Marinus J M Smulders

Marinus J M Smulders
Wageningen University & Research | WUR · Department of Plant Breeding

PhD (Nijmegen)

About

324
Publications
120,667
Reads
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Introduction
M J M (René) Smulders currently works at Plant Breeding, Wageningen University & Research. He does research on the opportunities of new plant breeding techniques, on developing tools for genetic mapping in polyploid crops including rose, and on how to make wheat varieties that are safe for people with coeliac disease.
Additional affiliations
April 2003 - present
Wageningen University & Research
Position
  • Business unit manager
January 2000 - December 2005
Plant Research International
Position
  • Research Group leader Identity and Genetic Diversity
September 1984 - May 1989
Radboud University
Position
  • PhD Student

Publications

Publications (324)
Article
Full-text available
Gene editing has the potential to make new crop varieties faster and more efficiently. New and more suitable crop varieties can increase sustainable agriculture, for instance, in the form of disease-resistant varieties that facilitate integrated pest management. The European Commission's proposal on the regulation of gene-edited and cisgenic plants...
Article
Full-text available
Most wild rose species in the Netherlands belong to Rosa section Caninae (dogroses), with Rosa arvensis (section Synstylae) and Rosa spinosissima (section Pimpinellifoliae) as other indigenous species. All species are rare, often found in small populations or as scattered individuals, except for Rosa canina and Rosa corymbifera. Conservation strate...
Article
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Plants edited with new genomic techniques (NGTs) currently fall under the Genetically Modified Organisms Directive (2001/18/EC) in the European Union. In the proposal of the European Commission, NGT plants are partially exempted from the regulations of this directive. The proposal makes a distinction between two categories of NGT plants: NGT-1 and...
Chapter
Full-text available
By using gene editing technologies such as CRISPR/Cas, precise modifications can be made in the genome. CRISPR/Cas is especially valuable for targeted mutagenesis in polyploids, as it can induce mutations of multiple alleles simultaneously, to obtain regenerants that are homozygous for the desired mutation. A range of gene-edited traits have been d...
Article
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While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with v...
Technical Report
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Advances in biotechnology in recent decades have led to the development of new genomic techniques (NGTs). In 2021, the Study on the status of new genomic techniques under Union law and in light of the Court of Justice ruling in Case C-528/16 was published, as requested by the Council of the European Union (Council Decision (EU) 2019/1904). The stud...
Article
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Quantitative trait locus (QTL) analysis allows to identify regions responsible for a trait and to associate alleles with their effect on phenotypes. When using biallelic markers to find these QTL regions, two alleles per QTL are modelled. This assumption might be close to reality in specific biparental crosses but is unrealistic in situations where...
Article
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Intercropping is both a well-established and yet novel agricultural practice, depending on one’s perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, s...
Article
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Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The...
Chapter
Cereal consumption by humans is older than agriculture. During preceding eras, humans gradually acquired the necessary knowledge and tools for processing and cultivation of cereals, making themselves unconsciously prepared to become the first farmers when climate improved at the end of the last Ice Age, some 12 thousand years ago, in the Near East...
Article
Full-text available
Motivation: The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher p...
Article
Full-text available
Plant breeding aims to develop improved crop varieties. Many crops have a polyploid and often highly heterozygous genome, which may make breeding of polyploid crops a real challenge. The efficiency of traditional breeding based on crossing and selection has been improved by using marker-assisted selection (MAS), and MAS is also being applied in pol...
Article
Full-text available
Key message Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Abstract Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenh...
Article
Full-text available
Key message In polyploids, linkage mapping is carried out using genotyping with discrete dosage scores. Here, we use probabilistic genotypes and we validate it for the construction of polyploid linkage maps. Abstract Marker genotypes are generally called as discrete values: homozygous versus heterozygous in the case of diploids, or an integer alle...
Article
Full-text available
The Netherlands’ field genebank collection of European wild apple ( Malus sylvestris ), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide p...
Preprint
Full-text available
Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The...
Preprint
Full-text available
Motivation The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher plo...
Article
Full-text available
Breeding innovations are relevant for sustainable agricultural development and food security, as new, resilient production systems require crop varieties optimally suited for these systems. In the societal debate around genetic engineering and other plant breeding innovations, ownership of patents on the technology used in the hands of large compan...
Preprint
Full-text available
Marker genotypes are generally called as discrete values: homozygous versus heterozygous in the case of diploids, or an integer allele dosage in the case of polyploids. Software for linkage map construction and/or QTL analysis usually relies on such discrete genotypes. However, it may not always be possible, or desirable, to assign definite values...
Article
Full-text available
Main conclusion Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Abstract Oil palm produces a quarter of the world’s total vegetable oil. In line with its...
Article
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On August 12, 2020, the U.S. Food and Drug Administration (FDA) has finalized a rule related to gluten-free labeling for foods containing fermented, hydrolyzed ingredients. The FDA believes that there is no scientifically valid analytical method effective for determining gluten in fermented or hydrolyzed foods. In the absence of an analytical metho...
Chapter
Consuming cereals, including wheat, is much older than agriculture. Wheat selection, cultivation, and processing gradually developed in prehistorical times. The wheat species einkorn, emmer, and spelt wheat remained major human staples until the last century when durum wheat for pasta products, and especially bread wheat oust the ancient grains fro...
Article
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Most alpha‐gliadin genes of the Gli‐D2 locus on the D genome of hexaploid bread wheat (Triticum aestivum) encode for proteins with epitopes that can trigger coeliac disease (CD), and several contain a 33‐mer peptide with six partly overlapping copies of three epitopes, which is regarded as a remarkably potent T cell stimulator. To increase genetic...
Article
Thanks to advances in next generation sequencing it is now straightforward to develop tens or even hundreds of thousands of SNP markers. Advances in genotyping technology have made it feasible to genotype progenies of crosses, panels of genotypes, or even a complete breeding program, by using arrays with tens of thousands of SNPs, or by random or t...
Article
Full-text available
Ingestion of gluten proteins (gliadins and glutenins) from wheat, barley and rye can cause coeliac disease (CD) in genetically predisposed individuals. The only remedy is a strict and lifelong gluten-free diet. There is a growing desire for coeliac-safe, whole-grain wheat-based products, as consumption of whole-grain foods reduces the risk of chron...
Article
Full-text available
Celiac disease (CD) affects a growing number of individuals worldwide. To elucidate the causes for this increase, future multidisciplinary collaboration is key to understanding the interactions between immunoreactive components in gluten-containing cereals and the human gastrointestinal tract and immune system and to devise strategies for CD preven...
Article
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We discuss whether genetic engineering and agroecology are compatible. For this, we investigated three cases of genetically engineered crops and considered agroecology as scientific discipline as well as a social movement. One case was the use of cisgenic modifications to make potato durably resistant to late blight, the second was the use of CRISP...
Article
Full-text available
Targeted and random mutagenesis of gene families require accurate quantification. Droplet digital PCR (ddPCR) enables high-throughput screening of copy number variation (CNV). We tested the accuracy of ddPCR for CNV analysis in the large α-gliadin gene family, using degenerate primers. First, duplex ddPCR assays measured α-gliadins in diploid (15–1...
Article
Full-text available
Background Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1–2% of the human population. Wheat varieties or accessions containing only safe gluten have not been identified and conventional breeding alone struggles to achieve such a goal, as the epitopes occur in gluten proteins encoded by fiv...
Article
Full-text available
The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and s...
Article
Full-text available
p>We developed an in-solution gluten exome capture system called GlutEnSeq (Gluten gene Enrichment and Sequencing), covering the sequence variation of thousands of prolamin genes from various Triticeae species and cultivars. We assessed the efficacy of this capture system in hexaploid wheat (Triticum aestivum L.) using Illumina sequencing. On-targe...
Article
Thanks to recent advances in high-throughput genotyping tools and software for genetic analyses, it is now possible to perform QTL mapping and genome-wide association analysis in tetraploid roses and to establish the effect of favorable SNP marker haplotype(s) (“plus-alleles”). The challenge is how to use these tools and technologies for rose breed...
Article
Full-text available
Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for...
Chapter
Full-text available
New plant breeding techniques such as CRISPR/Cas have the potential to improve sustainability in agriculture. Genome editing techniques can increase yields while reducing the use of pesticides. Researchers around the world are working on improving the nutritional value of plants. However, whether the new technologies will be used in Europe is uncer...
Article
Full-text available
Coeliac Disease (CD) is an auto-immune reaction to gluten in 1–2% of the human population. A gluten-free (GF) diet, excluding wheat, barley, and rye, is the only remedy. This diet is difficult to adhere to, partly because wheat gluten is added to many processed products for their viscoelastic properties. In addition, GF products are less healthy an...
Article
Full-text available
In the original publication of the article, Li et al. has been incorrectly cited in the following sentence “Interestingly, a complex trait par excellence, yield, was also shown to be amenable to an SDN-1 approach. Li et al. (2017) used CRISPR-Cas9 in rice to mutate the regulatory genes Gna1, DEP1, and GS3 and obtained plants with increased grain nu...
Article
Full-text available
The application of Good Agricultural Practice (GAP) contributes to many aspects of sustainable farming, including integrated control of weeds, diseases, and pests, and optimization of fertilization and irrigation. It is a relatively neglected issue in debates regarding the application of new technology, such as genetic modification (GM), which ofte...
Article
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Background: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across...
Chapter
In ornamental crops the development of genetic and molecular tools for breeding has been slow because of the large number of ornamental species, many of which are genetically complicated for breeding, being outbreeding crops, polyploid, and/or having a large genome. This is changing due to three recent developments: (i) next-generation sequencing c...
Article
Full-text available
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doub...
Article
Full-text available
Motivation: Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping...
Preprint
Full-text available
Rose is the world’s most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were ( i ) to develop the first high-quality reference genome sequence fo...
Preprint
Full-text available
Motivation Polyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping pl...
Article
Full-text available
During the 20th century, the economic position of oats (Avena sativa L.) decreased strongly in favour of higher yielding crops including winter wheat and maize. Presently, oat represents only ∼. 1.3% of the total world grain production, and its production system is fragmented. Nonetheless, current interest is growing because of recent knowledge on...
Article
Full-text available
Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differen...
Article
Full-text available
Sensitivity to lodging of oat varieties has been reduced in the last decades through the introduction of dwarfing genes. However, lodging may still cause significant yield loss, underscoring the need for new oat varieties with higher levels of lodging tolerance. In the present study, we analysed lodging and plant height in a collection of European...
Article
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...
Article
Full-text available
Key message: Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA...
Article
One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs...
Article
Full-text available
It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term "segmental allopolyploid" to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns....
Article
Full-text available
http://european-seed.com/genome-editing-new-plant-breeding-technique-opportunities-challenges/
Article
Full-text available
Persian walnut (Juglans regia L.) is the world’s most widely grown nut crop, but large-scale assessments and comparisons of the genetic diversity of the crop are notably lacking. To guide the conservation and utilization of Persian walnut genetic resources, genotypes (n = 189) from 25 different regions in 14 countries on three continents were sampl...
Article
Full-text available
(Open Access) Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include o300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array...
Article
Full-text available
Key message: Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with mi...
Article
Full-text available
The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented su...
Article
Boswellia papyrifera is used to produce frankincense, a bark resin that has been a commodity of domestic and international trade since ancient times. It is harvested from natural forests. The tropical dry forest (Terminalia-Combretum) woodland ecosystems in which B. papyrifera is one of the dominant species, are facing anthropogenic threats. In Eth...
Article
Various new plant breeding technique (NPBT) approaches have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here we review the opportunities of products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic...
Chapter
Full-text available
Cereals are among the oldest foods of humans. Wheat is one of these. In present times,several syndromes are, whether true or false, increasingly attributed to the consumption of wheat, with increasing costs for medical care and decreasing turnover for the food industry, especially the bakery sector. Many western societies show remarkable annual inc...
Article
Full-text available
The use of oats in the human diet has decreased over the past 70 years. This is an unfortunate development from the perspective of human health because oats have a high nutritional value and contain many compounds, including β-glucan, polyphenols, vitamins, and unsaturated fatty acids that are able to maintain or may even improve consumer’s health....
Technical Report
Full-text available
Prospects of New Plant Breeding Techniques in crops Plant breeding has resulted in numerous high-quality food, feed, ornamental and industrial crop varieties that are cultivated nowadays. Although traditional breeding based on the steps of crossing and selection remains an ongoing activity for crop improvement, it faces limitations as many crops h...