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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.

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    Genetic Variability of Morphological, Flowering, and Biomass Quality Traits in Hemp (Cannabis sativa L.)
    Petit, Jordi ; Salentijn, Elma M.J. ; Paulo, Maria João ; Thouminot, Claire ; Dinter, Bert Jan van; Magagnini, Gianmaria ; Gusovius, Hans Jörg ; Tang, Kailei ; Amaducci, Stefano ; Wang, Shaoliang ; Uhrlaub, Birgit ; Müssig, Jörg ; Trindade, Luisa M. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    Cannabis sativa - cell wall composition - fiber quality - flowering time - genetic variability - genotype-by-environment (G×E) interactions - hemp - sex determination

    Hemp (Cannabis sativa L.) is a bast-fiber crop well-known for the great potential to produce sustainable fibers. Nevertheless, hemp fiber quality is a complex trait, and little is known about the phenotypic variability and heritability of fiber quality traits in hemp. The aim of this study is to gain insights into the variability in fiber quality within the hemp germplasm and to estimate the genetic components, environmental components, and genotype-by-environment (G×E) interactions on fiber quality traits in hemp. To investigate these parameters, a panel of 123 hemp accessions was phenotyped for 28 traits relevant to fiber quality at three locations in Europe, corresponding to climates of northern, central, and southern Europe. In general, hemp cultivated in northern latitudes showed a larger plant vigor while earlier flowering was characteristic of plants cultivated in southern latitudes. Extensive variability between accessions was observed for all traits. Most cell wall components (contents of monosaccharides derived from cellulose and hemicellulose; and lignin content), bast fiber content, and flowering traits revealed large genetic components with low G×E interactions and high broad-sense heritability values, making these traits suitable to maximize the genetic gains of fiber quality. In contrast, contents of pectin-related monosaccharides, most agronomic traits, and several fiber traits (fineness and decortication efficiency) showed low genetic components with large G×E interactions affecting the rankings across locations. These results suggest that pectin, agronomic traits, and fiber traits are unsuitable targets in breeding programs of hemp, as their large G×E interactions might lead to unexpected phenotypes in untested locations. Furthermore, all environmental effects on the 28 traits were statistically significant, suggesting a strong adaptive behavior of fiber quality in hemp to specific environments. The high variability in fiber quality observed in the hemp panel, the broad range in heritability, and adaptability among all traits prescribe positive prospects for the development of new hemp cultivars of excellent fiber quality.

    A molecular network for functional versatility of HECATE transcription factors
    Gaillochet, Christophe ; Jamge, Suraj ; Wal, Froukje van der; Angenent, Gerco ; Immink, Richard ; Lohmann, Jan U. - \ 2018
    The Plant Journal 95 (2018)1. - ISSN 0960-7412 - p. 57 - 70.
    Arabidopsis thaliana - flowering time - HECATE - NGATHA - regulatory module - shoot apical meristem - transcription factor

    During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix–loop–helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.

    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.
    Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
    Bargsten, J.W. ; Nap, J.P.H. ; Sanchez Perez, G.F. ; Dijk, A.D.J. van - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229
    genome-wide association - protein function prediction - arabidopsis-thaliana - nucleotide polymorphisms - enrichment analysis - flowering time - complex traits - oryza-sativa - rice - architecture
    Background Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. Results The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. Conclusions Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
    QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population
    Tondelli, A. ; Francia, E. ; Visioni, A. ; Comadran, J. ; Mastrangelo, A.M. ; Akar, T. ; Al-Yassina, A. ; Ceccarelli, S. ; Grando, S. ; Eeuwijk, F.A. van; Thomas, W.T.B. ; Stanca, A.M. ; Romagosa, I. ; Pecchioni, N. - \ 2014
    Euphytica 197 (2014)1. - ISSN 0014-2336 - p. 73 - 86.
    quantitative trait loci - hordeum-vulgare - drought tolerance - agronomic traits - flowering time - abiotic stress - grain-yield - major genes - linkage map - wheat
    Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’
    Inferring the Gene Network Underlying the Branching of Tomato Inflorescence
    Astola, L. ; Stigter, J.D. ; Dijk, A.D.J. van; Daelen, R. van; Molenaar, J. - \ 2014
    PLoS ONE 9 (2014)4. - ISSN 1932-6203 - 7 p.
    flowering time - reproductive structure - regulatory networks - abscission zone - inference - meristem - lycopersicon - falsiflora - jointless
    The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior
    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
    Identification of seed-related QTL in Brassica rapa
    Bagheri, H. ; Pino del Carpio, D. ; Hanhart, C.J. ; Bonnema, A.B. ; Keurentjes, J.J.B. ; Aarts, M.G.M. - \ 2013
    Spanish Journal of Agricultural Research 11 (2013)4. - ISSN 1695-971X - p. 1085 - 1093.
    quantitative trait loci - genetic-linkage map - campestris l - turnip rape - flowering time - oilseed rape - oil content - color - inheritance - napus
    To reveal the genetic variation, and loci involved, for a range of seed-related traits, a new F2 mapping population was developed by crossing Brassica rapa ssp. parachinensis L58 (CaiXin) with B. rapa ssp. trilocularis R-o-18 (spring oil seed), both rapid flowering and self-compatible. A linkage map was constructed using 97 AFLPs and 21 SSRs, covering a map distance of 757 cM with an average resolution of 6.4 cM, and 13 quantitative trait loci (QTL) were detected for nine traits. A strong seed colour QTL (LOD 26) co-localized with QTL for seed size (LOD 7), seed weight (LOD 4.6), seed oil content (LOD 6.6), number of siliques (LOD 3) and number of seeds per silique (LOD 3). There was only a significant positive correlation between seed colour and seed oil content in the yellow coloured classes. Seed coat colour and seed size were controlled by the maternal plant genotype. Plants with more siliques tended to have more, but smaller, seeds and higher seed oil content. Seed colour and seed oil content appeared to be controlled by two closely linked loci in repulsion phase. Thus, it may not always be advantageous to select for yellow-seededness when breeding for high seed oil content in Brassicas.
    Epistatic natural allelic variation reveals a function of AGAMOUS-LIKE6 in axillary bud formation in Arabidopsis
    Huang, X. ; Effgen, S. ; Meyer, R.C. ; Theres, K. ; Koornneef, M. - \ 2012
    The Plant Cell 24 (2012)6. - ISSN 1040-4651 - p. 2364 - 2379.
    mads-box gene - quantitative trait loci - organ-identity proteins - inbred line population - transcription factor - meristem development - ectopic expression - apical dominance - flowering time - complex-formation
    In the Arabidopsis Multiparent Recombinant Inbred Line mapping population, a limited number of plants were detected that lacked axillary buds in most of the axils of the cauline (stem) leaves, but formed such buds in almost all rosette axils. Genetic analysis showed that polymorphisms in at least three loci together constitute this phenotype, which only occurs in late-flowering plants. Early flowering is epistatic to two of these loci, called REDUCED SHOOT BRANCHING1 (RSB1) and RSB2, which themselves do not affect flowering time. Map-based cloning and confirmation by transformation with genes from the region where RSB1 was identified by fine-mapping showed that a specific allele of AGAMOUS-Like6 from accession C24 conferred reduced branching in the cauline leaves. Site-directed mutagenesis in the Columbia allele revealed the causal amino acid substitution, which behaved as dominant negative, as was concluded from a loss-of-function mutation that showed the same phenotype in the late-flowering genetic background. This causal allele occurs at a frequency of 15% in the resequenced Arabidopsis thaliana accessions and correlated with reduced stem branching only in late-flowering accessions. The data show the importance of natural variation and epistatic interactions in revealing gene function
    Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
    Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
    Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
    Predicting the Impact of Alternative Splicing on Plant MADS Domain Protein Function
    Severing, E.I. ; Dijk, A.D.J. van; Morabito, G. ; Busscher-Lange, J. ; Immink, G.H. ; Ham, R.C.H.J. van - \ 2012
    PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 13 p.
    flowering time - box genes - transcription factors - arabidopsis-thaliana - messenger-rna - evolutionary analysis - exon duplication - organ identity - sequence - identification
    Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1–3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins
    Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs
    Malosetti, M. ; Eeuwijk, F.A. van; Boer, M. ; Casas, A. ; Elia, M. ; Bhat, P. ; Ramsay, L. ; Molina-Cano, J.L. - \ 2011
    Theoretical and Applied Genetics 122 (2011)8. - ISSN 0040-5752 - p. 1605 - 1616.
    quantitative trait loci - major genes - environmental covariables - flowering time - dwarfing gene - heading date - line crosses - inbred lines - markers - maize
    Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or kinship information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of markertrait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well. Electronic supplementary material
    Consistent phenological shifts in the making of biodiversity hotspots: the Cape flora.
    Warren, B. ; Bakker, F.T. ; Bellstedt, D.U. ; Bytebier, B. ; Claszen-Bockhoff, R. ; Dreyer, L.L. ; Edwards, A. ; Forest, F. ; Galley, C. ; Hardy, C.R. ; Linder, H.P. ; Muasya, A.M. ; Mummenhoff, K. ; Oberlander, K.C. ; Quint, M. ; Richardson, J.E. ; Savolainen, V. ; Schrire, B.D. ; Niet, T. van der; Verboom, G.A. ; Yesson, C. ; Hawkins, J.A. - \ 2011
    BMC Evolutionary Biology 11 (2011). - ISSN 1471-2148 - 11 p.
    climate-change - southern africa - ecological niches - flowering time - heterogeneous environments - evolutionary responses - adaptive radiation - rapid evolution - fossil record - sequence data
    Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.
    Comparative methods for association studies: a case study on metabolite variation in a Brassica rapa core collection
    Pino del Carpio, D. ; Basnet, R.K. ; Vos, C.H. de; Maliepaard, C.A. ; Paulo, M.J. ; Bonnema, A.B. - \ 2011
    PLoS ONE 6 (2011)5. - ISSN 1932-6203
    multilocus genotype data - genome-wide association - population-structure - random forests - linkage disequilibrium - flowering time - inference - classification - resistance - traits
    Background Association mapping is a statistical approach combining phenotypic traits and genetic diversity in natural populations with the goal of correlating the variation present at phenotypic and allelic levels. It is essential to separate the true effect of genetic variation from other confounding factors, such as adaptation to different uses and geographical locations. The rapid availability of large datasets makes it necessary to explore statistical methods that can be computationally less intensive and more flexible for data exploration. Methodology/Principal Findings A core collection of 168 Brassica rapa accessions of different morphotypes and origins was explored to find genetic association between markers and metabolites: tocopherols, carotenoids, chlorophylls and folate. A widely used linear model with modifications to account for population structure and kinship was followed for association mapping. In addition, a machine learning algorithm called Random Forest (RF) was used as a comparison. Comparison of results across methods resulted in the selection of a set of significant markers as promising candidates for further work. This set of markers associated to the metabolites can potentially be applied for the selection of genotypes with elevated levels of these metabolites. Conclusions/Significance The incorporation of the kinship correction into the association model did not reduce the number of significantly associated markers. However incorporation of the STRUCTURE correction (Q matrix) in the linear regression model greatly reduced the number of significantly associated markers. Additionally, our results demonstrate that RF is an interesting complementary method with added value in association studies in plants, which is illustrated by the overlap in markers identified using RF and a linear mixed model with correction for kinship and population structure. Several markers that were selected in RF and in the models with correction for kinship, but not for population structure, were also identified as QTLs in two bi-parental DH populations.
    Genome-wide computational function prediction of Arabidopsis thaliana proteins by integration of multiple data sources
    Kourmpetis, Y.I.A. ; Dijk, A.D.J. van; Ham, R.C.H.J. van; Braak, C.J.F. ter - \ 2011
    Plant Physiology 155 (2011). - ISSN 0032-0889 - p. 271 - 281.
    generalized linear-models - transcription factor - flowering time - cell-death - thaliana - gene - algorithm - networks - biology - family
    Although Arabidopsis thaliana is the best studied plant species, the biological role of one third of its proteins is still unknown. We developed a probabilistic protein function prediction method that integrates information from sequences, protein-protein interactions and gene expression. The method was applied to proteins from Arabidopsis thaliana. Evaluation of prediction performance showed that our method has improved performance compared to single source-based prediction approaches and two existing integration approaches. An innovative feature of our method is that enables transfer of functional information between proteins that are not directly associated with each other. We provide novel function predictions for 5,807 proteins. Recent experimental studies confirmed several of the predictions. We highlight these in detail for proteins predicted to be involved in flowering and floral organ development.
    Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato
    Li, Li ; Paulo, M.J. ; Eeuwijk, F.A. van; Gebhardt, C. - \ 2010
    Theoretical and Applied Genetics 121 (2010)7. - ISSN 0040-5752 - p. 1303 - 1310.
    sucrose-phosphate synthase - linkage disequilibrium - flowering time - rubisco activase - higher-plants - dna variation - late blight - maize - locus - photosynthesis
    Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q = 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q = 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed
    PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana
    Tessadori, F. ; Zanten, M. van; Pavlova, P. ; Clifton, R. ; Pontvianne, F. ; Snoek, L.B. ; Millenaar, F.F. ; Schulkes, R.K. ; Driel, R. van; Voesenek, L.A.C.J. ; Spillane, C. ; Pikaard, C.S. ; Fransz, P.F. ; Peeters, A.J.M. - \ 2009
    Plos Genetics 5 (2009)9. - ISSN 1553-7404 - 13 p.
    natural allelic variation - inbred line population - dna methylation - flowering time - genome regulation - genetic-variation - circadian clock - linkage map - h3 lysine-9 - heterochromatin
    Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process
    Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa
    Jianjun Zhao, Jianjun ; Jamar, D.C.L. ; Lou, P. ; Wang, Y. ; Wu, J. ; Wang, X. ; Bonnema, A.B. ; Koornneef, M. ; Vreugdenhil, D. - \ 2008
    Plant, Cell & Environment 31 (2008)7. - ISSN 0140-7791 - p. 887 - 900.
    phytic-acid - arabidopsis-thaliana - natural variation - comparative genomics - flowering time - linkage map - phosphorus - sequence - accumulation - resistance
    Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway
    Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves
    Lou, P. ; Jianjun Zhao, Jianjun ; He, Hongju ; Hanhart, C.J. ; Pino del Carpio, D. ; Verkerk, R. ; Custers, J.B.M. ; Koornneef, M. ; Bonnema, A.B. - \ 2008
    New Phytologist 179 (2008)4. - ISSN 0028-646X - p. 1017 - 1032.
    genetic-linkage map - arabidopsis-thaliana - auxin homeostasis - comparative genomics - insect resistance - natural variation - flowering time - biosynthesis - sequence - napus
    Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica rapa. Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F1s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. Both comparative genomic analyses based on Arabidopsis¿Brassica rapa synteny and mapping of candidate orthologous genes in B. rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL
    Applying modelling experiences from the past to shape crop systems biology : the need to converge crop physiology and functional genomics
    Yin, X. ; Struik, P.C. - \ 2008
    New Phytologist 179 (2008)3. - ISSN 0028-646X - p. 629 - 642.
    to-phenotype relationships - quantitative trait loci - in-silico plant - c-3 photosynthesis - genetic-control - flowering time - use efficiency - ecophysiological model - co2 concentrations - increase yield
    Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem
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