extensive green roofs

Lohr, D.; Schmitz, H.; Meinken, E. (2022)

31. International Horticultural Congress (IHC2022); II International symposium on greener cities: improving ecosystem services in a climate-changing world (greencities2022).

 

Green roofs play a crucial role in climate change mitigation strategies. On the one hand, they should reduce the risk of urban floods after heavy rainfalls. On the other hand, they should cool the city by evapotranspiration and avoid the formation of urban heat islands. However, concurrently most green roofs in Germany are extensive ones. They are designed as dry sites, with shallow and well-drained vegetation layers, no additional irrigation and greened with highly drought-adapted plants - mainly sedum. Indeed, during the last years a new kind of extensive green roofs – still with shallow vegetation layers – but equipped with sub-surface irrigation and voluminous retention elements as temporary water storage beneath the vegetation layer as well as greened with plants with high transpiration, were developed. But also these new kind of green roofs are facing a conflict of objectives between storm water retention and cooling performance.

To solve this conflict of objectives an adaptive and sensor based water management system was developed. It consists of two main components: Irrigation management of the plants and management of storm water runoff, especially the control of the retention element. For the irrigation management a decision matrix was developed which adapts the irrigation strategy, depending if cooling performance or water retention has higher priority. Prioritization is based on thermal discomfort and rain forecast. The decision matrix uses environmental data, data of the weather forecast and information about water resources (e.g. grey water, water supply in the retention element). For management of storm water, run-off is actively controlled and the vegetation layer used as temporary water storage. In combination with a retention element, this can quadruple water retention capacity of green roofs. The amount of water stored in the green roof system – especially the retention element – is mainly controlled on basis of real-time, radar-based precipitation data.

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Effect of co-composted biochar on nitrogen availability to spinach

Görl, J.; Lohr, D.; Meinken, E. (2022)

31. International Horticultural Congress (IHC2022); International symposium on plant nutrition, fertilization, soil management .

 

Co-composted biochar is suspected to be an effective sorbent for nitrate and thus might reduce nitrate leaching from agricultural soils. However, the underlying mechanism is unknown now and the effect on nitrogen availability is under discussion. In the current study, a pot trial with spinach was conducted to evaluate the influence of two co-composted biochars on nitrogen availability. Two wood-based biochars were co-composted with grass clippings and woody scrap material from landscaping activities. Additionally, a compost without biochar was prepared. Composts were mixed to an arable soil at rates of 30, 60 and 120 t ha-1 and nitrate was applied on basis of 100 kg N per hectare. Afterwards, mixtures were filled in balcony boxes, moisturized and placed in a greenhouse for 40 days. As control the soil without compost was treated in the same way. Furthermore, additional treatments without and with the highest application rate, but without nitrogen fertilization, were prepared. After the 40 days these balcony boxes were also fertilized with 100 kg ha-1 of nitrogen and spinach – pre-cultivated in press pots – was planted in all balcony boxes.

Irrespectively of application rates and – in case of the highest application rate – of date of nitrogen fertilization, no negative effect of co-composted biochar on N uptake was observed. In addition, the nitrogen balance for treatments with co-composted biochar was not significantly different from the control. However, for treatments with compost without biochar an increasing balance shortfall with increasing amounts of compost was observed. This might due to a nitrogen immobilization of woody residues. In view of the fact, that N uptake by plants was comparable and significant amounts of easily extractable nitrate were found in the soil at the end of the experiment, we assume that the co-composted biochars used in this experiment had no adsorption capacity for nitrate.


Estimation of plant availability of different phosphates by the CaCl2/DTPA and CAL method

Lohr, D.; Babel, B.; Lau, C.; Levaillant, N.; Prell, F.; Hauck, D. (2022)

31. International Horticultural Congress (IHC2022); International symposium on innovative technologies and production strategies for sustainable controlled environment horticulture .

 

Due to depletion of global phosphorus resources, there is an increasing interest in phosphorus recycling products as fertilizer for growing media. However, in contrast to currently used fertilizers, which are almost completely based on calcium phosphates, at least in sewage-sludge based recycling products a remarkably amounts of phosphorus can be bound to iron or aluminum. In previous studies, the CaCl2/DTPA (CAT) and CAL method partly underestimated plant availability of such sewage-sludge based recycling products, which might be due to a low solubility of iron- and aluminium-bound phosphorus in these two extractants. Thus, a pot trial with marigold was done: plants were fertilized with mono-calcium phosphate (MCaP), di-calcium phosphate (DCaP), tri-calcium phosphate (TCaP), aluminium phosphate (AlP) or iron phosphate (FeP) at growing media pH of 5.5 and 6.5, respectively. No effect on plant growth was observed for the three calcium phosphates irrespectively of pH. However, plant fresh weight was reduced if P was applied as FeP and AlP, whereby no effect of pH was found for AlP but for FeP. Against expectations, plant availability was poorer at the higher pH. In contrary to fresh weight, P uptake of plants decreases from mono- to tri-calcium phosphate and with increasing pH. For aluminium and iron phosphates results for P uptake was comparable to those reported for fresh weight. Whereas plant availability of the three calcium phosphates was well reflected by CAT and overestimated by CAL, P uptake from iron phosphate was strongly underestimated by CAT but matches CAL soluble P. Availability of aluminum phosphate was strongly underestimated by both extractants as well as by the combination of CAT and CAL soluble phosphorus. This supports previous findings for various sewage-sludge based products and raises the question of the need of other extractants.

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Suitability of dielectric soil moisture sensors for measuring the water supply status of green roofs

Schmitz, H.; Jüttner, I.; Lohr, D.; Meinken, E. (2022)

31. International Horticultural Congress (IHC2022); II International symposium on greener cities: improving ecosystem services in a climate-changing world (greencities2022).

 

Extensive green roofs are a key component of urban water management in the future. On the one hand, they should mitigate urban heat islands, for which evapotranspiration has to be maximized, and on the other hand, they are supposed to reduce the risk of urban floods after heavy precipitation events. To achieve these goals, an exact measurement of the water supply status is necessary. In arable soils as well as in organic growing media, dielectric sensors are widely common. However, there is only little knowledge about the suitability of this kind of sensors for mineral and coarse-textured substrates used for extensive green roofs. In the current research four dielectric sensors (EC-5, 10 HS, SMT 100 and Aquaflex TR) were tested using five different green roof substrates. The five substrates were filled in plastic boxes of 80 x 60 cm. Substrate height was 15 cm and the four sensors were placed at half height. Afterwards, white lupine was sown and cultivated up to a height of about 30 cm. For testing the sensors, the substrates were saturated with water and then they have been left to dry out until plants show severe signs of wilt. During dry out, the sensor signals as well as the weight of the boxes were recorded automatically every five minutes. For each substrate six consecutive drying cycles were done. With exception of the Aquaflex TR, for all sensors output signals were closely linear correlated to the weight loss and signal ranges were comparable for the six drying cycles. However, significant differences in output signals of the sensors between the five tested substrates were observed. This indicates a need for substrate specific calibrations. The relation between the output signal of the Aquaflex TR and the weight loss was not linear, but also reproducible and suitable to assess water supply status of plants.

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Bäume wandern himmelwärts

Rösler, S. (2022)

alpinwelt 03/2022, S. 28-29.

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Einheitliche Orientierungswerte für öffentliches Grün

Blum, P.; Böhme, C.; Kühnau, C.; Reinke, M.; Willen, L. (2022)

Stadt + Grün 71 (8), S. 19-23.

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Trials with perennials - what's going on in Germany?

Hertle, B. (2022)

Trial delegates meeting of the International Perennial Associaton at Boskoop .


Ethical consumption: Influencing factors of consumer´s intention to purchase Fairtrade roses

Berki-Kiss, D.; Menrad, K. (2022)

Cleaner and Circular Bioeconomy 2, 100008, S. 1-9.
DOI: 10.1016/j.clcb.2022.100008


Open Access
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Entwicklung eines finanziellen Anreizsystems für zusätzliche Klimaschutz- und Biodiversitätsleistungen im Wald

Böttcher, H.; Welle, T.; Endres, E.; Eberl, J.; Unseld, R.; Dieng, K.; .., .. (2022)

Climate Change 2022 (35), S. 1-159.


Open Access

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