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Vermeulen C.J.,University of Aarhus | Vermeulen C.J.,University of Groningen | Sorensen P.,Danish Institute of Agricultural Sciences | Kirilova Gagalova K.,University of Groningen | And 2 more authors.
Journal of Evolutionary Biology | Year: 2013

In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds. © 2013 European Society For Evolutionary Biology.


Berbel A.,Polytechnic University of Valencia | Ferrandiz C.,Polytechnic University of Valencia | Hecht V.,University of Tasmania | Dalmais M.,French National Institute for Agricultural Research | And 11 more authors.
Nature Communications | Year: 2012

Unravelling the basis of variation in inflorescence architecture is important to understanding how the huge diversity in plant form has been generated. Inflorescences are divided between simple, as in Arabidopsis, with flowers directly formed at the main primary inflorescence axis, and compound, as in legumes, where they are formed at secondary or even higher order axes. The formation of secondary inflorescences predicts a novel genetic function in the development of the compound inflorescences. Here we show that in pea this function is controlled by VEGETATIVE1 (VEG1), whose mutation replaces secondary inflorescences by vegetative branches. We identify VEG1 as an AGL79-like MADS-box gene that specifies secondary inflorescence meristem identity. VEG1 misexpression in meristem identity mutants causes ectopic secondary inflorescence formation, suggesting a model for compound inflorescence development based on antagonistic interactions between VEG1 and genes conferring primary inflorescence and floral identity. Our study defines a novel mechanism to generate inflorescence complexity. © 2012 Macmillan Publishers Limited. All rights reserved.


Sarup P.,University of Aarhus | Sorensen P.,Danish Institute of Agricultural Sciences | Loeschcke V.,University of Aarhus
Age | Year: 2011

We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were differentially expressed between selected and control flies when measured at the same chronological age. The longevity-selected flies consistently showed expression profiles more similar to control flies one age class younger than control flies of the same age. This finding is in accordance with a younger gene expression profile in longevity-selected lines. Among the genes down-regulated in longevity-selected lines, we found a clear over-representation of genes involved in immune functions, supporting the hypothesis of a life-shortening effect of an overactive immune system, known as inflammaging. We judged the physiological age as the level of cumulative mortality. Eighty-four genes were differentially expressed between the control and longevity-selected lines at the same physiological age, and the overlap between the same chronological and physiological age gene lists included 40 candidate genes for increased longevity. Among these candidates were genes with roles in starvation resistance, immune response regulation, and several that have not yet been linked to longevity. Investigating these genes would provide new knowledge of the pathways that affect life span in invertebrates and, potentially, mammals. © 2010 American Aging Association, Media, PA, USA.


Sarup P.,University of Aarhus | Sorensen J.G.,University of Aarhus | Kristensen T.N.,University of Aarhus | Kristensen T.N.,Danish Institute of Agricultural Sciences | And 4 more authors.
PLoS ONE | Year: 2011

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds. © 2011 Sarup et al.


Gorres J.H.,Danish Institute of Agricultural Sciences | Amador J.A.,University of Rhode Island
Journal of Nematology | Year: 2010

Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, V s, varied between 0.13 and 0.18 mL/gand increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total V s of bulk and burrow samples were not significant on any sampling date. Howe\er, differences were significant for pore size fractions at the scale of nematode body diameter. © The Society of Nematologists 2010.


Zink V.,Institute of Animal Science | Lassen J.,Danish Institute of Agricultural Sciences | Stipkova M.,Institute of Animal Science
Czech Journal of Animal Science | Year: 2012

The aim of this study was to estimate genetic parameters for female fertility and production traits in first-parity Czech Holstein cows and to quantify the effect of using this information on the accuracy of a selection index in seven different scenarios. In order to estimate genetic (co)variance components, theDMU software running an AI-REML algorithm was used. The analyses were made using a series of bivariate animal models. The pedigree included 164 125 animals and it was set up using a pruned animal modeldesign. The present study included the following female fertility traits for the first lactations: calving to the first insemination (CF), days open (DO), calving from the first to the last insemination (FL), and milk production traits: milk production (MLK), kg of fat (FAT), and kg of protein (PROT). The heritability for all the investigated fertility traits was low and close to 0. Moderate heritabilities for production traits ranging from0.20 (MLK) to 0.23 (PROT) were estimated. The strongest unfavourable correlation was found between PROT and DO (0.49). Other estimated correlations between fertility traits and production traits were moderate, ranging from 0.26 to 0.41. The results of this study evidence that cows with the poorest genetic potential forreproductive performance are those having high genetic potential for milk production and milk components. The results also show that the number of days from calving to new pregnancy depends on the production level. Seven investigated scenarios using selection index theory show a clear trend for increasing accuracy when more fertility traits were added as well as when higher numbers of daughters with information on reproduction traits per sire were available.


Zink V.,Institute of Animal Science | Stipkova M.,Institute of Animal Science | Lassen J.,Danish Institute of Agricultural Sciences
Journal of Dairy Science | Year: 2011

The aim of this study was to estimate genetic parameters for fertility traits and linear type traits in the Czech Holstein dairy cattle population. Phenotypic data regarding 12 linear type traits, measured in first lactation, and 3 fertility traits, measured in each of first and second lactation, were collected from 2005 to 2009 in the progeny testing program of the Czech-Moravian Breeders Corporation. The number of animals for each linear type trait was 59,467, except for locomotion, where 53,436 animals were recorded. The 3-generation pedigree file included 164,125 animals. (Co)variance components were estimated using AI-REML in a series of bivariate analyses, which were implemented via the DMU package. Fertility traits included days from calving to first service (CF1), days open (DO1), and days from first to last service (FL1) in first lactation, and days from calving to first service (CF2), days open (DO2), and days from first to last service (FL2) in second lactation. The number of animals with fertility data varied between traits and ranged from 18,915 to 58,686. All heritability estimates for reproduction traits were low, ranging from 0.02 to 0.04. Heritability estimates for linear type traits ranged from 0.03 for locomotion to 0.39 for stature. Estimated genetic correlations between fertility traits and linear type traits were generally neutral or positive, whereas genetic correlations between body condition score and CF1, DO1, FL1, CF2 and DO2 were mostly negative, with the greatest correlation between BCS and CF2 (-0.51). Genetic correlations with locomotion were greatest for CF1 and CF2 (-0.34 for both). Results of this study show that cows that are genetically extreme for angularity, stature, and body depth tend to perform poorly for fertility traits. At the same time, cows that are genetically predisposed for low body condition score or high locomotion score are generally inferior in fertility. © 2011 American Dairy Science Association.


PubMed | National Institute for Biotechnology and Genetic Engineering NIBGE, Food and Biotechnology Research Center, Forman Christian College and Danish Institute of Agricultural Sciences
Type: Journal Article | Journal: Transgenic research | Year: 2016

Phytate is a major constituent of wheat seeds and chelates metal ions, thus reducing their bioavailability and so the nutritional value of grains. Transgenic plants expressing heterologous phytase are expected to enhance degradation of phytic acid stored in seeds and are proposed to increase the in vitro bioavailability of mineral nutrients. Wheat transgenic plants expressing Aspergillus japonicus phytase gene (phyA) in wheat endosperm were developed till T


Aldana-Jague E.,Catholic University of Louvain | Heckrath G.,Danish Institute of Agricultural Sciences | Macdonald A.,Rothamsted Research | van Wesemael B.,Catholic University of Louvain | Van Oost K.,Catholic University of Louvain
Geoderma | Year: 2016

Traditional methods to assess the soil organic carbon (SOC) content based on soil sampling and analysis are time consuming and expensive, and the results are influenced by the sampling design. The aim of this study was to investigate the potential of UAS (Unmanned Aerial Systems) multi-spectral imagery (480-1000 nm) for estimating the SOC content in bare cultivated soils at a high spatial resolution (12 cm). We performed UAS analysis on the Hoosfield Spring Barley experiment at Rothamsted (UK) where adjacent plots with distinctly different SOC contents, due to different long-term management practices, provide a valuable resource to evaluate this approach. We acquired images (wavelength: 480-550-670-780-880-1000 nm) at an altitude of 120 m over an area of 2 ha using a multi-spectral camera mounted on an UAS. The high-resolution images captured small-scale variations at the soil surface (e.g. shadows, tillage and wheels marks). After a projection in new dimensions by a PCA, we calibrated a support vector machine regression using observations from conventional soil sampling and SOC measurements. The performance of the calibration had a R2 of 0.98 and a RMSE of 0.17%C. A cross-validation showed that the model was robust, with an average R2 of 0.95 and a RMSE of 0.21%. An external validation dataset was used to evaluate the predicted spatial patterns of SOC content and a good fit with an RMSE 0.26%C was obtained. Although this study shows that the methodology has a clear potential for use in precision agriculture or monitoring important soil properties following changes in management, we also identify and discuss its limitations and current shortcomings. © 2016 Elsevier B.V.


Sakin E.,Danish Institute of Agricultural Sciences | Seyrek A.,Danish Institute of Agricultural Sciences
Romanian Agricultural Research | Year: 2015

Understanding the relationship between terrestrial biomass and climate is necessary to predict the effects of climate changes on carbon stocks. Biomass distribution is affected by geographical and climatic parameters and limits carbon accumulation to soil. This study evaluates biomass, precipitation, and carbon correlations of wheat, lentil and barley left to agricultural rainfall. During 2011 to 2012, total precipitation was 381.3 mm, and biomass was 914.49 grams of dry matter m-2(530.41 g Cm-2), during 2012 to 2013, there were 1013.58 grams of dry matter m-2(587.88 g Cm-2) that were obtained with 381.3 mm of precipitation. In parallel with a 1 mm increase in precipitation, 2.89 grams of dry matter m-2 (1.68 g Cm-2) were found during 2011 to 2012 and 2.66 grams of dry matter m-2 (1.54 g Cm-2) were found in 2012 to 2013. A strong correlation was found between precipitation and biomass (P<0.001; R2= 0.6551 in wheat, P<0.001; R2= 0.5458 in lentil and P<0.001; R2= 0.6687 in barley). In addition, a strong correlation was found between total annual carbon and total annual precipitation (P<0.001; R2= 0.5221 barley + lentil and P<0.001; R2= 0.6221 wheat + lentil). © 2015, National Agricultural Research and Development Institute Fundulea. All rights reserved.

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