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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    Distinct bhaplotype structure at the innate immune receptor Toll-like receptor 2 across bank vole populations and lineages in Europe
    Morger, Jennifer, J. ; Raberg, Lars, L. ; Hille, Sabine, S. ; Brink, N.W. van den - \ 2015
    Biological Journal of the Linnean Society 116 (2015)1. - ISSN 0024-4066 - p. 124 - 133.
    major histocompatibility complex - positive darwinian selection - balancing selection - clethrionomys-glareolus - contrasting patterns - genetic-variation - northern spain - small mammals - mhc - polymorphism
    Parasite-mediated selection may contribute to the maintenance of genetic variation at host immune genes over long time scales. To date, the best evidence for the long-term maintenance of immunogenetic variation in natural populations comes from studies on the major histocompatibility complex (MHC) genes, whereas evidence for such processes from other immune genes remains scarce. In the present study, we show that, despite pronounced population differentiation and the occurrence of numerous private alleles within populations, the innate immune gene Toll-like receptor 2 (TLR2) displays a distinct haplotype structure in 21 bank vole (Myodes glareolus) populations across Europe. Haplotypes from all populations grouped in four clearly differentiated clusters, with the three main clusters co-occurring in at least three previously described mitochondrial lineages. This pattern indicates that the distinct TLR2 haplotype structure may precede the split of the mitochondrial lineages 0.19–0.56 Mya and suggests that haplotype clusters at this innate immune receptor are maintained over prolonged time in wild bank vole populations
    An economic analysis of sweet sorghum cultivation for ethanol production in North China
    Liu, H. ; Ren, L. ; Spiertz, J.H.J. ; Zhu, Y. ; Xie, G.H. - \ 2015
    Global change biology Bioenergy 7 (2015)5. - ISSN 1757-1693 - p. 1176 - 1184.
    biomass production - genetic-variation - sugar content - plastic film - west china - yield - feedstock - bicolor - juice - irrigation
    Sweet sorghum [Sorghum bicolor (L.) Moench] is a promising non-food energy crop. The objective of this study was to determine the economic costs and input sensitivity of sweet sorghum compared to cotton, maize, and sunflower, at two saline-alkali sites in Shandong (Wudi County) and Inner Mongolia (Wuyuan County) provinces of China. The data were collected quantitatively based on a face-to-face interview with 100 and 67 sweet sorghum growers at the two sites, respectively. The sweet sorghum grown at Wudi had lower external input (5469 CNY ha-1), higher net return (7305 CNY ha-1) and benefit-cost ratio (2.36) than its reference crop, cotton (18 454 CNY ha-1; 3615 CNY ha-1; 1.24). At Wuyuan, the sweet sorghum showed contrasting economic performance (19 541 CNY ha-1; 3438 CNY ha-1; 0.91), which was largely because of the higher labor costs compared to sunflower (10 896 CNY ha-1; 15 133 CNY ha-1; 2.49); and maize (9108 CNY ha-1; 14 760 CNY ha-1; 2.76). The productivity of sweet sorghum per unit of external input costs (kg CNY-1) was 13.12 for Wudi and only 3.26 for Wuyuan. Based on the Cobb-Douglas production function, the external inputs of diesel and seed had a significantly positive impact on the profitability of sweet sorghum at Wudi but not at Wuyuan. However, thecosts of irrigation and film cover were significantly negative. The energy crop, sweet sorghum, showed a better return to scale on investment than cotton and sunflower.
    On selection for flowering time plasticity in response to density
    Vermeulen, P.J. - \ 2015
    New Phytologist 205 (2015)1. - ISSN 0028-646X - p. 429 - 439.
    arabidopsis-thaliana - phenotypic plasticity - shade-avoidance - adaptive plasticity - impatiens-capensis - dependent selection - plant-populations - genetic-variation - local adaptation - life-history
    Different genotypes often exhibit opposite plastic responses in the timing of the onset of flowering with increasing plant density. In experimental studies, selection for accelerated flowering is generally found. By contrast, game theoretical studies predict that there should be selection for delayed flowering when competition increases. Combining different optimality criteria, the conditions under which accelerated or delayed flowering in response to density would be selected for are analysed with a logistic growth simulation model. To maximize seed production at the whole-stand level (simple optimization), selection should lead to accelerated flowering at high plant density, unless very short growing seasons select for similar onset of flowering at all densities. By contrast, selection of relative individual fitness will lead to delayed flowering when season length is long and/or growth rates are high. These different results give a potential explanation for the observed differences in direction of the plastic responses within and between species, including homeostasis, as a result of the effect of the variation in season length on the benefits of delayed flowering. This suggests that limited plasticity can evolve without the costs and limits that are currently thought to constrain the evolution of plasticity.
    Genomic relationships computed from either next- generation sequence or array SNP data
    Perez Enciso, M. - \ 2014
    Journal of Animal Breeding and Genetics 131 (2014)2. - ISSN 0931-2668 - p. 85 - 96.
    genetic-variation - complex traits - selection - pig - predictions - genotype - samples - cattle
    The use of sequence data in genomic prediction models is a topic of high interest, given the decreasing prices of current next'-generation sequencing technologies (NGS) and the theoretical possibility of directly interrogating the genomes for all causal mutations. Here, we compare by simulation how well genetic relationships (G) could be estimated using either NGS or ascertained SNP arrays. DNA sequences were simulated using the coalescence according to two scenarios: a cattle' scenario that consisted of a bottleneck followed by a split in two breeds without migration, and a pig' model where Chinese introgression into international pig breeds was simulated. We found that introgression results in a large amount of variability across the genome and between individuals, both in differentiation and in diversity. In general, NGS data allowed the most accurate estimates of G, provided enough sequencing depth was available, because shallow NGS (4x) may result in highly distorted estimates of G elements, especially if not standardized by allele frequency. However, high-density genotyping can also result in accurate estimates of G. Given that genotyping is much less noisy than NGS data, it is suggested that specific high-density arrays (similar to 3M SNPs) that minimize the effects of ascertainment could be developed in the population of interest by sequencing the most influential animals and rely on those arrays for implementing genomic selection.
    Natural variation in stomatal response to closing stimuli among Arabidopsis thaliana accessions after exposure to lowe VPD as a tool to recognize the mechanism of disturbed stomatal functioning
    Ali Niaei Fard, S. ; Meeteren, U. van - \ 2014
    Journal of Experimental Botany 65 (2014)22. - ISSN 0022-0957 - p. 6529 - 6542.
    relative-air-humidity - vapor-pressure-deficit - abscisic-acid - tradescantia-virginiana - genetic-variation - corylus-maxima - water status - guard-cells - plants - drought
    Stomatal responses to closing stimuli are disturbed after long-term exposure of plants to low vapour pressure deficit (VPD). The mechanism behind this disturbance is not fully understood. Genetic variation between naturally occurring ecotypes can be helpful to elucidate the mechanism controlling stomatal movements in different environments. We characterized the stomatal responses of 41 natural accessions of Arabidopsis thaliana to closing stimuli (ABA and desiccation) after they had been exposed for 4 days to moderate VPD (1.17 kPa) or low VPD (0.23 kPa). A fast screening system was used to test stomatal response to ABA using chlorophyll fluorescence imaging under low O2 concentrations of leaf discs floating on ABA solutions. In all accessions stomatal conductance (gs) was increased after prior exposure to low VPD. After exposure to low VPD, stomata of 39 out of 41 of the accessions showed a diminished ABA closing response; only stomata of low VPD-exposed Map-42 and C24 were as responsive to ABA as moderate VPD-exposed plants. In response to desiccation, most of the accessions showed a normal stomata closing response following low VPD exposure. Only low VPD-exposed Cvi-0 and Rrs-7 showed significantly less stomatal closure compared with moderate VPD-exposed plants. Using principle component analysis (PCA), accessions could be categorized to very sensitive, moderately sensitive, and less sensitive to closing stimuli. In conclusion, we present evidence for different stomatal responses to closing stimuli after long-term exposure to low VPD across Arabidopsis accessions. The variation can be a useful tool for finding the mechanism of stomatal malfunctioning.
    Reciprocal interactions between native and introduced populations of common milkweed, Asclepias syriaca, and the specialist aphid, Aphis nerii
    Bukovinszky, T. ; Gols, R. ; Agrawal, A.A. ; Roge, C. ; Bezemer, T.M. ; Biere, A. ; Harvey, J.A. - \ 2014
    Basic and Applied Ecology 15 (2014)5. - ISSN 1439-1791 - p. 444 - 452.
    oleander aphid - biological-control - density-dependence - genetic-variation - local adaptation - natural enemies - invasive plants - host plants - herbivores - evolution
    Following its introduction into Europe (EU), the common milkweed (Asclepias syriaca) has been free of most specialist herbivores that are present in its native North American (NA) range, except for the oleander aphid Aphis nerii. We compared EU and NA populations of A. nerii on EU and NA milkweed populations to test the hypothesis that plant–insect interactions differ on the two continents. First, we tested if herbivore performance is higher on EU plants than on NA plants, because the former have escaped most of their herbivores and have perhaps been selected for lower defence levels following introduction. Second, we compared two A. nerii lines (one from each continent) to test whether genotypic differences in the herbivore may influence species interactions in plant–herbivore communities in the context of species introductions. The NA population of A. nerii developed faster, had higher fecundity and attained higher population growth rates than the EU population. There was no overall significant continental difference in aphid resistance between the plants. However, milkweed plants from EU supported higher population growth rates and faster development of the NA line of A. nerii than plants from NA. In contrast, EU aphids showed similar (low) performance across plant populations from both continents. In a second experiment, we examined how chewing herbivores indirectly mediate interactions between milkweeds and aphids, and induced A. syriaca plants from each continent by monarch caterpillars (Danaus plexippus) to compare the resulting changes in plant quality on EU aphid performance. As specialist chewing herbivores of A. syriaca are only present in NA, we expected that plants from the two continents may affect aphid growth in different ways when they are challenged by a specialist chewing herbivore. Caterpillar induction decreased aphid developmental times on NA plants, but not on EU plants, whereas fecundity and population growth rates were unaffected by induction on both plant populations. The results show that genetic variation in the plants as well as in the herbivores can determine the outcome of plant–herbivore interactions.
    Effects of ambient temperature, feather cover, and housing system on energy partitioning and performance in laying hens
    Krimpen, M.M. van; Binnendijk, G.P. ; Anker, I. van den; Heetkamp, M.J.W. ; Kwakkel, R.P. ; Brand, H. van den - \ 2014
    Journal of Animal Science 92 (2014)11. - ISSN 0021-8812 - p. 5019 - 5031.
    residual feed consumption - physical-activity - genetic-variation - egg-production - fowl - poultry - requirements - selection - patterns
    Environmental factors, such as ambient temperature (T), feather cover (FC), and housing system (HS), probably affect energy requirements of laying hens. Using a 3 × 2 × 2 factorial arrangement, interaction effects of T (11, 16, and 21°C), FC (100 and 50%), and HS (cage and floor housing) on energy partitioning and performance of laying hens were investigated. Six batches of 70 H&N Brown Nick laying hens, divided over 2 respiration chambers, were exposed to the T levels in three 2-wk periods. Heat production (HP) was determined by indirect calorimetry. The ME intake was calculated by subtracting energy in manure/litter from that in feed and wood shavings. The NE was calculated by subtracting HP from ME. The ME intake increased by 1% for each degree reduction in T. In hens with intact plumage, HP was not affected by T, whereas at decreasing T, HP increased in hens with 50% FC (P <0.01). At 21°C, HP was not affected by HS, whereas in the floor system, HP at 16 and 11°C was 5.8 and 3.0% higher, respectively, than in cages (P <0.05). The NE for production was 25.7% higher in cages compared to the floor system (P <0.05). In cages, 24.7% of NE for production was spent on body fat deposition, whereas in the floor system, 9.0% of NE for production was released from body fat reserves. The ME intake was predicted by the equation (R2 = 0.74) ME intake (kJ/d) = 612 BW0.75 – (8.54 × T) + (28.36 × ADG) + (10.43 × egg mass) – (0.972 × FC). Hen performances were not affected by treatments, indicating the adaptive capacity of young laying hens to a broad range of environmental conditions.
    A novel Botrytis species is associated with a newly emergent foliar disease in cultivated Hemerocallis
    Grant-Downton, R.T. ; Terhem, R.B. ; Kapralov, M. ; Mehdi, S. ; Rodriguez-Enriquez, M.J. ; Gurr, S.J. ; Kan, J.A.L. van; Dewey, F.M. - \ 2014
    PLoS ONE 9 (2014)6. - ISSN 1932-6203 - 11 p.
    genetic-variation - south-carolina - plant - cinerea - host - infection - elliptica - fungi - armillaria - diversity
    Foliar tissue samples of cultivated daylilies (Hemerocallis hybrids) showing the symptoms of a newly emergent foliar disease known as ‘spring sickness’ were investigated for associated fungi. The cause(s) of this disease remain obscure. We isolated repeatedly a fungal species which proved to be member of the genus Botrytis, based on immunological tests. DNA sequence analysis of these isolates, using several different phyogenetically informative genes, indicated that they represent a new Botrytis species, most closely related to B. elliptica (lily blight, fire blight) which is a major pathogen of cultivated Lilium. The distinction of the isolates was confirmed by morphological analysis of asexual sporulating cultures. Pathogenicity tests on Hemerocallis tissues in vitro demonstrated that this new species was able to induce lesions and rapid tissue necrosis. Based on this data, we infer that this new species, described here as B. deweyae, is likely to be an important contributor to the development of ‘spring sickness’ symptoms. Pathogenesis may be promoted by developmental and environmental factors that favour assault by this necrotrophic pathogen. The emergence of this disease is suggested to have been triggered by breeding-related changes in cultivated hybrids, particularly the erosion of genetic diversity. Our investigation confirms that emergent plant diseases are important and deserve close monitoring, especially in intensively in-bred plants.
    Defining the role of common variation in the genomic and biological architecture of adult human height
    Wood, A.R. ; Esko, T. ; Yang, J. ; Dhonukshe-Rutten, R.A.M. ; Groot, C.P.G.M. de - \ 2014
    Nature Genetics 46 (2014). - ISSN 1061-4036 - p. 1173 - 1186.
    genetic-variation - complex traits - heritability - mutations - snps
    Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ~2,000, ~3,700 and ~9,500 SNPs explained ~21%, ~24% and ~29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/ß-catenin and chondroitin sulfate–related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.
    Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle
    Binsbergen, R. van; Bink, M.C.A.M. ; Calus, M.P.L. ; Eeuwijk, F.A. van; Hayes, B.J. ; Hulsegge, B. ; Veerkamp, R.F. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 25 p.
    haplotype-phase inference - genotype imputation - linkage disequilibrium - wide association - breeding programs - genetic-variation - complex traits - population - prediction - design
    Background The use of whole-genome sequence data can lead to higher accuracy in genome-wide association studies and genomic predictions. However, to benefit from whole-genome sequence data, a large dataset of sequenced individuals is needed. Imputation from SNP panels, such as the Illumina BovineSNP50 BeadChip and Illumina BovineHD BeadChip, to whole-genome sequence data is an attractive and less expensive approach to obtain whole-genome sequence genotypes for a large number of individuals than sequencing all individuals. Our objective was to investigate accuracy of imputation from lower density SNP panels to whole-genome sequence data in a typical dataset for cattle. Methods Whole-genome sequence data of chromosome 1 (1737 471 SNPs) for 114 Holstein Friesian bulls were used. Beagle software was used for imputation from the BovineSNP50 (3132 SNPs) and BovineHD (40 492 SNPs) beadchips. Accuracy was calculated as the correlation between observed and imputed genotypes and assessed by five-fold cross-validation. Three scenarios S40, S60 and S80 with respectively 40%, 60%, and 80% of the individuals as reference individuals were investigated. Results Mean accuracies of imputation per SNP from the BovineHD panel to sequence data and from the BovineSNP50 panel to sequence data for scenarios S40 and S80 ranged from 0.77 to 0.83 and from 0.37 to 0.46, respectively. Stepwise imputation from the BovineSNP50 to BovineHD panel and then to sequence data for scenario S40 improved accuracy per SNP to 0.65 but it varied considerably between SNPs. Conclusions Accuracy of imputation to whole-genome sequence data was generally high for imputation from the BovineHD beadchip, but was low from the BovineSNP50 beadchip. Stepwise imputation from the BovineSNP50 to the BovineHD beadchip and then to sequence data substantially improved accuracy of imputation. SNPs with a low minor allele frequency were more difficult to impute correctly and the reliability of imputation varied more. Linkage disequilibrium between an imputed SNP and the SNP on the lower density panel, minor allele frequency of the imputed SNP and size of the reference group affected imputation reliability.
    Mate preference of female blue tits varies with experimental photoperiod
    Reparaz, L.B. ; Oers, K. van; Naguib, M. ; Doutrelant, C. ; Visser, M.E. ; Caro, S.P. - \ 2014
    PLoS ONE 9 (2014)3. - ISSN 1932-6203 - 8 p.
    parus-caeruleus populations - sexually selected trait - great tits - extrapair paternity - body-size - reproductive-performance - cyanistes-caeruleus - plumage coloration - european starlings - genetic-variation
    Organisms use environmental cues to time their life-cycles and among these cues, photoperiod is the main trigger of reproductive behaviours such as territory defence or song activity. Whether photoperiod is also important for another behaviour closely associated with reproduction, mate choice, is unknown. In many bird species, mate choice occurs at two different times during the annual cycle that strongly differ in daylength: in late winter when photoperiod is short and social mates are chosen, and again around egg-laying when photoperiod is longer and extra-pair mates are chosen. This duality makes the role that photoperiod plays on mate choice behaviours intriguing. We investigated the effect of photoperiod on mate choice using three experimental photoperiodic treatments (9 L:15 D, 14 L:10 D, 18 L:6 D), using blue tits (Cyanistes caeruleus) as a biological model. We show that female choice was stronger under long photoperiods. In addition, female blue tits spent significantly more time near males with long tarsi and long wings. This latter preference was only expressed under long photoperiods, suggesting that some indices of male quality only become significant to females when they are strongly photostimulated, and therefore that females could select their social and extra-pair mates based on different phenotypic traits. These results shed light on the roles that photoperiod may play in stimulating pair-bonding and in refining female selectivity for male traits.
    Effects of parental and own early developmental conditions on the phenotype expression in zebra finches (Taeniopygia guttata)
    Krause, E.T. ; Naguib, M. - \ 2014
    Evolutionary Ecology 28 (2014)2. - ISSN 0269-7653 - p. 263 - 275.
    risk-taking behavior - tits parus-major - catch-up growth - nutritional conditions - personality-traits - great tits - brood size - neonatal nutrition - genetic-variation - metabolic-rate
    The performance of an individual can be critically influenced by its experience early in life as well as trans-generationally by the conditions experienced by its parents. However, it remains unclear whether or not the early experience of parents and offspring interact with each other and adapt offspring when the parental and own early environ-mental conditions match. Here, zebra finches (Taeniopygia guttata) that had experienced either early low or high nutritional conditions raised their offspring under either matched or mismatched nutritional conditions. Parental and offspring early conditions both separately affected the offspring's adult phenotype, but early conditions experienced by parents and offspring did not interact as predicted. Offspring that grew up under conditions matching those their parents had experienced did not do better than those that grew up in a mis-matched environment. Thus, transgenerational effects remain a lifelong burden to the offspring acting in addition to the offspring's own early life experience. The lack of evidence for adaptive programming to matching environmental conditions may result from non-predictive environments under natural conditions in such opportunistic breeders.
    Are there evolutionary consequences of plant–soil feedbacks along soil gradients?
    Schweitzer, J.A. ; Juric, I. ; Voorde, T.F.J. van de; Clay, K. ; Putten, W.H. van der; Bailey, J.K. - \ 2014
    Functional Ecology 28 (2014)1. - ISSN 0269-8463 - p. 55 - 64.
    microbial communities - frequency-dependence - genetic-variation - local adaptation - invasive plant - temperate tree - diversity - ecosystems - selection - ecology
    1.Both abiotic and biotic gradients exist in soils and several of these gradients have been shown to select for plant traits. Moreover, plants possess a multitude of traits that can lead to strong niche construction (i.e., plant-induced changes to soils). Our objectives in this paper are to outline both empirical and theoretical evidence for the evolutionary consequences of plant-soil linkages and feedbacks on plants along soil heterogeneity gradients. 2.We describe a simple mathematical model of plant evolution to explore the relationship between the sign and magnitude of feedback and the divergence of plant traits. We also constructed an individual-based simulation model to study the conditions under which plant-soil feedbacks occur, niche construction evolves and plant traits diverge. 3.This approach allows us to address specific hypotheses regarding relationships between positive and negative plant-soil feedback with variation in niche construction, the strength of selective gradients and the relative importance of local adaptation vs. feedbacks. 4.The models suggest that feedbacks between soils and plants may commonly result in evolutionary interactions. The simulation model indicates that plant traits can diverge with niche construction and traits can be selected for in response to niche construction. However, the magnitude of feedbacks and how strongly they evolve depends on the amount of gene flow and the strength of selective gradients over time. 5.These results suggest that plant-soil feedback can lead to evolution in plants and reveals new research directions for further inquiry. Questions addressing trade-offs and relationships between positive and negative feedbacks as well as adaptation and maladaptation of plant traits represent important frontiers in plant-soil feedback studies.
    Co-Variation between Seed dormancy, growth rate and flowering time changes with latitude in Arabidopsis thaliana
    Debieu, M. ; Tang, C. ; Stich, B. ; Sikosek, T. ; Effgen, S. ; Josephs, E. ; Schmitt, J. ; Nordborg, M. ; Koornneef, M. ; Meaux, J. De - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    natural allelic variation - genome-wide association - quantitative-trait loci - life-history - genetic-variation - clinal variation - plant-growth - native range - germination - adaptation
    Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis
    Heritability of cortisol response to confinement stress in European sea bass dicentrarchus labrax
    Volckaert, F.A.M. ; Hellemans, B. ; Batargias, C. ; Louro, B. ; Massault, C. ; Houdt, J.K.J. Van; Haley, C. ; Koning, D.J. de; Canario, A.V.M. - \ 2012
    Genetics, Selection, Evolution 44 (2012). - ISSN 0999-193X
    tilapia oreochromis-niloticus - input earthen ponds - cyprinus-carpio l. - genetic-variation - rainbow-trout - disease resistance - body-weight - atlantic salmon - growth - traits
    Background: In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stress, is less studied. In this study, we have estimated heritabilities of two growth traits (body weight and length) and of cortisol response to confinement stress in the European sea bass. Findings: The F1 progeny analysed (n = 922) belonged to a small effective breeding population with contributions from an unbalanced family structure of just 10 males and 2 females. Heritability values ranged from 0.54 (+/- 0.21) for body weight to 0.65 (+/- 0.22) for standard body length and were low for cortisol response i.e. 0.08 (+/- 0.06). Genetic correlations were positive (0.94) between standard body length and body weight and negative between cortisol and body weight and between cortisol and standard body length (-0.60 and -0.55, respectively). Conclusion: This study confirms that in European sea bass, heritability of growth-related traits is high and that selection on such traits has potential. However, heritability of cortisol response to stress is low in European sea bass and since it is known to vary greatly among species, further studies are necessary to understand the reasons for these differences.
    Genotype-by-temperature interactions may help to maintain clonal diversity in asterionella formosa (Bacillariophyceae)
    Gsell, A.S. ; Domis, L.N.D. ; Przytulska-Bartosiewicz, A. ; Mooij, W.M. ; Donk, E. van; Ibelings, B.W. - \ 2012
    Journal of Phycology 48 (2012)5. - ISSN 0022-3646 - p. 1197 - 1208.
    diatom ditylum-brightwellii - fresh-water phytoplankton - reaction norms - phenotypic plasticity - genetic-variation - centric diatom - cell-size - environment interactions - marine-phytoplankton - skeletonema-costatum
    Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity. To test the influence of temperature as a selection force in continually (seasonally) changing aquatic systems we carried out reaction norms experiments on co-occurring clonal genotypes of a ubiquitous diatom species, Asterionella formosa Hassall, across an environmentally relevant range of temperatures. We report within population genetic diversity and extensive diversity in genotype-specific reaction norms in growth rates and cell size traits. Our results showed genotype by environment interactions, indicating that no genotype could outgrow all others across all temperature environments. Subsequently, we constructed a model to simulate the relative proportion of each genotype in a hypothetical population based on genotype and temperature-specific population growth rates. This model was run with different seasonal temperature patterns. Our modeling exercise showed a succession of two to several genotypes becoming numerically dominant depending on the underlying temperature pattern. The results suggest that (temperature) context dependent fitness may contribute to the maintenance of genetic diversity in isolated populations of clonally reproducing microorganisms in temporally variable environments.
    Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians
    Hulzen, K.J.E. van; Schopen, G.C.B. ; Arendonk, J.A.M. van; Nielen, M. ; Koets, A.P. ; Schrooten, C. ; Heuven, H.C.M. - \ 2012
    Journal of Dairy Science 95 (2012)5. - ISSN 0022-0302 - p. 2740 - 2748.
    single nucleotide polymorphisms - estimated breeding values - quantitative trait loci - genetic-variation - johnes-disease - linkage disequilibrium - short-communication - us holsteins - infection - cattle
    Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.
    Single nucleotide polymorphisms (SNPs) involved in insulin resistance, weight regulation, lipid metabolism and inflammation in relation to metabolic syndrome: an epidemiological study
    Povel, C.M. ; Boer, J.M.A. ; Onland-Moret, N. ; Dolle, M.E. ; Feskens, E.J.M. ; Schouw, Y.T. van der - \ 2012
    Cardiovascular Diabetology 11 (2012)1. - ISSN 1475-2840
    genome-wide association - c-reactive protein - coronary-artery-disease - mendelian randomization - genetic-variation - heart-disease - loci - risk - variants - traits
    Background: Mechanisms involved in metabolic syndrome (MetS) development include insulin resistance, weight regulation, inflammation and lipid metabolism. Aim of this study is to investigate the association of single nucleotide polymorphisms (SNPs) involved in these mechanisms with MetS. Methods: In a random sample of the EPIC-NL study (n = 1886), 38 SNPs associated with waist circumference, insulin resistance, triglycerides, HDL cholesterol and inflammation in genome wide association studies (GWAS) were selected from the 50K IBC array and one additional SNP was measured with KASPar chemistry. The five groups of SNPs, each belonging to one of the metabolic endpoints mentioned above, were associated with MetS and MetS-score using Goeman's global test. For groups of SNPs significantly associated with the presence of MetS or MetS-score, further analyses were conducted. Results: The group of waist circumference SNPs was associated with waist circumference (P=0.03) and presence of MetS (P=0.03). Furthermore, the group of SNPs related to insulin resistance was associated with MetS score (P
    Growth and yield performance of Jerusalem artichoke clones in a semiarid region of China
    Liu, Z.X. ; Spiertz, J.H.J. ; Sha, J. ; Xue, S. ; Xie, G.H. - \ 2012
    Agronomy Journal 104 (2012)6. - ISSN 0002-1962 - p. 1538 - 1546.
    helianthus-tuberosus-l. - spring wheat cultivars - drought resistance - genetic-variation - water - ethanol - energy - stems - land
    This study investigated biomass yield and growth characteristics of 26 Jerusalem artichoke (Helianthus tuberosus L.) clones and assessed it as a bioenergy crop for a semiarid region of the Loess Plateau in China. Genotype, year, and genotype ´ year interaction contributed to differences in crop development, growth characteristics, and biomass yields (dry matter). Generally, biomass yields in 2011 were lower than in 2008, mainly due to a more severe soil moisture deficit in 2011. Shoot and tuber biomass yields (STBY) ranged from 18.9 to 35.0 Mg ha–1 in 2008 and from 16.1 to 24.8 Mg ha–1 in 2011. Clones HUB-2 and BJ-4 produced the highest shoot biomass yield (SBY), amounting to 31.3 and 25.6 Mg ha–1, respectively, in the wetter year but higher drought sensitivity. Clones HUN-2, SD-2, and SHH-1 produced the second highest SBY, which varied between 14.3 and 20.1 Mg ha–1. Clones GZ-1, HEN-1, HUB-1, IM-1, and SX-2 are recommended for tuber production and produced tuber yields >8 Mg ha–1 in both seasons. Clones SD-2 and SHH-1 exhibited drought sensitivity indices
    Indel-II region deletion sizes in the white spot syndrome virus genome correlate with shrimp disease outbreaks in southern Vietnam
    Tran Thi Tuyet, H. ; Zwart, M.P. ; Phuong, N.T. ; Oanh, D.T.H. ; Jong, M.C.M. de; Vlak, J.M. - \ 2012
    Diseases of Aquatic Organisms 99 (2012)2. - ISSN 0177-5103 - p. 153 - 162.
    penaeus-monodon - bacilliform virus - genetic-variation - wssv - virulence - pathogenesis - thailand - sequence - province - fitness
    Sequence comparisons of the genomes of white spot syndrome virus (WSSV) strains have identified regions containing variable-length insertions/deletions (i.e. indels). Indel-I and Indel-II, positioned between open reading frames (ORFs) 14/15 and 23/24, respectively, are the largest and the most variable. Here we examined the nature of these 2 indel regions in 313 WSSV-infected Penaeus monodon shrimp collected between 2006 and 2009 from 76 aquaculture ponds in the Mekong Delta region of Vietnam. In the Indel-I region, 2 WSSV genotypes with deletions of either 5950 or 6031 bp in length compared with that of a reference strain from Thailand (WSSV-TH-96-II) were detected. In the Indel-II region, 4 WSSV genotypes with deletions of 8539, 10970, 11049 or 11866 bp in length compared with that of a reference strain from Taiwan (WSSV-TW) were detected, and the 8539 and 10970 bp genotypes predominated. Indel-II variants with longer deletions were found to correlate statistically with WSSV-diseased shrimp originating from more intensive farming systems. Like Indel-I lengths, Indel-II lengths also varied based on the Mekong Delta province from which farmed shrimp were collected
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