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.

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    We will mail you new results for this query: keywords==Plant breeding
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Exploring the treasure of plant molecules with integrated biorefineries
Torres, Andres F. ; Xu, Xuan ; Nikiforidis, Constantinos V. ; Bitter, Johannes H. ; Trindade, Luisa M. - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Biobased economy - Biomass deconstruction - Biorefinery - Cross-disciplinary - Plant breeding - Plant compounds - Process technology

Despite significant progress toward the commercialization of biobased products, today’s biorefineries are far from achieving their intended goal of total biomass valorization and effective product diversification. The problem is conceptual. Modern biorefineries were built around well-optimized, cost-effective chemical synthesis routes, like those used in petroleum refineries for the synthesis of fuels, plastics, and solvents. However, these were designed for the conversion of fossil resources and are far from optimal for the processing of biomass, which has unique chemical characteristics. Accordingly, existing biomass commodities were never intended for modern biorefineries as they were bred to meet the needs of conventional agriculture. In this perspective paper, we propose a new path toward the design of efficient biorefineries, which capitalizes on a cross-disciplinary synergy between plant, physical, and catalysis science. In our view, the best opportunity to advance profitable and sustainable biorefineries requires the parallel development of novel feedstocks, conversion protocols and synthesis routes specifically tailored for total biomass valorization. Above all, we believe that plant biologists and process technologists can jointly explore the natural diversity of plants to synchronously develop both, biobased crops with designer chemistries and compatible conversion protocols that enable maximal biomass valorization with minimum input utilization. By building biorefineries from the bottom-up (i.e., starting with the crop), the envisioned partnership promises to develop cost-effective, biomass-dedicated routes which can be effectively scaled-up to deliver profitable and resource-use efficient biorefineries.

Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour
Alves, Mara Lisa ; Carbas, Bruna ; Gaspar, Daniel ; Paulo, Manuel ; Brites, Cláudia ; Mendes-Moreira, Pedro ; Brites, Carla Moita ; Malosetti, Marcos ; Eeuwijk, Fred Van; Vaz Patto, Maria Carlota - \ 2019
BMC Plant Biology 19 (2019)1. - ISSN 1471-2229
Bread - Candidate genes - Nutritional quality - Pasting behavior - Plant breeding - Portuguese maize germplasm - Zea mays L.

Background: Maize is a crop in high demand for food purposes and consumers worldwide are increasingly concerned with food quality. However, breeding for improved quality is a complex task and therefore developing tools to select for better quality products is of great importance. Kernel composition, flour pasting behavior, and flour particle size have been previously identified as crucial for maize-based food quality. In this work we carried out a genome-wide association study to identify genomic regions controlling compositional and pasting properties of maize wholemeal flour. Results: A collection of 132 diverse inbred lines, with a considerable representation of the food used Portuguese unique germplasm, was trialed during two seasons, and harvested samples characterized for main compositional traits, flour pasting parameters and mean particle size. The collection was genotyped with the MaizeSNP50 array. SNP-trait associations were tested using a mixed linear model accounting for genetic relatedness. Fifty-seven genomic regions were identified, associated with the 11 different quality-related traits evaluated. Regions controlling multiple traits were detected and potential candidate genes identified. As an example, for two viscosity parameters that reflect the capacity of the starch to absorb water and swell, the strongest common associated region was located near the dull endosperm 1 gene that encodes a starch synthase and is determinant on the starch endosperm structure in maize. Conclusions: This study allowed for identifying relevant regions on the maize genome affecting maize kernel composition and flour pasting behavior, candidate genes for the majority of the quality-associated genomic regions, or the most promising target regions to develop molecular tools to increase efficacy and efficiency of quality traits selection (such as "breadability") within maize breeding programs.

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding
Eeuwijk, Fred A. van; Bustos-Korts, Daniela ; Millet, Emilie J. ; Boer, Martin P. ; Kruijer, Willem ; Thompson, Addie ; Malosetti, Marcos ; Iwata, Hiroyoshi ; Quiroz, Roberto ; Kuppe, Christian ; Muller, Onno ; Blazakis, Konstantinos N. ; Yu, Kang ; Tardieu, Francois ; Chapman, Scott C. - \ 2019
Plant Science 282 (2019). - ISSN 0168-9452 - p. 23 - 39.
Crop growth model - Genomic prediction - Genotype-by-environment-interaction - Genotype-to-phenotype model - Mixed model - Multi-environment model - Multi-trait model - Phenotyping - Phenotyping platform - Physiology - Plant breeding - Prediction - Reaction norm - Response surface - Statistical genetics

New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.

Plant breeding and diversity : A troubled relationship?
Louwaars, Niels P. - \ 2018
Euphytica 214 (2018)7. - ISSN 0014-2336
Biodiversity policy - Diversity bottleneck - Genetic diversity - Genetic resources - Multiline - Nagoya Protocol - Participatory plant breeding - Plant breeding - Seed regulations - Trait breeding

Plant breeding collects, induces and rearranges genetic diversity followed by selection. Breeding may contribute to diversity in farmers’ fields or significantly reduce it. History has numerous examples of both. The diversity of many crops have gone through domestication, dispersal and modernization bottlenecks. Between these major decreasing processes, diversity has picked up through different evolutionary processes, and plant breeding affected by policies. Major negative effects of plant breeding on diversity have been recorded following the modernization bottleneck, but alternative breeding strategies have come up as well, both in the formal system and in the interphase between formal and farmers’ seed systems. Multiline breeding and participatory plant breeding are introduced as examples to also analyse effects of current developments in technology and policy. This paper intends to shed some light on the questions: how will current developments in technology and policy affect crop genetic diversity? Are we heading for a new bottleneck—either a molecular or a policy bottleneck, or a combination of both? Or could the future become more diverse? We look at the relationship between breeding, policies, and crop genetic diversity in farming systems with a birds-eye view. Notably because of current policy trends we warn for a new diversity bottleneck.

QTLTableMiner++: Semantic mining of QTL tables in scientific articles
Singh, Gurnoor ; Kuzniar, Arnold ; Mulligen, Erik M. van; Gavai, Anand ; Bachem, Christian W. ; Visser, Richard G.F. ; Finkers, Richard - \ 2018
BMC Bioinformatics 19 (2018). - ISSN 1471-2105
Ontologies - Plant breeding - QTL - Quantitative trait locus - Semantic interoperability - Table mining
Background: A quantitative trait locus (QTL) is a genomic region that correlates with a phenotype. Most of the experimental information about QTL mapping studies is described in tables of scientific publications. Traditional text mining techniques aim to extract information from unstructured text rather than from tables. We present QTLTableMiner++ (QTM), a table mining tool that extracts and semantically annotates QTL information buried in (heterogeneous) tables of plant science literature. QTM is a command line tool written in the Java programming language. This tool takes scientific articles from the Europe PMC repository as input, extracts QTL tables using keyword matching and ontology-based concept identification. The tables are further normalized using rules derived from table properties such as captions, column headers and table footers. Furthermore, table columns are classified into three categories namely column descriptors, properties and values based on column headers and data types of cell entries. Abbreviations found in the tables are expanded using the Schwartz and Hearst algorithm. Finally, the content of QTL tables is semantically enriched with domain-specific ontologies (e.g. Crop Ontology, Plant Ontology and Trait Ontology) using the Apache Solr search platform and the results are stored in a relational database and a text file. Results: The performance of the QTM tool was assessed by precision and recall based on the information retrieved from two manually annotated corpora of open access articles, i.e. QTL mapping studies in tomato (Solanum lycopersicum) and in potato (S. tuberosum). In summary, QTM detected QTL statements in tomato with 74.53% precision and 92.56% recall and in potato with 82.82% precision and 98.94% recall. Conclusion: QTM is a unique tool that aids in providing QTL information in machine-readable and semantically interoperable formats.
Food processing and breeding strategies for coeliac-safe and healthy wheat products
Jouanin, Aurélie ; Gilissen, Luud J.W.J. ; Boyd, Lesley A. ; Cockram, James ; Leigh, Fiona J. ; Wallington, Emma J. ; Broeck, Hetty C. van den; Meer, Ingrid M. van der; Schaart, Jan G. ; Visser, Richard G.F. ; Smulders, Rene - \ 2018
Food Research International 110 (2018). - ISSN 0963-9969 - p. 11 - 21.
Coeliac disease - Food processing - Genome editing - Gliadin - Gluten - Mutation breeding - Plant breeding - T cell epitope
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.
Genomic prediction within and across biparental families : Means and variances of prediction accuracy and usefulness of deterministic equations
Schopp, Pascal ; Müller, Dominik ; Wientjes, Yvonne C.J. ; Melchinger, Albrecht E. - \ 2017
G3 : Genes Genomes Genetics 7 (2017)11. - ISSN 2160-1836 - p. 3571 - 3586.
Biparental families - GBLUP deterministic accuracy - Genomic prediction - Genomic selection - Genpred shared data resources - Linkage disequilibrium - Plant breeding
A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zea mays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines. We analyzed PA within each BPF for 50 simulated polygenic traits, using genomic best linear unbiased prediction (GBLUP) models trained with individuals from either full-sib (FSF), half-sib (HSF), or unrelated families (URF) for various sizes (Ntrain) of the training set and different heritabilities (h2). In addition, we modified two deterministic equations for forecasting PA to account for inbreeding and genetic variance unexplained by the training set. Averaged across traits, PA was high within FSF (0.41-0.97) with large variation only for Ntrain, 50 and h2 <0:6: For HSF and URF, PA was on average ~40-60% lower and varied substantially among different combinations of BPFs used for model training and prediction as well as different traits. As exemplified by HSF results, PA of across-family GP can be very low if causal variants not segregating in the training set account for a sizeable proportion of the genetic variance among predicted individuals. Deterministic equations accurately forecast the PA expected over many traits, yet cannot capture trait-specific deviations. We conclude that model training within BPFs generally yields stable PA, whereas a high level of uncertainty is encountered in across-family GP. Our study shows the extent of variation in PA that must be at least reckoned with in practice and offers a starting point for the design of training sets composed of multiple BPFs.
Concepts and strategies of organic plant breeding in light of novel breeding techniques
Nuijten, Edwin ; Messmer, Monika M. ; Lammerts van Bueren, Edith - \ 2017
Sustainability 9 (2017)1. - ISSN 2071-1050
Alternative techniques - Future perspectives - Guiding principles - Organic farming - Plant breeding

In this paper, we describe the development of a set of guiding principles for the evaluation of breeding techniques by the organic sector over time. The worldwide standards of organic agriculture (OA) do not allow genetic engineering (GE) or any products derived from genetic engineering. The standards in OA are an expression of the underlying principles of health, ecology, fairness and care. The derived norms are process and not product oriented. As breeding is considered part of the process in agriculture, GE is not a neutral tool for the organic sector. The incompatibility between OA and GE is analyzed, including the "novel breeding techniques". Instead, alternative breeding approaches are pursued based on the norms and values of organic agriculture not only on the technical level but also on the social and organizational level by including other value chain players and consumers. The status and future perspectives of the alternative directions for organic breeding are described and discussed.

Functional characterization of the powdery mildew susceptibility gene SmMLO1 in eggplant (Solanum melongena L.)
Bracuto, Valentina ; Appiano, Michela ; Ricciardi, Luigi ; Göl, Deniz ; Visser, Richard G.F. ; Bai, Yuling ; Pavan, Stefano - \ 2017
Transgenic Research 26 (2017)3. - ISSN 0962-8819 - p. 323 - 330.
Eggplant - MLO - Plant breeding - Powdery mildew - Resistance
Eggplant (Solanum melongena L.) is one of the most important vegetables among the Solanaceae and can be a host to fungal species causing powdery mildew (PM) disease. Specific homologs of the plant Mildew Locus O (MLO) gene family are PM susceptibility factors, as their loss of function results in a recessive form of resistance known as mlo resistance. In a previous work, we isolated the eggplant MLO homolog SmMLO1. SmMLO1 is closely related to MLO susceptibility genes characterized in other plant species. However, it displays a peculiar non-synonymous substitution that leads to a T → M amino acid change at protein position 422, in correspondence of the MLO calmodulin-binding domain. In this study, we performed the functional characterization of SmMLO1. Transgenic overexpression of SmMLO1 in a tomato mlo mutant compromised resistance to the tomato PM pathogen Oidium neolycopersici, thus indicating that SmMLO1 is a PM susceptibility factor in eggplant. PM susceptibility was also restored by the transgenic expression of a synthetic gene, named s-SmMLO1, encoding a protein identical to SmMLO1, except for the presence of T at position 422. This indicates that the T → M polymorphism does not affect the protein role as PM susceptibility factor. Overall, the results of this work are of interest for the functional characterization of MLO proteins and the introduction of PM resistance in eggplant using reverse genetics.
Rationalization of genes for resistance to Bremia lactucae in lettuce
Parra, Lorena ; Maisonneuve, Brigitte ; Lebeda, Ales ; Schut, Johan ; Christopoulou, Marilena ; Jeuken, Marieke ; McHale, Leah ; Truco, Maria Jose ; Crute, Ian ; Michelmore, Richard - \ 2016
Euphytica 210 (2016)3. - ISSN 0014-2336 - p. 309 - 326.
Dm gene - Lactuca spp. - Lettuce downy mildew - Plant breeding - Quantitative trait locus - Resistance genes

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce worldwide. Breeding for resistance to this disease is a major priority for most lettuce breeding programs. Many genes and factors for resistance to B. lactucae have been reported by multiple researchers over the past ~50 years. Their nomenclature has not been coordinated, resulting in duplications and gaps in nominations. We have reviewed the available information and rationalized it into 51 resistance genes and factors and 15 quantitative trait loci along with supporting documentation as well as genetic and molecular information. This involved multiple rounds of consultation with many of the original authors. This paper provides the foundation for naming additional genes for resistance to B. lactucae in the future as well as for deploying genes to provide more durable resistance.

Domestication selected for deceleration of the circadian clock in cultivated tomato
Müller, Niels A. ; Wijnen, Cris L. ; Srinivasan, Arunkumar ; Ryngajllo, M. ; Ofner, I. ; Lin, Tao ; Ranjan, Aashish ; West, Donelly ; Maloof, J.N. ; Sinha, Neelima R. ; Huang, Sanwen ; Zamir, Dani ; Jimenez-Gomez, J.M. - \ 2016
Nature Genetics 48 (2016). - ISSN 1061-4036 - p. 89 - 93.
Plant breeding - Plant genetics - Transcriptomics
The circadian clock is a critical regulator of plant physiology and development, controlling key agricultural traits in crop plants1. In addition, natural variation in circadian rhythms is important for local adaptation2, 3, 4. However, quantitative modulation of circadian rhythms due to artificial selection has not yet been reported. Here we show that the circadian clock of cultivated tomato (Solanum lycopersicum) has slowed during domestication. Allelic variation of the tomato homolog of the Arabidopsis gene EID1 is responsible for a phase delay. Notably, the genomic region harboring EID1 shows signatures of a selective sweep. We find that the EID1 allele in cultivated tomatoes enhances plant performance specifically under long day photoperiods, suggesting that humans selected slower circadian rhythms to adapt the cultivated species to the long summer days it encountered as it was moved away from the equator.
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
Bassil, N.V. ; Davis, T.M. ; Zhang, Hailong ; Ficklin, Stephen ; Mittmann, Mike ; Webster, Teresa ; Mahoney, Lise ; Wood, David ; Alperin, E.S. ; Rosyara, U.R. ; Koehorst-vanc Putten, Herma ; Monfort, Amparo ; Sargent, D.J. ; Amaya, Iraida ; Denoyes, Beatrice ; Bianco, Luca ; Dijk, Thijs van; Pirani, Ali ; Iezzoni, Amy ; Main, Dorrie ; Peace, Cameron ; Yang, Yilong ; Whitaker, Vance ; Verma, Sujeet ; Bellon, Laurent ; Brew, Fiona ; Herrera, Raul ; Weg, Eric van de - \ 2015
BMC Genomics 16 (2015)1. - ISSN 1471-2164
Fragaria - Genotyping array - Plant breeding - Polyploidy - Reduced ploidy - Single nucleotide polymorphism - Strawberry

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. Results: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. Conclusions: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

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