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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    Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions
    Prinzenberg, Aina E. ; Campos-Dominguez, Lucia ; Kruijer, Willem ; Harbinson, Jeremy ; Aarts, Mark G.M. - \ 2020
    Plant, Cell & Environment 43 (2020)8. - ISSN 0140-7791 - p. 2000 - 2013.
    Arabidopsis - cold - GWAS - natural variation - photosynthesis

    Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (ΦPSII) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in ΦPSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in ΦPSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.

    The Role of Transcriptional Regulation in Hybrid Vigor
    Botet, Ramon ; Keurentjes, Joost J.B. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    Arabidopsis thaliana - breeding - gene expression - genetic regulation - heterosis - hybrid vigor - natural variation - speciation

    The genetic basis of hybrid vigor in plants remains largely unsolved but strong evidence suggests that variation in transcriptional regulation can explain many aspects of this phenomenon. Natural variation in transcriptional regulation is highly abundant in virtually all species and thus a potential source of heterotic variability. Allele Specific Expression (ASE), which is tightly linked to parent of origin effects and modulated by complex interactions in cis and in trans, is generally considered to play a key role in explaining the differences between hybrids and parental lines. Here we discuss the recent developments in elucidating the role of transcriptional variation in a number of aspects of hybrid vigor, thereby bridging old paradigms and hypotheses with contemporary research in various species.

    A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits
    Snoek, Basten ; Volkers, Rita ; Nijveen, Harm ; Petersen, Carola ; Dirksen, Philipp ; Sterken, Mark ; Nakad, Rania ; Riksen, Joost ; Rosenstiel, P.C. ; Stastna, J.J. ; Braekman, B.P. ; Harvey, S.C. ; Schulenburg, Hinrich ; Kammenga, Jan - \ 2019
    Wageningen University & Research
    Multi-parent RILs - Caenorhabditis elegans - QTL - life-history - natural variation - genetic map
    Background The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. Results To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11Â kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. Conclusion Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
    Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene
    Julkowska, Magdalena M. ; Klei, Karlijn ; Fokkens, Like ; Schranz, Eric - \ 2016
    Journal of Experimental Botany 67 (2016)8. - ISSN 0022-0957 - p. 2127 - 2138.
    Arabidopsis - development - GWAS - natural variation - rosette size - salt stress

    Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850), flowering locus KH-domain containing protein and a DUF1639-containing protein. Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth.

    Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formation
    Hoedjes, K.M. ; Smid, H.M. ; Schijlen, E.G.W.M. ; Vet, L.E.M. ; Vugt, J.J.F.A. van - \ 2015
    BMC Genomics 16 (2015). - ISSN 1471-2164
    natural variation - antisense transcription - protein-synthesis - foraging success - parasitic wasps - drosophila - vitripennis - pathway - consolidation - opportunities
    Background Cellular processes underlying memory formation are evolutionary conserved, but natural variation in memory dynamics between animal species or populations is common. The genetic basis of this fascinating phenomenon is poorly understood. Closely related species of Nasonia parasitic wasps differ in long-term memory (LTM) formation: N. vitripennis will form transcription-dependent LTM after a single conditioning trial, whereas the closely-related species N. giraulti will not. Genes that were differentially expressed (DE) after conditioning in N. vitripennis, but not in N. giraulti, were identified as candidate genes that may regulate LTM formation. Results RNA was collected from heads of both species before and immediately, 4 or 24 hours after conditioning, with 3 replicates per time point. It was sequenced strand-specifically, which allows distinguishing sense from antisense transcripts and improves the quality of expression analyses. We determined conditioning-induced DE compared to naïve controls for both species. These expression patterns were then analysed with GO enrichment analyses for each species and time point, which demonstrated an enrichment of signalling-related genes immediately after conditioning in N. vitripennis only. Analyses of known LTM genes and genes with an opposing expression pattern between the two species revealed additional candidate genes for the difference in LTM formation. These include genes from various signalling cascades, including several members of the Ras and PI3 kinase signalling pathways, and glutamate receptors. Interestingly, several other known LTM genes were exclusively differentially expressed in N. giraulti, which may indicate an LTM-inhibitory mechanism. Among the DE transcripts were also antisense transcripts. Furthermore, antisense transcripts aligning to a number of known memory genes were detected, which may have a role in regulating these genes. Conclusion This study is the first to describe and compare expression patterns of both protein-coding and antisense transcripts, at different time points after conditioning, of two closely related animal species that differ in LTM formation. Several candidate genes that may regulate differences in LTM have been identified. This transcriptome analysis is a valuable resource for future in-depth studies to elucidate the role of candidate genes and antisense transcription in natural variation in LTM formation.
    Systemic Regulation of RAS/MAPK Signaling by the Serotonin Metabolite 5-HIAA
    Schmid, T. ; Snoek, L.B. ; Fröhli, E. ; Bent, M.L. van der; Kammenga, J.E. ; Hajnal, A. - \ 2015
    Plos Genetics 11 (2015)5. - ISSN 1553-7404 - 16 p.
    caenorhabditis-elegans - c-elegans - natural variation - vulvar induction - complex disease - receptor - protein - gene - kinase - activation
    Human cancer is caused by the interplay of mutations in oncogenes and tumor suppressor genes and inherited variations in cancer susceptibility genes. While many of the tumor initiating mutations are well characterized, the effect of genetic background variation on disease onset and progression is less understood. We have used C. elegans genetics to identify genetic modifiers of the oncogenic RAS/MAPK signaling pathway. Quantitative trait locus analysis of two highly diverged C. elegans isolates combined with allele swapping experiments identified the polymorphic monoamine oxidase A (MAOA) gene amx-2 as a negative regulator of RAS/MAPK signaling. We further show that the serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), which is a product of MAOA catalysis, systemically inhibits RAS/MAPK signaling in different organs of C. elegans. Thus, MAOA activity sets a global threshold for MAPK activation by controlling 5-HIAA levels. To our knowledge, 5-HIAA is the first endogenous small molecule that acts as a systemic inhibitor of RAS/MAPK signaling.
    The laboratory domestication of Caenorhabditis elegans
    Sterken, M.G. ; Snoek, L.B. ; Kammenga, J.E. ; Andersen, E.C. - \ 2015
    Trends in Genetics 31 (2015)6. - ISSN 0168-9525 - p. 224 - 231.
    life-history traits - c. elegans - natural variation - social-behavior - npr-1 - genetics - yeast - environment - populations - diversity
    Model organisms are of great importance to our understanding of basic biology and to making advances in biomedical research. However, the influence of laboratory cultivation on these organisms is underappreciated, and especially how that environment can affect research outcomes. Recent experiments led to insights into how the widely used laboratory reference strain of the nematode Caenorhabditis elegans compares with natural strains. Here we describe potential selective pressures that led to the fixation of laboratory-derived alleles for the genes npr1, glb-5, and nath-10. These alleles influence a large number of traits, resulting in behaviors that affect experimental interpretations. Furthermore, strong phenotypic effects caused by these laboratory-derived alleles hinder the discovery of natural alleles. We highlight strategies to reduce the influence of laboratory-derived alleles and to harness the full power of C. elegans.
    Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought
    El-Soda, M. ; Kruijer, Willem ; Malosetti, M. ; Koornneef, M. ; Aarts, M.G.M. - \ 2015
    Plant, Cell & Environment 38 (2015)3. - ISSN 0140-7791 - p. 585 - 599.
    genome-wide association - natural variation - abiotic stress - inbred lines - qtl analysis - growth - reveals - protein - genetics - adaptation
    Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome-wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co-located with a QTL mapped in the RIL population
    Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species
    Hoedjes, K.M. ; Smid, H.M. ; Vet, L.E.M. ; Werren, J.H. - \ 2014
    Heredity 113 (2014). - ISSN 0018-067X - p. 542 - 550.
    long-term-memory - natural variation - parasitic wasps - learning rate - drosophila - evolution - consolidation - dynamics - pteromalidae - hymenoptera
    Genes involved in the process of memory formation have been studied intensively in model organisms; however, little is known about the mechanisms that are responsible for natural variation in memory dynamics. There is substantial variation in memory retention among closely related species in the parasitic wasp genus Nasonia. After a single olfactory conditioning trial, N. vitripennis consolidates long-term memory that lasts at least 6 days. Memory of the closely related species N. giraulti is present at 24¿h but is lost within 2 days after a single trial. The genetic basis of this interspecific difference in memory retention was studied in a backcrossing experiment in which the phenotype of N. giraulti was selected for in the background of N. vitripennis for up to five generations. A genotyping microarray revealed five regions that were retained in wasps with decreased memory retention. Independent introgressions of individual candidate regions were created using linked molecular markers and tested for memory retention. One region on chromosome 1 (spanning ~5.8¿cM) and another on chromosome 5 (spanning ~25.6¿cM) resulted in decreased memory after 72¿h, without affecting 24-h-memory retention. This phenotype was observed in both heterozygous and homozygous individuals. Transcription factor CCAAT/enhancer-binding protein and a dopamine receptor, both with a known function in memory formation, are within these genomic regions and are candidates for the regulation of memory retention. Concluding, this study demonstrates a powerful approach to study variation in memory retention and provides a basis for future research on its genetic basis.
    Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective
    Wijnen, C.L. ; Keurentjes, J.J.B. - \ 2014
    Current Opinion in Plant Biology 18 (2014). - ISSN 1369-5266 - p. 103 - 109.
    genome-wide association - inbred line population - functional genomics - thaliana accession - induced mutations - natural variation - identification - plant - mutagenesis - phenotypes
    The use of genetic resources for the analysis of quantitative traits finds its roots in crop breeding but has seen a rejuvenation in Arabidopsis thaliana thanks to specific tools and genomic approaches. Although widely used in numerous crop and natural species, many approaches were first developed in this reference plant. We will discuss the scientific background and historical use of mapping populations in Arabidopsis and highlight the technological innovations that drove the development of novel strategies. We will especially lay emphasis on the methodologies used to generate the diverse population types and designate possible applications. Finally we highlight some of the most recent developments in generating genetic mapping resources and suggest specific usage for these novel tools and concepts.
    Genetic dissection of leaf development in Brassica rapa using a ‘geneticalgenomics’ approach
    Xiao, D. ; Wang, H. ; Basnet, R.K. ; Jianjun Zhao, Jianjun ; Lin, K. ; Hou, X. ; Bonnema, A.B. - \ 2014
    Plant Physiology 164 (2014)3. - ISSN 0032-0889 - p. 1309 - 1325.
    quantitative trait loci - flowering time - arabidopsis-thaliana - morphological traits - functional divergence - natural variation - duplicated genes - organ growth - expression - cell
    The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene BRASSICA RAPA KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; BRASSICA RAPA ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; BRASSICA RAPA LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, BRASSICA RAPA FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa.
    Octopamine-like immunoreactive neurons in the brain and subesophageal ganglion of the parasitic wasps Nasonia vitripennis and N. giraulti
    Haverkamp, A. ; Smid, H.M. - \ 2014
    Cell and Tissue Research 358 (2014)2. - ISSN 0302-766X - p. 313 - 329.
    long-term-memory - honey-bee - schistocerca-gregaria - cotesia-glomerata - natural variation - drosophila brain - nervous-system - locust brain - plant odors - fruit-fly
    Octopamine is an important neuromodulator in the insect nervous system, influencing memory formation, sensory perception and motor control. In this study, we compare the distribution of octopamine-like immunoreactive neurons in two parasitic wasp species of the Nasonia genus, N. vitripennis and N. giraulti. These two species were previously described as differing in their learning and memory formation, which raised the question as to whether morphological differences in octopaminergic neurons underpinned these variations. Immunohistochemistry in combination with confocal laser scanning microscopy was used to reveal and compare the somata and major projections of the octopaminergic neurons in these wasps. The brains of both species showed similar staining patterns, with six different neuron clusters being identified in the brain and five different clusters in the subesophageal ganglion. Of those clusters found in the subesophageal ganglion, three contained unpaired neurons, whereas the other three consisted in paired neurons. The overall pattern of octopaminergic neurons in both species was similar, with no differences in the numbers or projections of the ventral unpaired median (VUM) neurons, which are known to be involved in memory formation in insects. In one other cluster in the brain, located in-between the optic lobe and the antennal lobe, we detected more neurons in N. vitripennis compared with N. giraulti. Combining our results with findings made previously in other Hymenopteran species, we discuss possible functions and some of the ultimate factors influencing the evolution of the octopaminergic system in the insect brain.
    Unravelling reward value: the effect of host value on memory retention in Nasonia parasitic wasps
    Hoedjes, K.M. ; Kralemann, L.E.M. ; Vugt, J.J.F.A. van; Vet, L.E.M. ; Smid, H.M. - \ 2014
    Animal Behaviour 96 (2014). - ISSN 0003-3472 - p. 1 - 7.
    long-term-memory - sex-ratio - natural variation - pieris-rapae - drosophila - quality - vitripennis - succession - preference - behavior
    Learning can be instrumental in acquiring new skills or optimizing behaviour, but it is also costly in terms of energy and when maladaptive associations are formed: the balance between costs and benefits affects memory dynamics. Numerous studies have demonstrated that memory dynamics of animal species depend on the value of the reward during conditioning, even when animals are inexperienced with this reward. How an animal perceives reward value depends on a number of aspects, including the quantity or quality of the reward in terms of energy or fitness for the animal, the internal state of the animal and previous experience. The reliability of the learned association is another aspect, which can be assessed through the frequency of experiences, or through perception of inherent properties of the reward. The reward in oviposition learning of parasitic wasps is a host to parasitize. Different host species can differ in their reward value. This study focused on a specific aspect of reward value, namely host value, i.e. the number and size of emerging offspring, and tested the effect on oviposition learning in parasitic wasps of the genus Nasonia. We conditioned parasitic wasps of the species Nasonia vitripennis and Nasonia giraulti using three different host species as a reward, which differed greatly in their value as a host. However, for both parasitic wasp species, the resulting memory formation was independent of the value of the host. We discuss factors that may be responsible for this observation.
    Identification of quantitative trait loci and a candidate locus for freezing tolerance in controlled and outdoor environments in the overwintering crucifer Boechera stricta.
    Heo, J. ; Feng, D. ; Niu, X. ; Mitchell-Olds, T. ; Tienderen, P.H. van; Tomes, D. ; Schranz, M.E. - \ 2014
    Plant, Cell & Environment 37 (2014)11. - ISSN 0140-7791 - p. 2459 - 2469.
    cold-acclimation - arabidopsis-thaliana - chlorophyll fluorescence - transcription factor - natural variation - frost tolerance - genes - temperature - wheat - expression
    Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of Boechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day (LD), short-day (SD) and in an outdoor environment (OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single- and multi-trait analyses, three main-effect quantitative trait loci (QTL) were identified. QTL on linkage group (LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co-localization of photosynthetic performance and freezing tolerance effects supports these traits being co-regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C-repeat binding factor locus, known regulators of chilling and freezing responses in Arabidopsis thaliana and other species.
    Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis
    He, H. ; Souza Vidigal, D. De; Snoek, L.B. ; Schnabel, S.K. ; Nijveen, H. ; Hilhorst, H. ; Bentsink, L. - \ 2014
    Journal of Experimental Botany 65 (2014)22. - ISSN 0022-0957 - p. 6603 - 6615.
    sativa miller brassicaceae - abscisic-acid biosynthesis - maturation environment - drought tolerance - natural variation - key enzyme - dormancy - germination - thaliana - temperature
    Seed performance after dispersal is highly dependent on parental environmental cues, especially during seed formation and maturation. Here we examine which environmental factors are the most dominant in this respect and whether their effects are dependent on the genotypes under investigation. We studied the influence of light intensity, photoperiod, temperature, nitrate, and phosphate during seed development on five plant attributes and thirteen seed attributes, using 12 Arabidopsis genotypes that have been reported to be affected in seed traits. As expected, the various environments during seed development resulted in changed plant and/or seed performances. Comparative analysis clearly indicated that, overall, temperature plays the most dominant role in both plant and seed performance, whereas light has a prominent impact on plant traits. In comparison to temperature and light, nitrate mildly affected some of the plant and seed traits while phosphate had even less influence on those traits. Moreover, clear genotype-by-environment interactions were identified. This was shown by the fact that individual genotypes responded differentially to the environmental conditions. Low temperature significantly increased seed dormancy and decreased seed longevity of NILDOG1 and cyp707a1-1, whereas low light intensity increased seed dormancy and decreased seed longevity of NILDOG3 and NILDOG6. This also indicates that different genetic and molecular pathways are involved in the plant and seed responses. By identifying environmental conditions that affect the dormancy vs longevity correlation in the same way as previously identified naturally occurring loci, we have identified selective forces that probably shaped evolution for these important seed traits.
    Genotype x environment interaction QTL mapping in plants: lessons from Arabidopsis
    El-Soda, M. ; Malosetti, M. ; Zwaan, B.J. ; Koornneef, M. ; Aarts, M.G.M. - \ 2014
    Trends in Plant Science 19 (2014)6. - ISSN 1360-1385 - p. 390 - 398.
    quantitative trait loci - genome-wide association - adaptive phenotypic plasticity - flowering time - natural variation - mixed-model - missing heritability - drought tolerance - complex traits - life-history
    Plant growth and development are influenced by the genetic composition of the plant (G), the environment (E), and the interaction between them (G × E). To produce suitable genotypes for multiple environments, G × E should be accounted for and assessed in plant-breeding programs. Here, we review the genetic basis of G × E and its consequence for quantitative trait loci (QTL) mapping in biparental and genome-wide association (GWA) mapping populations. We also consider the implications of G × E for understanding plant fitness trade-offs and evolutionary ecology
    A rapid and massive gene expression shift marking adolescent transition in C. elegans
    Snoek, L.B. ; Sterken, M.G. ; Volkers, R.J.M. ; Klatter, M. ; Bosman, K.J. ; Bevers, R.P.J. ; Riksen, J.A.G. ; Smant, G. ; Cossins, A.R. ; Kammenga, J.E. - \ 2014
    Scientific Reports 4 (2014). - ISSN 2045-2322
    caenorhabditis-elegans - natural variation - genome - populations - robustness - diversity - profiles - genotype - project - age
    Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution time series we found that in adolescent worms over 10,000 genes changed their expression. These genes were clustered according to their expression patterns. One cluster involved in chromatin remodelling showed a brief up-regulation around 50 h post-hatch. At the same time a spectacular shift in expression was observed. Sequence comparisons for this cluster across many genotypes revealed diversifying selection. Strongly up-regulated genes showed signs of purifying selection in non-coding regions, indicating that adolescence-active genes are constrained on their regulatory properties. Our findings improve our understanding of adolescent transition and help to eliminate experimental artefacts due to incorrect developmental timing.
    Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population
    Bagheri, H. ; Soda, M. El; Kim, H.K. ; Fritsche, S. ; Jung, C. ; Aarts, M.G.M. - \ 2013
    International Journal of Molecular Sciences 14 (2013)8. - ISSN 1661-6596 - p. 15561 - 15577.
    synechocystis sp pcc-6803 - quantitative trait loci - vitamin-e content - arabidopsis-thaliana - hydroxyphenylpyruvate dioxygenase - tocopherol biosynthesis - plastoquinone synthesis - functional-analysis - natural variation - alpha-tocopherol
    The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs) controlling seed tocopherol and seedling metabolite concentrations. RIL population parent L58 had a higher level of glucosinolates and phenylpropanoids, whereas levels of sucrose, glucose and glutamate were higher in the other RIL population parent, R-o-18. QTL related to seed tocopherol (-, -, -, -, -/- and total tocopherol) concentrations were detected on chromosomes A3, A6, A9 and A10, explaining 11%-35% of the respective variation. The locus on A3 co-locates with the BrVTE1gene, encoding tocopherol cyclase. NMR spectroscopy identified the presence of organic/amino acid, sugar/glucosinolate and aromatic compounds in seedlings. QTL positions were obtained for most of the identified compounds. Compared to previous studies, novel loci were found for glucosinolate concentrations. This work can be used to design markers for marker-assisted selection of nutritional compounds in B. rapa.
    Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley
    Barboza, L. ; Effgen, S. ; Alonso-Blanco, C. ; Kooke, R. ; Keurentjes, J.J.B. ; Koornneef, M. - \ 2013
    Proceedings of the National Academy of Sciences of the United States of America 110 (2013)39. - ISSN 0027-8424 - p. 15818 - 15823.
    quantitative trait loci - gibberellin biosynthesis - natural variation - thaliana - gene - populations - model - polymorphism - association - adaptation
    Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-offunction mutations at GA locus 5 (GA5), which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are found in different populations from southern, western, and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu’s H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes, this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants
    Whole Genome and Tandem Duplicate Retention facilitated Glucosinolate Pathway Diversification in the Mustard Family.
    Hofberger, J.A. ; Lyons, E. ; Edger, P.P. ; Pires, J.C. ; Schranz, M.E. - \ 2013
    Genome Biology and Evolution 5 (2013). - ISSN 1759-6653 - p. 2155 - 2173.
    quantitative trait locus - arabidopsis-thaliana - gene duplication - secondary metabolism - insect resistance - natural variation - provides insight - biosynthesis - evolution - plants
    Plants share a common history of successive whole genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and Tandem Duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the Mustard Family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all Mustard Family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny. The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95 and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared to the 22% average for all protein-coding genes in Arabidopsis, 52 and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. While 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of tandem- and whole genome duplication events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.
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