Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Next-generation biological control: the need for integrating genetics and genomics
    Leung, Kelley ; Ras, Erica ; Ferguson, Kim B. ; Ariëns, Simone ; Babendreier, Dirk ; Bijma, Piter ; Bourtzis, Kostas ; Brodeur, Jacques ; Bruins, Margreet A. ; Centurión, Alejandra ; Chattington, Sophie R. ; Chinchilla-Ramírez, Milena ; Dicke, Marcel ; Fatouros, Nina E. ; González-Cabrera, Joel ; Groot, Thomas V.M. ; Haye, Tim ; Knapp, Markus ; Koskinioti, Panagiota ; Hesran, Sophie Le; Lyrakis, Manolis ; Paspati, Angeliki ; Pérez-Hedo, Meritxell ; Plouvier, Wouter N. ; Schlötterer, Christian ; Stahl, Judith M. ; Thiel, Andra ; Urbaneja, Alberto ; Zande, Louis van de; Verhulst, Eveline C. ; Vet, Louise E.M. ; Visser, Sander ; Werren, John H. ; Xia, Shuwen ; Zwaan, Bas J. ; Magalhães, Sara ; Beukeboom, Leo W. ; Pannebakker, Bart A. - \ 2020
    Biological Reviews (2020). - ISSN 1464-7931
    artificial selection - biological control - genetics - genome assembly - genomics - insect breeding - microbiome - modelling

    Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

    Archived experimental data on heritability of wing truncation in flightless Adalia bipunctata
    Lommen, Suzanne T.E. ; Koops, Kees G. ; Cornelder, Bardo A. ; Jong, Peter W. de; Brakefield, Paul M. - \ 2019
    Wageningen University & Research
    Adalia bipunctata - artificial selection - biological control - breeding design - Coccinellidae - Coleoptera - flightless - genetics - heritability - ladybird beetle - natural enemy - selective breeding - wing length - winglessness
    Original empirical data published in Lommen STE, Koops CG et al. 2019 Genetics and selective breeding of variation in wing truncation in a flightless aphid control agent. Entomologia Experimentalis et Applicata 167: 636-645. doi:10.1111/eea.12810
    Genetics and Breeding of Lupinus mutabilis: An Emerging Protein Crop
    Gulisano, Agata ; Alves, Sofia ; Martins, João Neves ; Trindade, Luisa M. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    breeding - genetics - lupin - Lupinus mutabilis - plant protein - protein crop

    Protein crops have gained increasing interest in recent years, as a transition towards plant-protein based diets appears pivotal to ensure global food security and preserve the environment. The Andean species Lupinus mutabilis emerges as an ideal protein crop with great potential for Europe and other regions with temperate climates. This species is characterized by oil and protein content similar to soybean and is highly valued for its adaptability to colder climates and low input agriculture on marginal land. However, its introduction outside the Andes has yet to take off. To date, L. mutabilis remains an under-studied crop, lacking high yield, early maturity and a consistent breeding history. This review paper identifies L. mutabilis limitations and potential uses, and suggests the main breeding targets for further improvement of this crop. It also highlights the potential of new molecular tools and available germplasm resources that can now be used to establish L. mutabilis as a viable protein crop.

    Combinations of Spok genes create multiple meiotic drivers in Podospora
    Vogan, Aaron A. ; Ament-Velásquez, S.L. ; Granger-Farbos, Alexandra ; Svedberg, Jesper ; Bastiaans, Eric ; Debets, Alfons J.M. ; Coustou, Virginie ; Yvanne, Hélène ; Clavé, Corinne ; Saupe, Sven J. ; Johannesson, Hanna - \ 2019
    eLife 8 (2019). - ISSN 2050-084X
    evolutionary biology - fungi - gene drive - genetics - genomic conflict - genomics - Podospora - selfish genetic element - spore killer

    Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages.

    Hoe kies je de beste stieren voor je bedrijf?
    Hoving, A.H. ; Ducro, B.J. - \ 2019
    Wageningen : Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research
    animal breeding - dairy cattle - genetics - teaching materials - intermediate vocational training - animal welfare - animal production - animal health
    Docentenhandleiding bij lesmateriaal ‘Hoe kies je de beste stieren voor je bedrijf?’ Powerpoint ‘Hoe kies je de beste stieren voor je bedrijf?’ Excel file ‘Een selectie van de stierenkaart’.
    Genotyping data MiMe offspring VIGS
    Calvo Baltanas, V. ; Wijnker, T.G. - \ 2019
    genetics - MiMe generated offspring - VIGS derived - virus-induced gene silencing (VIGS)
    Genotyping data regarding the offpsring generated from crosses of F1LerxCol hybrids to the transgenic line male sterile Ler. The genotyping markers used for genotyping are listed in the first rows. The first two columns contain the different lines genotyped. The blue color (B) identify a marker corresponding to a homozygous Ler allele while the green marker (H) corresponds to heterozygous Col-Ler.
    Genotyping Data Hyperrecombinant offspring VIGS
    Calvo Baltanas, V. ; Wijnker, T.G. - \ 2019
    genetics - genotyping - increase of recombination VIGS - recombination - virus-induced gene silencing (VIGS)
    Offspring generated from the crosses of F1 lerxcol plants in which RECQ4 and/or FIGL1 were pressumably knocked-down. Expected lines were expected to be hyperrecombinant but they display the same recombination events as compared to a wild-type population. The genoyping markers used can be seen in the first two rows while the first two columns display the total number of lines used. The markers in blue (B) corresopnd to homozygous Ler alleles while the green ones (H) correspond to the presence of a Col-Ler alleles.
    Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus
    Habig, Michael ; Kema, Gert Hj ; Holtgrewe Stukenbrock, Eva - \ 2018
    eLife 7 (2018). - ISSN 2050-084X - 20 p.
    accessory chromosome - B chromosome - chromosomes - gene expression - genetics - genomics - meiotic drive - selfish genetic elements - tetrad analysis - Zymoseptoria tritici

    Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.

    Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle
    Løvendahl, P. ; Difford, G.F. ; Li, B. ; Chagunda, M.G.G. ; Huhtanen, P. ; Lidauer, M.H. ; Lassen, J. ; Lund, P. - \ 2018
    Animal 12 (2018)s2. - ISSN 1751-7311 - p. s336 - s349.
    digestibility - genetics - holobiont - microbiome - ranking

    It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.

    Counts of bovine monocyte subsets prior to calving are predictive for postpartum occurrence of mastitis and metritis
    Pomeroy, Brianna ; Sipka, Anja ; Hussen, Jamal ; Eger, Melanie ; Schukken, Ynte - \ 2017
    Cornell University
    medicine - cell biology - genetics - ecology - immunology - mathematical sciences - developmental biology - infectious diseases - computational biology
    The heightened susceptibility to infectious diseases in postpartum dairy cows is often attributed to immune dysfunction associated with the transition period. However, the cell populations involved in this immune dysfunction and the dynamics between those populations are not well defined. Monocytes play a crucial role in governing initial immune response in bacterial infections. Bovine monocytes are subdivided in classical (CD14+/CD16−), intermediate (CD14+/CD16+) and non-classical monocytes (CD14−/CD16+) with distinct phenotypic and functional differences. This study investigated the relationship of monocyte subsets counts in blood at 42 and 14 days prior to expected calving date to occurrence of metritis and mastitis within 2 weeks postpartum. In the enrolled prospective cohort of 27 German Holstein cows, housed at the Institute of Animal Nutrition of the Friedrich-Loeffler-Institute Braunschweig, Germany, n = 13 developed metritis and/or mastitis postpartum. A multivariable logistic regression was used to analyze the relationship between prepartum cell counts of monocyte subsets and neutrophils with postpartum disease. Our model revealed that higher counts of the two CD14+ monocyte subsets were predictive of disease. In contrast, higher numbers of the CD14− monocyte subset were negatively associated with disease. Interestingly, the neutrophil count, a common hallmark for inflammatory response, was not associated with the outcome variable at either time point. The results indicate that the number and composition of monocyte subsets before calving are related to the susceptibility to infectious disease within 2 weeks postpartum. Furthermore the oppositional effect of CD14+ and CD14− subsets strengthens the hypothesis that these subsets have different functional roles in the inflammatory response in dairy cows.
    Data from: Maternal effects in a wild songbird are environmentally plastic but only marginally alter the rate of adaptation
    Ramakers, J.J.C. ; Cobben, M.M.P. ; Bijma, P. ; Reed, T.E. ; Visser, M.E. ; Gienapp, P. - \ 2017
    Wageningen University & Research
    adaptation - bird - evolution - experimental - fitness - genetics - quantative - maternal effects
    Despite ample evidence for the presence of maternal effects (MEs) in a variety of traits and strong theoretical indications for their evolutionary consequences, empirical evidence to what extent MEs can influence evolutionary responses to selection remains ambiguous. We tested the degree to which MEs can alter the rate of adaptation of a key life-history trait, clutch size, using an individual-based model approach parameterized with experimental data from a long-term study of great tits (Parus major). We modeled two types of MEs: (i) an environmentally plastic ME, in which the relationship between maternal and offspring clutch size depended on the maternal environment via offspring condition, and (ii) a fixed ME, in which this relationship was constant. Although both types of ME affected the rate of adaptation following an abrupt environmental shift, the overall effects were small. We conclude that evolutionary consequences of MEs are modest at best in our study system, at least for the trait and the particular type of ME we considered here. A closer link between theoretical and empirical work on MEs would hence be useful to obtain accurate predictions about the evolutionary consequences of MEs more generally.
    Reverse Breeding : Creating parental lines for a heterozygous plant
    Schaart, J.G. ; Wiel, C.C.M. van de - \ 2017
    Wageningen : Wageningen University
    plants - cultivation - genetics - crossing
    Video about breeding and genetics
    Reverse Breeding : Complications
    Schaart, J.G. ; Wiel, C.C.M. van de - \ 2017
    Wageningen : Wageningen University
    cultivation - genetics - plants - crossbreds
    Video recording about breeding and genetics
    Unravelling the genetic base of the meiotic recombination landscapes in two varieties of the button mushroom, Agaricus bisporus
    Sedaghat Telgerd, Narges - \ 2017
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): A.S.M. Sonnenberg. - Wageningen : Wageningen University - ISBN 9789463436953 - 142
    fungi - agaricus bisporus - mushrooms - genetics - breeding - meiosis - recombination - schimmels - agaricus bisporus - paddestoelen - genetica - veredelen - meiose - recombinatie

    The button mushroom, Agaricus bisporus var. bisporus, is one of the most cultivated mushrooms worldwide. Even though wild isolates of this variety have a broad genetic variation, the traditional and present-day hybrids only have a very narrow genetic base. The button mushroom has a typical meiotic recombination landscape (MRL) in which crossover (CO) events are predominantly restricted to the extreme ends of the chromosomes. This has been one of the main obstacles for mushroom breeders in improving or generating new mushroom hybrids due to a considerable linkage drag. A wild variety of A. bisporus, i.e., burnettii appeared to have CO spread more evenly across the genome. The existence of two extremely different MRLs in two compatible A. bisporus varieties offers an excellent opportunity to study the genetic basis for positioning CO in meiosis. The main objective of the research presented in this thesis initially was to examine meiosis of the var. burnettii in more detail and subsequently to identify genomic regions revealing the difference in MRL of the two A. bisporus varieties. The availability of genome sequences in the bisporus variety has produced many more informative markers such as SNP. We aimed to de novo sequence one of the haplotypes of a heterokaryotic strain of the burnettii variety using the PacBio sequencing technique and resequencing the other haplotype using Illumina HiSeq. In parallel to this, we used Genotyping by Sequencing (GBS) to construct the first linkage map of the burnettii variety, showing a more or less even distribution of COs across the genome. The constructed linkage map has also proved to be a useful tool for de novo assembly of the burnettii variety genome sequence. In addition, we performed comparative genome sequence studies between the burnettii variety and the previously sequenced genomes of two of the bisporus variety homokaryons, indicating high levels of collinearity between all three genomes. The only chromosomal rearrangement to be found was on chromosome 10, where an inversion of ~ 800 kb in the burnettii variety was detected compared to the var. bisporus genomes. As a starting point for unravelling the genetic basis underlying MRL in the A. bisporus, we performed quantitative trait loci (QTL) analysis using bisporus and burnettii varieties. An inter-varietal population was developed from a cross between a constituent nucleus of the bisporus and the burnettii variety. This population contains 178 haploid progenies which were genotyped by 210 SNP markers to construct a genetic linkage map, which proves to be a solid foundation for exploring the genetic control of MRL of A. bisporus. In addition, we performed a comparative genetic mapping study using the genetic maps of the bisporus variety Horst U1, the burnettii variety Bisp119/9 and the inter-varietal hybrid by selecting markers having similar positions in these three maps. In contrast to the bisporus variety where CO events are mainly restricted to chromosome ends, the burnettii variety shows a more or less equal distribution of CO events across the entire genome. The recombination landscape of the inter-varietal hybrid shows an intermediate pattern to that of both varieties. The MRL trait is expressed as a CO event in the offspring of each individual of the inter-varietal mapping population. For this reason, the individuals of the inter-varietal mapping population were intercrossed and outcrossed to generate three types of second generation hybrids. Two compatible tester homokaryons derived from the bisporus and burnettii varieties were used for outcrossing. Subsequently, the haploid progenies from each type of second generation hybrids were isolated to generate three types of segregating populations. The haploid progenies from segregating populations were genotyped with SNP markers covering the whole length of all the chromosomes. Recombination frequencies were determined at distal ends and elsewhere on the chromosomes and used to compare recombination frequencies between chromosomes within each population as well as between segregating populations across all chromosomes. A prerequisite for successful QTL mapping the MRL is to select segregating populations in which the segregation of MRL is clear. We observed that segregating populations outcrossed with the bisporus tester homokaryon were the most useful populations to generate haploid offspring in which COs are assessed for further QTL study of MRL at the time when this research was carried out. To map genomic regions involved in the different MRLs of A. bisporus, 71 homokaryotic offspring of the inter-varietal hybrid were outcrossed with an unrelated tester homokaryon of the bisporus variety. Subsequently, the haploid progenies were isolated from each hybrid and genotyped with SNP markers. Marker pairs were generated for the end regions of chromosomes to assess CO there or anywhere else on the chromosomes for each segregating population. QTL mapping analysis revealed two QTLs located on chromosome l and three others located on chromosomes IV, VI and VII. The QTLs identified span large parts of their respective chromosomes; therefore further strategies are needed for a more precise assessment and localisation of MRL.

    On the genetic mechanisms of nutrient-dependent lifespan and reproduction
    Zandveld, Jelle - \ 2017
    Wageningen University. Promotor(en): B.J. Zwaan, co-promotor(en): A.J.M. Debets. - Wageningen : Wageningen University - ISBN 9789463436861 - 209
    genetics - lifespan - reproduction - nutrients - drosophila melanogaster - fungi - diet - evolution - genetica - levensduur - voortplanting - voedingsstoffen - drosophila melanogaster - schimmels - dieet - evolutie

    Dietary restriction (DR), a moderate reduction in nutrient intake, improves health or extends lifespan across many species. Moreover, recent insights have shown that also the effects of specific nutrients are of importance for the beneficial effects of DR rather than intake alone. However, we still lack much insight through what mechanisms the lifespan increase through diet changes is exactly mediated.

    To further increase our understanding of the genetic mechanisms of nutrient-dependent lifespan, in Chapter 2, 3, 4, and 5 I employed different methods of genetic interventions (i.e. a genetic knockout, natural genetic variation and experimental evolution) using the model species Drosophila melanogaster and Podospora anserina. To test whether the genetic interventions affected the diet response, a broad range of diets was applied, thereby taking the recent insights of nutritional geometry into account. Furthermore, the response of the fly’s whole-genome transcription to different dietary treatments were assessed in Chapter 6 and 7 to identify and potentially disentangle genetic mechanisms for lifespan from those for reproduction.

    Chapter 2 addressed the effects of a triple knockout in the insulin-IGF signalling (IIS) pathway, namely for three genes encoding insulin-like peptides in Drosophila (dilp2-3,5). The mutant showed a strong elevation of lifespan that was irrespective of food type, but also a strong reduction of the female fly fecundity. In addition, this assay also revealed that the same knockout can yield different interpretations for its function in the fly’s diet response, which was strongly dependent per diet dimension under consideration (i.e. varying yeast, sugar, or its ratio in the diet). This observation set the stage for other experimental chapters in this thesis, where a broad range of diets was applied to depict the exact genotypic effects that are involved in the lifespan response to diet. For example, in Chapter 2, interactive effects were observed between dilp2-3,5 knockout and the lifespan response to dietary sugar, but however, not for the yeast component of the diet.

    In Chapter 3, for the same experimental diets, gene expression responses in dilp2-3,5 knockout flies were measured to describe the general dynamics on the pathway level. Interestingly, expression of the remaining fly head-expressed dilp, dilp6, was elevated on higher yeast levels upon dilp2-3,5 knockout. Therefore, compensatory mechanisms within IIS might still partly mediate the lifespan response to yeast.

    In Chapter 4 the natural genetic variation for the response to DR was explored in wild-derived strains of the fungus Podospora anserina. By applying a broad range of glucose concentrations in a synthetic medium, we constructed reaction norms for 62 natural occurring strains and showed considerable natural variation in the shape of the reaction norms, including the glucose concentration at which lifespan increased and how steeply the fungus’ lifespan responds to diet (the slope S). Furthermore, I identified a significant correlation between a strain’s general lifespan and both parameters, suggesting that the lifespan response to diet partly acts through a mechanism involved in the fungus’ lifespan determination under high nutrient, growth and reproduction permissive, conditions. On moderate glucose restriction levels we showed that a reduced reproduction was not always associated with lifespan extension, which indicates that decoupling of these traits (that often trade-off) can be achieved.

    An evolutionary perspective on diet response and the connection between reproduction and lifespan, two often interconnected traits in lifespan research, was provided in Chapter 5. Here, experimental evolution (EE) was performed in Drosophila melanogaster to test whether improved reproductive capacity (i.e. local adaptation) to three nutritionally distinct diets directly affected the lifespan response. Adaptation to the distinct nutritional conditions, had no consistent effect on the lifespan response to diet. Other life-history traits that I assessed could more consistently be associated with the evolutionary nutritional treatments, which together suggested that the adaptive genetic mechanisms increasing the fly’s reproduction were not necessarily interconnected singly with a change of lifespan, but rather with a change in the whole life-history strategy.

    By exploring the fly’s whole-genome transcription response in a continuously changing environ­ment, Chapter 6 continued on the evolutionary relevance of lifespan responses to diet. This type of fluctuations may better reflect the fly’s natural ecological setting than the continuous diets typically applied in whole-genome transcription laboratory studies. This revealed that flies were able to respond quickly to diet fluctuations throughout lifespan by drastically changing their transcription pattern and, moreover, my results indicated that a large part of the whole-genome transcription response could be attributed to the female fly’s reproduction. Because I measured the response of multiple life-history traits to the fluctuating diet changes, I was able to decouple groups of genes associated with lifespan from those associated with reproduction. This is an important step in the direction of unravelling the genetic architecture that specifically mediates the lifespan response to diet, which can be especially useful in whole-genome transcription studies.

    In Chapter 7, the consistencies between studies for their whole-genome transcription responses upon DR were investigated. This revealed large transcriptomic variations on different regulatory levels, i.e. the level of whole-genome transcription, most significant genes, and also gene ontology. To test whether the observed inconsistent whole-genome transcription responses were primarily a reflection of the fly’s reproduction, such as observed in Chapter 6, a new cohort of flies was subjected to different regimes that resulted in very different age-dependent reproduction patterns. By assessing whole-genome transcription in this cohort at two time points, the gene expression changes reflected the age-dependent reproduction patterns observed, rather than the lifespan phenotypes. Similar to Chapter 6, this again highlighted the importance of measuring multiple life-history traits for associating whole-genome transcription responses to lifespan effects of dietary restriction.

    In Chapter 8 the acquired insights across the experimental chapters were synthesized, discussing the importance of assessing a broad range of nutrients for the interpretation of any genotypic effect, and in addition discussing the value of measuring multiple life-history traits for genetic associations. In this chapter I also suggested directions for future research in Drosophila and Podospora that may be valuable for further unravelling and understanding the mechanisms of diet responses in other organisms, including in humans.

    Anosmia - A Clinical Review
    Boesveldt, Sanne ; Postma, Elbrich M. ; Boak, Duncan ; Welge-Luessen, Antje ; Schöpf, Veronika ; Mainland, Joel D. ; Martens, Jeffrey ; Ngai, John ; Duffy, Valerie B. - \ 2017
    Chemical Senses 42 (2017)7. - ISSN 0379-864X - p. 513 - 523.
    genetics - neural reorganization - olfactory dysfunction - quality of life - stem cell regeneration - treatment

    Anosmia and hyposmia, the inability or decreased ability to smell, is estimated to afflict 3-20% of the population. Risk of olfactory dysfunction increases with old age and may also result from chronic sinonasal diseases, severe head trauma, and upper respiratory infections, or neurodegenerative diseases. These disorders impair the ability to sense warning odors in foods and the environment, as well as hinder the quality of life related to social interactions, eating, and feelings of well-being. This article reports and extends on a clinical update commencing at the 2016 Association for Chemoreception Sciences annual meeting. Included were reports from: a patient perspective on losing the sense of smell with information on Fifth Sense, a nonprofit advocacy organization for patients with olfactory disorders; an otolaryngologist's review of clinical evaluation, diagnosis, and management/treatment of anosmia; and researchers' review of recent advances in potential anosmia treatments from fundamental science, in animal, cellular, or genetic models. As limited evidence-based treatments exist for anosmia, dissemination of information on anosmia-related health risks is needed. This could include feasible and useful screening measures for olfactory dysfunction, appropriate clinical evaluation, and patient counseling to avoid harm as well as manage health and quality of life with anosmia.

    Investigating the fruit texture genetic control in apple and its interplay with the production of volatile compounds using multi-family based analysis and genome wide association mapping
    Guardo, Mario Di - \ 2017
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): W.E. van de Weg; F. Costa. - Wageningen : Wageningen University - ISBN 9789463432054 - 177
    malus domestica - apples - fruit - fruit growing - genetics - plant breeding - genome analysis - malus domestica - appels - fruit - fruitteelt - genetica - plantenveredeling - genoomanalyse

    Although varying with context, quality of fresh fruits includes several properties such as color, texture, flavor and health promoting compounds. This thesis focused on two important quality aspects, namely texture and aroma in apple, and defining the genomic regions involved in the control of these two features. The genetic control of texture and VOCs production have been investigated using two marker-trait association analysis approaches: Pedigree Based Analysis (PBA) and Genome Wide Association Study (GWAS). In chapter 2, ASSIsT (Automatic SNP ScorIng Tool), a software dedicated for the efficient calling and filtering of SNPs from Illumina InfiniumÒ arrays is presented. ASSIsT builds on GenomeStudio® derived data and identifies markers showing reliable genotype calls (bi-allelic segregation pattern). In addition, ASSIsT identifies and re-edits SNP calls of markers showing additional alleles (null alleles or additional SNPs in the probe annealing site). Chapter 3 aimed to dissect the genetic control of fruit firmness in apple during storage through PBA and employing 24 bi-parental families (1216 individuals) connected by a common pedigree structure. Ten QTLs were identified encompassing eight linkage groups, which unravelled a QTL dynamics over storage shedding light on the specific genetic control at each time-point. Chapter 4: aimed to comprehensively decipher the genetic control of fruit texture. Two complementing QTL mapping approaches were employed together with a novel and high sophisticated phenotyping device for fruit texture. The PBA was carried out on six full-sib pedigreed families (416 individuals), while the GWAS was performed on a collection of 233 apple accessions. The texture analyser employed (TAXT-AED texture analyser) allowed the measurement of both the mechanical properties (firmness) and the acoustic properties (crispness) of fruit texture. The QTL results indicated chromosome 10 being associated in changes of the mechanical properties of fruit texture, while chromosomes 2 and 14 were more associated to the acoustic response. In Chapter 5 the interplay between texture and volatile organic compounds (VOCs) was investigated in 162 apple accessions. The array of volatile compounds phenotyped was implemented into a GWAS identifying seven chromosomes harbouring important candidate genes for aroma, such as MdAAT1 and MdIGS. Next, volatilome and fruit texture data were integrated revealing a negative correlation between these two features.

    Nesting behaviour of broiler breeders
    Oever, Anne van den; Rodenburg, T.B. ; Bolhuis, J.E. ; Ven, L.J.F. van de; Kemp, B. - \ 2017
    In: Xth European Symposium on Poultry Welfare, 19-22 June 2017, Ploufragan - France. - World's Poultry Science Association (WPSA) - p. 23 - 23.
    broiler breeders - nesting behaviour - genetics - nest design - housing - climate
    Broilers have been selected for growth related characteristics, which are negatively correlated to reproductive traits. This genetic background creates challenges in broiler breeders, as the hens do not make optimal use of the nests provided. This project aims to investigate what factors determine nesting behaviour, i.e. where a broiler breeder hen prefers to lay her eggs. Factors such as genetic background, social interactions, physical characteristics of the nest and climate might interfere with the natural nesting behaviour of the hen. Also fundamental trade-offs between different motivations, such as hunger, comfort and safety, might influence nesting behaviour. Behaviour and use of space will be measured in experimental set-ups in order to gain insight in the importance of different system components. This knowledge will be used to optimise housing conditions and develop strategies that stimulate the hen to lay her egg in the nest. The performance of this improved system will be tested in field experiments to investigate the transferability of results from experimental to field conditions.
    Automatic ultra-wideband sensor detection shows selection on feather pecking increases activity in laying hens
    Haas, E.N. de; Eijk, J.A.J. van der; Rodenburg, T.B. - \ 2017
    In: Xth European Symposium on Poultry Welfare, 19-22 June 2017, Ploufragan - France. - World's Poultry Science Association (WPSA) - p. 101 - 101.
    broiler breeders - nesting behaviour - genetics - nest design - housing - climate - laying hens - feather pecking - ultra-wideband tracking - activity - sensor technology
    Broilers have been selected for growth related characteristics, which are negatively correlated to reproductive traits. This genetic background creates challenges in broiler breeders, as the hens do not make optimal use of the nests provided. This project aims to investigate what factors determine nesting behaviour, i.e. where a broiler breeder hen prefers to lay her eggs. Factors such as genetic background, social interactions, physical characteristics of the nest and climate might interfere with the natural nesting behaviour of the hen. Also fundamental trade-offs between different motivations, such as hunger, comfort and safety, might influence nesting behaviour. Behaviour and use of space will be measured in experimental set-ups in order to gain insight in the importance of different system components. This knowledge will be used to optimise housing conditions and develop strategies that stimulate the hen to lay her egg in the nest. The performance of this improved system will be tested in field experiments to investigate the transferability of results from experimental to field conditions.
    Behavioural and physiological characterisation of laying hen lines divergently selected on feather pecking
    Eijk, J.A.J. van der; Lammers, A. ; Rodenburg, T.B. - \ 2017
    In: Xth European Symposium on Poultry Welfare, 19-22 June 2017, Ploufragan - France. - World's Poultry Science Association (WPSA) - p. 60 - 60.
    broiler breeders - nesting behaviour - genetics - nest design - housing - climate - laying hens - feather pecking - fearfulness - coping style - stress - imune system
    Broilers have been selected for growth related characteristics, which are negatively correlated to reproductive traits. This genetic background creates challenges in broiler breeders, as the hens do not make optimal use of the nests provided. This project aims to investigate what factors determine nesting behaviour, i.e. where a broiler breeder hen prefers to lay her eggs. Factors such as genetic background, social interactions, physical characteristics of the nest and climate might interfere with the natural nesting behaviour of the hen. Also fundamental trade-offs between different motivations, such as hunger, comfort and safety, might influence nesting behaviour. Behaviour and use of space will be measured in experimental set-ups in order to gain insight in the importance of different system components. This knowledge will be used to optimise housing conditions and develop strategies that stimulate the hen to lay her egg in the nest. The performance of this improved system will be tested in field experiments to investigate the transferability of results from experimental to field conditions.
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