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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    Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar
    Clifton-Brown, John ; Harfouche, Antoine ; Casler, Michael D. ; Dylan Jones, Huw ; Macalpine, William J. ; Murphy-Bokern, Donal ; Smart, Lawrence B. ; Adler, Anneli ; Ashman, Chris ; Awty-Carroll, Danny ; Bastien, Catherine ; Bopper, Sebastian ; Botnari, Vasile ; Brancourt-Hulmel, Maryse ; Chen, Zhiyong ; Clark, Lindsay V. ; Cosentino, Salvatore ; Dalton, Sue ; Davey, Chris ; Dolstra, Oene ; Donnison, Iain ; Flavell, Richard ; Greef, Joerg ; Hanley, Steve ; Hastings, Astley ; Hertzberg, Magnus ; Hsu, Tsai Wen ; Huang, Lin S. ; Iurato, Antonella ; Jensen, Elaine ; Jin, Xiaoli ; Jørgensen, Uffe ; Kiesel, Andreas ; Kim, Do Soon ; Liu, Jianxiu ; McCalmont, Jon P. ; McMahon, Bernard G. ; Mos, Michal ; Robson, Paul ; Sacks, Erik J. ; Sandu, Anatolii ; Scalici, Giovanni ; Schwarz, Kai ; Scordia, Danilo ; Shafiei, Reza ; Shield, Ian ; Slavov, Gancho ; Stanton, Brian J. ; Swaminathan, Kankshita ; Trindade, Luisa M. - \ 2019
    Global change biology Bioenergy 11 (2019)1. - ISSN 1757-1693 - p. 118 - 151.
    bioenergy - feedstocks - lignocellulose - M. sacchariflorus - M. sinensis - Miscanthus - Panicum virgatum - perennial biomass crop - Populus spp. - Salix spp.

    Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output–input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.

    Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels
    Weijde, Tim van der; Lessa Alvim Kamei, Claire ; Severing, Eduard ; Torres Salvador, Andres Francisco ; Gomez, Leonardo D. ; Dolstra, Oene ; Maliepaard, Chris A. ; McQueen-Mason, Simon J. ; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2017
    BMC Genomics 18 (2017). - ISSN 1471-2164 - 15 p.
    Biofuel - Biomass quality - Cell wall composition - Conversion efficiency - Genetic map - Miscanthus - Quantitative trait loci (QTL) - Saccharification efficiency - Yield

    Background: Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. Results: To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. Conclusion: In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.

    Extending miscanthus cultivation with novel germplasm at six contrasting sites
    Kalinina, Olena ; Nunn, Christopher ; Sanderson, Ruth ; Hastings, Astley F.S. ; Weijde, Tim van der; Özgüven, Mensure ; Tarakanov, Ivan ; Schüle, Heinrich ; Trindade, Luisa M. ; Dolstra, Oene ; Schwarz, Kai Uwe ; Iqbal, Yasir ; Kiesel, Andreas ; Mos, Michal ; Lewandowski, Iris ; Clifton-Brown, John C. - \ 2017
    Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
    Establishment - Marginal land - Miscanthus - Multi-location field trials - Novel hybrids - Productivity

    Miscanthus is a genus of perennial rhizomatous grasses with C4 photosynthesis which is indigenous in a wide geographic range of Asian climates. The sterile clone, Miscanthus × giganteus (M. × giganteus), is a naturally occurring interspecific hybrid that has been used commercially in Europe for biomass production for over a decade. Although, M. × giganteus has many outstanding performance characteristics including high yields and low nutrient offtakes, commercial expansion is limited by cloning rates, slow establishment to a mature yield, frost, and drought resistance. In this paper, we evaluate the performance of 13 novel germplasm types alongside M. × giganteus and horticultural “Goliath” in trials in six sites (in Germany, Russia, The Netherlands, Turkey, UK, and Ukraine). Mean annual yields across all the sites and genotypes increased from 2.3 ± 0.2 t dry matter ha−1 following the first year of growth, to 7.3 ± 0.3, 9.5 ± 0.3, and 10.5 ± 0.2 t dry matter ha−1 following the second, third, and fourth years, respectively. The highest average annual yields across locations and four growth seasons were observed for M. × giganteus (9.9 ± 0.7 t dry matter ha−1) and interspecies hybrid OPM-6 (9.4 ± 0.6 t dry matter ha−1). The best of the new hybrid genotypes yielded similarly to M. × giganteus at most of the locations. Significant effects of the year of growth, location, species, genotype, and interplay between these factors have been observed demonstrating strong genotype × environment interactions. The highest yields were recorded in Ukraine. Time needed for the crop establishment varied depending on climate: in colder climates such as Russia the crop has not achieved its peak yield by the fourth year, whereas in the hot climate of Turkey and under irrigation the yields were already high in the first growing season. We have identified several alternatives to M. × giganteus which have provided stable yields across wide climatic ranges, mostly interspecies hybrids, and also Miscanthus genotypes providing high biomass yields at specific geographic locations. Seed-propagated interspecific and intraspecific hybrids, with high stable yields and cheaper reliable scalable establishment remain a key strategic objective for breeders.

    Stability of cell wall composition and saccharification efficiency in Miscanthus across diverse environments
    Weijde, Tim van der; Dolstra, Oene ; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2017
    Frontiers in Plant Science 7 (2017). - ISSN 1664-462X
    Biomass quality - Ethanol - Genotype-by-environment interaction - GGE biplot - Miscanthus - Multi-location trial - Near-infrared spectroscopy (NIRS) - Stability

    To investigate the potential effects of differences between growth locations on the cell wall composition and saccharification efficiency of the bioenergy crop miscanthus, a diverse set of 15 accessions were evaluated in six locations across Europe for the first 3 years following establishment. High-throughput quantification of cellulose, hemicellulose and lignin contents, as well as cellulose and hemicellulose conversion rates was achieved by combining near-infrared reflectance spectroscopy (NIRS) and biochemical analysis. Prediction models were developed and found to predict biomass quality characteristics with high accuracy. Location significantly affected biomass quality characteristics in all three cultivation years, but location-based differences decreased toward the third year as the plants reached maturity and the effect of location-dependent differences in the rate of establishment reduced. In all locations extensive variation in accession performance was observed for quality traits. The performance of the different accessions in the second and third cultivation year was strongly correlated, while accession performance in the first cultivation year did not correlate well with performance in later years. Significant genotype-by-environment (G × E) interactions were observed for most traits, revealing differences between accessions in environmental sensitivity. Stability analysis of accession performance for calculated ethanol yields suggested that selection for good and stable performance is a viable approach. Environmental influence on biomass quality is substantial and should be taken into account in order to match genotype, location and end-use of miscanthus as a lignocellulose feedstock.

    Impact of drought stress on growth and quality of miscanthus for biofuel production
    Weijde, Tim van der; Huxley, Laurie M. ; Hawkins, Sarah ; Eben Haeser Sembiring, Eben ; Farrar, Kerrie ; Dolstra, Oene ; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2017
    Global change biology Bioenergy 9 (2017)4. - ISSN 1757-1693 - p. 770 - 782.
    Cell wall composition - Cellulose - Drought tolerance - Hemicellulose - Lignin - Miscanthus - Saccharification efficiency
    Miscanthus has a high potential as a biomass feedstock for biofuel production. Drought tolerance is an important breeding goal in miscanthus as water deficit is a common abiotic stress and crop irrigation is in most cases uneconomical. Drought may not only severely reduce biomass yields, but also affect biomass quality for biofuel production as cell wall remodeling is a common plant response to abiotic stresses. The quality and plant weight of 50 diverse miscanthus genotypes were evaluated under control and drought conditions (28 days no water) in a glasshouse experiment. Overall, drought treatment decreased plant weight by 45%. Drought tolerance - as defined by maintenance of plant weight - varied extensively among the tested miscanthus genotypes and ranged from 30% to 110%. Biomass composition was drastically altered due to drought stress, with large reductions in cell wall and cellulose content and a substantial increase in hemicellulosic polysaccharides. Stress had only a small effect on lignin content. Cell wall structural rigidity was also affected by drought conditions; substantially higher cellulose conversion rates were observed upon enzymatic saccharification of drought-treated samples with respect to controls. Both cell wall composition and the extent of cell wall plasticity under drought varied extensively among all genotypes, but only weak correlations were found with the level of drought tolerance, suggesting their independent genetic control. High drought tolerance and biomass quality can thus potentially be advanced simultaneously. The extensive genotypic variation found for most traits in the evaluated miscanthus germplasm provides ample scope for breeding of drought-tolerant varieties that are able to produce substantial yields of high-quality biomass under water deficit conditions. The higher degradability of drought-treated samples makes miscanthus an interesting crop for the production of second-generation biofuels in marginal soils.
    Evaluation of Miscanthus sinensis biomass quality as feedstock for conversion into different bioenergy products
    Weijde, Tim van der; Kiesel, Andreas ; Iqbal, Yasir ; Muylle, Hilde ; Dolstra, Oene ; Visser, Richard G.F. ; Lewandowski, Iris ; Trindade, Luisa M. - \ 2017
    Global change biology Bioenergy 9 (2017)1. - ISSN 1757-1693 - p. 176 - 190.
    Miscanthus sinensis - Anaerobic digestion - Bioethanol - Biogas - Biomass quality - Cell wall composition - Combustion - Enzymatic saccharification - Lignin

    Miscanthus is a promising fiber crop with high potential for sustainable biomass production for a biobased economy. The effect of biomass composition on the processing efficiency of miscanthus biomass for different biorefinery value chains was evaluated, including combustion, anaerobic digestion and enzymatic saccharification for the production of bioethanol. Biomass quality and composition was analyzed in detail using stem and leaf fractions of summer (July) and winter (March) harvested biomass of eight compositionally diverse Miscanthus sinensis genotypes. Genotype performance in tests for enzymatic saccharification, anaerobic digestion and combustion differed extensively. The variation between the best and the worst performing genotype was 18% for biogas yield (ml g-1 dm) and 42% for saccharification efficiency (glucose release as %dm). The ash content of the best performing genotype was 62% lower than that of the genotype with the highest ash content and showed a considerably high ash melting temperature during combustion. Variation between genotypes in biomass quality for the different thermochemical bioconversion processes was shown to be strongly correlated to differences in biomass composition. The most important traits that contributed favorably to biogas yields and saccharification efficiency were a high content of trans-ferulic acid, a high ratio of para-coumaric acid to lignin and a low lignin content. Additionally, a high content of hemicellulosic polysaccharides positively affected saccharification efficiency. Low contents of ash and inorganic elements positively affect biomass quality for combustion and low potassium and chloride contents contributed to a higher ash melting temperature. These results demonstrate the potential for optimizing and exploiting M. sinensis as a multipurpose lignocellulosic feedstock, particularly for bioenergy applications.

    Effects of environmental factors on bruising sensitivity of button mushrooms (Agaricus bisporus)
    Gao, W. ; Baars, J.J.P. ; Dolstra, O. ; Visser, R.G.F. ; Zhang, Jin-Xia ; Sonnenberg, A.S.M. - \ 2016
    Mycosystema = Junwu Xuebao 11 (2016). - ISSN 1672-6472 - p. 1375 - 1386.
    White button mushrooms are fragile and discolor soon after mechanical bruising. This hampers the development of
    mechanical harvesting for button mushrooms and causes loss of postharvest quality. The extent of discoloration can be affected
    by environmental conditions. A factorial design analysis was conducted to screen the effect of factors influencing the bruising
    sensitivity of button mushrooms, and to find out a combination of environmental factors generating the largest variation among
    bruising sensitive and bruising resistant strains. In this way a maximal variation of the trait ‘bruising sensitivity’ can be induced in
    segregating populations intended to map this trait. Three environmental factors were investigated on four genotypes (strains),
    i.e., thickness of the casing layer (2.5cm and 5cm), wetness of casing (dry and normal), and relative humidity in the growing
    room (80% and 87%). Analysis of variance (ANOVA) showed that genotype (strain) was a significant factor influencing bruising
    sensitivity as well as casing thickness. Significant factor interaction effects were observed. The factor combination generating the
    largest difference in bruising sensitivity between the four strains was identified, i.e., a thickness of the casing layer of 5cm,
    normal humidity of the casing, and 87% for relative humidity in the growing room.
    Progress on optimizing miscanthus biomass production for the european bioeconomy : Results of the EU FP7 project OPTIMISC
    Lewandowski, Iris ; Clifton-Brown, John ; Trindade, Luisa M. ; Linden, Gerard C. van der; Schwarz, Kai Uwe ; Müller-Sämann, Karl ; Anisimov, Alexander ; Chen, C.L. ; Dolstra, Oene ; Donnison, Iain S. ; Farrar, Kerrie ; Fonteyne, Simon ; Harding, Graham ; Hastings, Astley ; Huxley, Laurie M. ; Iqbal, Yasir ; Khokhlov, Nikolay ; Kiesel, Andreas ; Lootens, Peter ; Meyer, Heike ; Mos, Michal ; Muylle, Hilde ; Nunn, Chris ; Özgüven, Mensure ; Roldán-Ruiz, Isabel ; Schüle, Heinrich ; Tarakanov, Ivan ; Weijde, Tim van der; Wagner, Moritz ; Xi, Qingguo ; Kalinina, Olena - \ 2016
    Frontiers in Plant Science 7 (2016). - ISSN 1664-462X - 23 p.
    Bioeconomy - Costs - Genotypes - LCA - Marginal land - Miscanthus - Stress tolerance - Value chains

    This paper describes the complete findings of the EU-fundedresearch project OPTIMISC,which investigated methods to optimize the production and use of miscanthus biomass. Miscanthus bioenergy and bioproduct chains were investigated by trialing 15 diverse germplasm types in a range of climatic and soil environments across central Europe,Ukraine,Russia,and China. The abiotic stress tolerances of a wider panel of 100 germplasm types to drought,salinity,and low temperatures were measured in the laboratory and a field trial in Belgium. Asmall selection of germplasmtypes was evaluated for performance in grasslands on marginal sites in Germany and the UK. The growth traits underlying biomass yield and quality were measured to improve regional estimates of feedstock availability. Several potential high-value bioproducts were identified. The combined results provide recommendations to policymakers,growers and industry. The major technical advances in miscanthus production achieved by OPTIMISC include: (1) demonstration that novel hybrids can out-yield the standard commercially grown genotype Miscanthus x giganteus; (2) characterization of the interactions of physiological growth responses with environmental variation within andbetween sites; (3) quantification of biomass-quality-relevant traits; (4) abiotic stress tolerances of miscanthus genotypes; (5) selections suitable for production on marginal land; (6) field establishment methods for seeds using plugs; (7) evaluation of harvesting methods; and (8) quantification of energy used in densification (pellet) technologies with a range of hybrids with differences in stem wall properties. End-user needs were addressed by demonstrating the potential of optimizing miscanthus biomass composition for the production of ethanol and biogas as well as for combustion. The costs and life-cycle assessment of seven miscanthus-based value chains,including small- and large-scale heat and power,ethanol,biogas,and insulation material production,revealed GHG-emission- and fossil-energy-saving potentials of up to 30.6 t CO2eq C ha−1 y−1 and 429 GJ ha−1 y−1 ,respectively. Transport distance was identified as an important cost factor. Negative carbon mitigation costs of –78€−1 CO2eq C were recorded for local biomass use. The OPTIMISC results demonstrate the potential of miscanthus as a crop for marginal sites and provide information and technologies for the commercial implementation of miscanthus-based value chains.

    Supercritical CO2 extraction as an effective pretreatment step for wax extraction in a miscanthus biorefinery
    Attard, Thomas M. ; McElroy, C.R. ; Gammons, Richard J. ; Slattery, John M. ; Supanchaiyamat, Nontipa ; Kamei, Claire Lessa Alvim ; Dolstra, Oene ; Trindade, Luisa M. ; Bruce, Neil C. ; McQueen-Mason, Simon J. ; Shimizu, Seishi ; Hunt, Andrew J. - \ 2016
    ACS sustainable chemistry & engineering 4 (2016)11. - ISSN 2168-0485 - p. 5979 - 5988.
    Carbon dioxide - Extraction - Miscanthus - Saccharification - Supercritical - Waxes

    The use of supercritical carbon dioxide (scCO2) to extract valuable lipophilic compounds from miscanthus was investigated and subsequent enzymatic saccharification was carried out to determine the impact of scCO2 extraction on downstream processing of miscanthus. Two miscanthus genotypes (Miscanthus x. giganteus and Miscanthus sinensis) were investigated and characterized. A diverse range of molecules were detected including long-chain hydrocarbons, fatty acids, n-policosanols, aldehydes, wax esters, sterols and steroid ketones. Quantification data indicates that there is a considerable difference among each species in the quantities of specific compounds. The waxes also exhibited significant differences in melting temperature, thus illustrating the opportunity for utilization in various applications. In addition to the isolation of valuable chemical compounds, the scCO2 pretreatment also had a beneficial effect on the downstream processing of the biomass. The total sugars released after saccharification was found to increase by around 20% when coupled with scCO2 extraction, as compared to untreated samples.

    Maize feedstocks with improved digestibility reduce the costs and environmental impacts of biomass pretreatment and saccharification
    Torres Salvador, A.F. ; Slegers, Ellen ; Noordam-Boot, C.M.M. ; Dolstra, O. ; Vlaswinkel, L. ; Boxtel, A.J.B. van; Visser, R.G.F. ; Trindade, L.M. - \ 2016
    Biotechnology for Biofuels 9 (2016). - ISSN 1754-6834 - 15 p.
    Background - Despite the recognition that feedstock composition influences biomass conversion efficiency, limited information exists as to how bioenergy crops with reduced recalcitrance can improve the economics and sustainability of cellulosic fuel conversion platforms. We have compared the bioenergy potential—estimated as total glucose productivity per hectare (TGP)—of maize cultivars contrasting for cell wall digestibility across processing conditions of increasing thermochemical severity. In addition, exploratory environmental impact and economic modeling were used to assess whether the development of bioenergy feedstocks with improved cell wall digestibility can enhance the environmental performance and reduce the costs of biomass pretreatment and enzymatic conversion.
    Results - Systematic genetic gains in cell wall degradability can lead to significant advances in the productivity (TGP) of cellulosic fuel biorefineries under low severity processing; only if gains in digestibility are not accompanied by substantial yield penalties. For a hypothetical maize genotype combining the best characteristics available in the evaluated cultivar panel, TGP under mild processing conditions (~3.7 t ha−1) matched the highest realizable yields possible at the highest processing severity. Under this scenario, both, the environmental impacts and processing costs for the pretreatment and enzymatic saccharification of maize stover were reduced by 15 %, given lower chemical and heat consumption.
    Conclusions - Genetic improvements in cell wall composition leading to superior cell wall digestibility can be advantageous for cellulosic fuel production, especially if “less severe” processing regimes are favored for further development. Exploratory results indicate potential cost and environmental impact reductions for the pretreatment and enzymatic saccharification of maize feedstocks exhibiting higher cell wall degradability. Conceptually, these results demonstrate that the advance of bioenergy cultivars with improved biomass degradability can enhance the performance of currently available biomass-to-ethanol conversion systems.
    Orphan Crops Browser : a bridge between model and orphan crops
    Kamei, Claire Lessa Alvim ; Severing, E.I. ; Dechesne, Annemarie ; Furrer, Heleen ; Dolstra, Oene ; Trindade, L.M. - \ 2016
    Molecular Breeding 36 (2016)1. - ISSN 1380-3743 - p. 1 - 18.
    Bioinformatics tool - Breeding targets - De novo transcriptome - Orphan crops - Orthologous genes

    Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information. Our goal was to develop a tool that enables molecular breeders, without extensive bioinformatics knowledge, to efficiently study de novo transcriptome data from any orphan crop (http://www.bioinformatics.nl/denovobrowser/db/species/index). The Orphan Crops Browser has been designed to facilitate the following tasks (1) search and identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data from a set of related species and (2) design specific and degenerate primers for expression studies in the orphan crop of interest. To demonstrate the usability and reliability of the browser, it was used to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis. Expression studies in miscanthus stem internode tissue differing in maturation were subsequently carried out, to follow the expression of these genes during lignification. Our results showed a negative correlation between lignin content and gene expression. The present data are in agreement with recent findings in maize and other crops, and it is further discussed in this paper.

    Genetic map construction and QTL analysis of nitrogen use efficiency in spinach (Spinacia oleracea L.)
    Chan Navarrete, Jose Rafael ; Dolstra, Oene ; Kaauwen, Martijn van; Lammerts van Bueren, Edith T. ; Linden, Gerard van der - \ 2016
    Euphytica 208 (2016)3. - ISSN 0014-2336 - p. 621 - 636.
    Genetic map - Nitrogen use efficiency (NUE) - Quantitative trait locus (QTL) - Spinacia oleracea

    Cultivation of spinach requires high amounts of nitrogen (N), which puts a strain on the environment. A sustainable solution to this problem is to breed for crops with higher N use efficiency (NUE). The aim of this study was to provide tools for molecular breeding and to elucidate the genetic variation of factors contributing to NUE in spinach. A cross was made between two F1 hybrid cultivars contrasting in NUE. Several F1 progeny were self-pollinated and based on evaluation of the F2 generation, a mapping F2 population (335 individuals) of a single F1 was selected. SNP markers for the genetic map were discovered by RNA sequencing of the two parent cultivars, and 283 SNP markers were used to produce a genetic map comprising of six linkage groups (P01–P06), ranging in size from 46 to 116 cM. NUE related traits were determined for a set of F2:3 families grown under low and high N conditions in a hydroponics system under an Ingestad N-addition model. Interval mapping analysis detected 39 trait-specific QTLs, with several QTLs accumulating on P01 and P02 of the linkage map. The QTLs and in particular the P01 and P02 regions provide potential targets for the improvement of NUE in spinach.

    Impact of Different Lignin Fractions on Saccharification Efficiency in Diverse Species of the Bioenergy Crop Miscanthus
    Weijde, Tim van der; Torres Salvador, Andres Francisco ; Dolstra, Oene ; Dechesne, Annemarie ; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2016
    Bio Energy Research 9 (2016)1. - ISSN 1939-1234 - p. 146 - 156.
    Acetyl bromide lignin - Acid detergent lignin - Bioenergy - Klason lignin - Miscanthus - Saccharification efficiency

    Lignin is a key factor limiting saccharification of lignocellulosic feedstocks. In this comparative study, various lignin methods—including acetyl bromide lignin (ABL), acid detergent lignin (ADL), Klason lignin (KL), and modified ADL and KL determination methods—were evaluated for their potential to assess saccharification efficiency. Six diverse accessions of the bioenergy crop miscanthus were used for this analysis, which included accessions of Miscanthus sinensis, Miscanthus sacchariflorus, and hybrid species. Accessions showed large variation in lignin content. Lignin estimates were different between methods, but (highly) correlated to each other (0.54 ≤ r ≤ 0.94). The strength of negative correlations to saccharification efficiency following either alkaline or dilute acid pretreatment differed between lignin estimates. The strongest and most consistent correlations (−0.48 ≤ r ≤ −0.85) were obtained with a modified Klason lignin method. This method is suitable for high throughput analysis and was the most effective in detecting differences in lignin content (p <0.001) between accessions.

    Cell Wall Diversity in Forage Maize : Genetic Complexity and Bioenergy Potential
    Torres, A.F. ; Noordam-Boot, C.M.M. ; Dolstra, Oene ; Weijde, Tim van der; Combes, Eliette ; Dufour, Philippe ; Vlaswinkel, Louis ; Visser, R.G.F. ; Trindade, L.M. - \ 2015
    Bio Energy Research 8 (2015)1. - ISSN 1939-1234 - p. 187 - 202.
    Biofuel - Cell wall composition - Maize - Pretreatment - QTL - Saccharification

    Genetic studies are ideal platforms for assessing the extent of genetic diversity, inferring the genetic architecture, and evaluating complex trait interrelations for cell wall compositional and bioconversion traits relevant to bioenergy applications. Through the characterization of a forage maize doubled haploid (DH) population, we indicate the substantial degree of highly heritable (h2 > ~65 %) diversity in cell wall composition and bioconversion potential available within this important agronomic species. In addition to variation in lignin content, extensive genotypic diversity was found for the concentration and composition of hemicelluloses, the latter found to exert an influence on the recalcitrance of maize cell walls. Our results also demonstrate that forage maize harbors considerable variation for the release of cell wall glucose following pretreatment and enzymatic saccharification. In fact, the extent of variability observed for bioconversion efficiency (nearly 30 % between population extremes) greatly exceeded ranges reported in previous studies. In our population, a total of 52 quantitative trait loci (QTL) were detected for biomass compositional and bioconversion characters across 8 chromosomes. Noteworthy, from eight QTL related to bioconversion properties, five were previously unidentified and warrant further investigation. Ultimately, our results substantiate forage maize germplasm as a valid genetic resource for advancing cell wall degradability traits in bioenergy maize-breeding programs. However, since useful variation for cell wall traits is defined by QTL with “minor” effects (R2 = ~10 %), cultivar development for bio-based applications will rely on advanced marker-assisted selection procedures centered on detecting and increasing the frequency of favorable QTL alleles in elite flint and dent germplasm.

    Extent of genotypic variation for maize cell wall bioconversion traits across environments and among hybrid combinations
    Torres, A.F. ; Noordam-Boot, C.M.M. ; Dolstra, O. ; Vlaswinkel, L. ; Visser, R.G.F. ; Trindade, L.M. - \ 2015
    Euphytica 206 (2015)2. - ISSN 0014-2336 - p. 501 - 511.
    The utilization of maize stover as a substrate for bioenergy production demands the development of dual-purpose hybrid varieties combining both, optimal grain yield and improved biomass processing amenability. In this study, our objectives were to assess how contrasting environments influence the expression of cell wall composition and bioconversion traits relevant to cellulosic fuel production, and to study how these traits are inherited in hybrid combinations. To this end, a panel of maize double haploid (DH) lines and their corresponding test-cross (TC) offspring were tested under different locations (primarily in the Netherlands) and characterized for a variety of cell wall compositional and bioconversion features relevant to cellulosic fuel production. Overall, the DH and TC sets displayed extensive genotypic diversity in cell wall composition, polymeric ultrastructure and bioconversion characteristics. Heritability for the different traits was generally high (h 2 > ~0.60); essentially implying that systematic differences between genotypes remained constant across divergent environmental conditions. Moreover, correlations between the performance of DH lines and related TC hybrids were significant and favorable for most investigated traits. Strong associations (r > ~0.50) were especially prominent for cell wall lignin content, degree of substitution of cell wall glucuronoarabinoxylans and cell wall convertibility following pretreatment and enzymatic hydrolysis. In conclusion, complex cell wall bioconversion traits constitute accessible and reliable selection criteria for incorporation in modern breeding programs seeking to advance bio-based maize hybrid varieties. The high heritability and environmental stability of these traits guarantee high selection efficacy during the development of superior DH/inbred material; and their predominantly additive nature prescribe that preliminary selection at the inbred level will guarantee similar correlated genetic gains in hybrid breeding.
    Voorstel voor een co-existentie monitoringsprogramma t.b.v. het naast elkaar bestaan van genetisch gemodificeerde (GG) en niet GG-teelten in toekomstige praktijksituaties. 1. Maïs
    Wiel, C.C.M. van de; Kok, E.J. ; Scholtens, I.M.J. ; Dolstra, O. ; Smulders, M.J.M. ; Lotz, L.A.P. - \ 2015
    Wageningen UR - 33
    akkerbouw - veldgewassen - maïs - genetische modificatie - vermengen - uitkruisen - transgene planten - nederland - arable farming - field crops - maize - genetic engineering - blending - outcrossing - transgenic plants - netherlands
    In het rapport wordt een voorstel voor een concreet co-existentiemonitoringprogramma (CMP) voor maïs beschreven dat is aangepast aan de specifieke gewaseigenschappen van maïs. De gemaakte keuzen t.b.v. een pragmatische invulling van het voorgestelde CMP worden in de opvolgende hoofdstukken toegelicht op basis van de huidige stand van zaken in het wetenschappelijk onderzoek aan (trans)genverspreiding in maïs. Er is nog beperkte ervaring met een CMP in maïs, bijvoorbeeld in Portugal, Tsjechië en Slowakije waar Bt MON810 maïs op beperkte schaal verbouwd wordt. Er is ook geen (Europese) standaard voor een CMP, maar er is wel voor maïs als eerste een Best Practice Document door het European Co-existence Bureau (ECoB) van het JRC uitgebracht (Rizov & Rodríguez-Cerezo 2014).
    Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population
    Gitonga, V.W. ; Koning, C.F.S. ; Verlinden, K. ; Dolstra, O. ; Visser, R.G.F. ; Maliepaard, C.A. ; Krens, F.A. - \ 2014
    BMC Genetics 15 (2014). - ISSN 1471-2156 - 23 p.
    x-chromosome - genome - recombination - qtl - snps - pigs
    Background Global trade has ensured that the ornamental horticulture continues to grow worldwide, with rose hybrids being the most economically important genus (Rosa x hybrida). Due to changes in global trade and an increase in energy costs the ornamental industry has seen a shift in the production and sale of flowers from the US and Europe alone to production in Africa and Latin America. As Kenya is a major exporter of roses to Europe we studied the genetic variation and heritability of specific morphological traits in a tetraploid population grown in the Netherlands and in Kenya. The aim was to estimate genotype by environment interaction (G???E) and to investigate the implications of (G???E) for rose breeding. Results A tetraploid rose population (K5) from a cross between two tetraploid parents was field tested over two seasons in the Netherlands (summer and winter) and two locations in Kenya (Nairobi and Njoro). Ten traits were compared per genotype across the four environments. There were differences in trait association across the four environments showing that the traits were partially influenced by the environment.The traits that had a low ratio of ?2 ge/?2 g also showed a high value for heritability. For the traits number of petals, prickles on petioles, prickles on stems the interaction is minimal. For the traits chlorophyll content, stem width and side shoots we observed a much higher interaction ratio of 0.83, 1.43 and 3.13 respectively. The trait number of petals had the highest heritability of 0.96 and the lowest ?2 ge/?2 g ratio (0.08). The trait number of side shoots (SS) with the lowest heritability (0.40) also had the highest ?2 ge/?2 g ratio of 3.13. Conclusion Results attained by this experiment showed that we have different magnitudes of non-crossover G???E interactions. For the traits number of petals, prickles on stems and prickles on petioles with a low interaction and high heritability, selection can be done at any of the environments. Thus, these traits can be confirmed at the breeding site. For the traits stem width, side shoots and chlorophyll content that had a higher interaction selection for or against these traits should be done at the production location or at least be verified there.
    Genetic diversity of nitrogen use efficiency in spinach (Spinacia oleraces L.) cultivars using the Ingestad model on hydroponics
    Chan-Navarrete, R. ; Kawai, A. ; Dolstra, O. ; Lammerts Van Bueren, E. ; Linden, C.G. van der - \ 2014
    Euphytica 199 (2014)1-2. - ISSN 0014-2336 - p. 155 - 166.
    nitrate accumulation - crop plants - growth - vegetables - nutrition - photosynthesis - leaves - yield - acid - allocation
    Spinach is a leafy vegetable that requires a high N fertilization to have a satisfactory yield and quality, in part because it has poor nitrogen use efficiency (NUE). Therefore, there is a need to breed for cultivars with an excellent NUE. To this end the genetic diversity for NUE-related traits was studied in a diverse set of commercial cultivars. This set was evaluated in a hydroponic system using the Ingestad model; the system was set at a relative growth rate of 0.14 and 0.18 g g-1 day-1 (low and high N, respectively). Experiments were performed at low and high plant density. Traits monitored for single plants included fresh and dry weight, leaf area, specific leaf area, dry weight ratio between root and shoot, and chlorophyll content. The high density experiment showed more genotypic variation for the observed traits than the low density one. Biomass production was considerably lower at low than at high N. Path analysis revealed that leaf area had the highest direct effect on NUE, while specific leaf area was an important trait determining variation in NUE at low N. Slow and fast growing genotypes were shown to use different strategies to utilize N, and these strategies are expressed differently at high and low N availability. This indicates that improving spinach for NUE is feasible using the analysed genotypes as source material, and different strategies can be targeted for adaptation of spinach cultivars to low N conditions.
    Genetic Variation and Combining Ability Analysis of Bruising Sensitivity in Agaricus bisporus
    Gao, W. ; Baars, J.J.P. ; Dolstra, O. ; Visser, R.G.F. ; Sonnenberg, A.S.M. - \ 2013
    PLoS ONE 8 (2013)10. - ISSN 1932-6203
    schizophyllum-commune - growth-rate - inheritance - populations - improvement - mushrooms - selection - yield
    Advanced button mushroom cultivars that are less sensitive to mechanical bruising are required by the mushroom industry, where automated harvesting still cannot be used for the fresh mushroom market. The genetic variation in bruising sensitivity (BS) of Agaricus bisporus was studied through an incomplete set of diallel crosses to get insight in the heritability of BS and the combining ability of the parental lines used and, in this way, to estimate their breeding value. To this end nineteen homokaryotic lines recovered from wild strains and cultivars were inter-crossed in a diallel scheme. Fifty-one successful hybrids were grown under controlled conditions, and the BS of these hybrids was assessed. BS was shown to be a trait with a very high heritability. The results also showed that brown hybrids were generally less sensitive to bruising than white hybrids. The diallel scheme allowed to estimate the general combining ability (GCA) for each homokaryotic parental line and to estimate the specific combining ability (SCA) of each hybrid. The line with the lowest GCA is seen as the most attractive donor for improving resistance to bruising. The line gave rise to hybrids sensitive to bruising having the highest GCA value. The highest negative SCA possibly indicates heterosis effects for resistance to bruising. This study provides a foundation for estimating breeding value of parental lines to further study the genetic factors underlying bruising sensitivity and other quality-related traits, and to select potential parental lines for further heterosis breeding. The approach of studying combining ability in a diallel scheme was used for the first time in button mushroom breeding. Citation: Gao W, Baars JJP, Dolstra O, Visser RGF, Sonnenberg ASM (2013) G
    Association mapping of salt tolerance in barley (Hordeum vulgare L.)
    Nguyen Viet Long, L. ; Dolstra, O. ; Malosetti, M. ; Kilian, B. ; Graner, A. ; Visser, R.G.F. ; Linden, C.G. van der - \ 2013
    Theoretical and Applied Genetics 126 (2013)9. - ISSN 0040-5752 - p. 2335 - 2351.
    genome-wide association - abiotic stress tolerance - quantitative trait loci - linkage disequilibrium - population-structure - salinity stress - expression analysis - ion homeostasis - wild barley - molecular markers
    A spring barley collection of 192 genotypes from a wide geographical range was used to identify quantitative trait loci (QTLs) for salt tolerance traits by means of an association mapping approach using a thousand SNP marker set. Linkage disequilibrium (LD) decay was found with marker distances spanning 2–8 cM depending on the methods used to account for population structure and genetic relatedness between genotypes. The association panel showed large variation for traits that were highly heritable under salt stress, including biomass production, chlorophyll content, plant height, tiller number, leaf senescence and shoot Na+, shoot Cl- and shoot, root Na+/K+ contents. The significant correlations between these traits and salt tolerance (defined as the biomass produced under salt stress relative to the biomass produced under control conditions) indicate that these traits contribute to (components of) salt tolerance. Association mapping was performed using several methods to account for population structure and minimize false-positive associations. This resulted in the identification of a number of genomic regions that strongly influenced salt tolerance and ion homeostasis, with a major QTL controlling salt tolerance on chromosome 6H, and a strong QTL for ion contents on chromosome 4H.
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