Herman J van Eck

Wageningen University, Wageningen, Gelderland, Netherlands

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Publications (77)281.52 Total impact

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    ABSTRACT: Key message: A 20K SNP array was developed and a comprehensive set of tetraploid cultivar was genotyped. This allowed us to identify footprints of the breeding history in contemporary breeding material such as identification of introgression segments, selection and founder signatures. A non-redundant subset of 15,138 previously identified SNPs and 4454 SNPs originating from the SolCAP project were combined into a 20k Infinium SNP array for genotyping a total of 569 potato genotypes. In this study we describe how this SNP array (encoded SolSTW array) was designed and analysed with fitTetra, software designed for autotetraploids. Genotypes from different countries and market segments, complemented with historic cultivars and important progenitors, were genotyped. This comprehensive set of genotypes combined with the deliberate inclusion of a large proportion of SNPs with a low minor allele frequency allowed us to distinguish genetic variation contributed by introgression breeding. This "new" (post 1945) genetic variation is located on specific chromosomal regions and enables the identification of SNP markers linked to R-genes. In addition, when the genetic composition of modern cultivars was compared with cultivars released before 1945, it appears that 96 % of the genetic variants present in those ancestral cultivars remains polymorphic in modern cultivars. Hence, genetic erosion is almost absent in potato. Finally, we studied population genetic processes shaping the genetic composition of the modern European potato including drift, selection and founder effects. This resulted in the identification of major founders contributing to contemporary germplasm.
    Full-text · Article · Aug 2015 · Theoretical and Applied Genetics
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    ABSTRACT: Background In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned. Results For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1–3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5. Conclusions Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1578-1) contains supplementary material, which is available to authorized users.
    Full-text · Article · May 2015 · BMC Genomics
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    ABSTRACT: This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.
    Full-text · Article · Dec 2014 · Potato Research
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    ABSTRACT: One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.
    No preview · Article · Aug 2014 · Molecular Genetics and Genomics
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    ABSTRACT: Key message Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Abstract Two association mapping panels were analysed for marker–trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
    No preview · Article · Jan 2014 · Theoretical and Applied Genetics
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    Full-text · Dataset · Jun 2013
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    Muhammad Sohail Khan · Herman J. van Eck · Paul C. Struik
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    ABSTRACT: The objective of this paper is to evaluate the performance of the conventional system of classifying maturity type in potato and to provide a concept of maturity type based on crop physiology. We present an approach in which physiological traits are used to quantify and assess maturity type unam- biguously for a set of varieties covering a wide range of maturity classes and a diploid F1 population separating for maturity and well-adapted to Dutch grow- ing conditions, both grown in six environments. We defined physiological maturity based on four traits: the duration of maximum green canopy, the area under the green canopy cover progress curve, and the rate and duration of tuber bulking. The results indicated that physiological maturity type criteria tended to define maturity classes less ambiguously than the conventional criterion. Moreover, the conventional criterion was subject to more random noise and lacked stability and/or repeatability compared with the physiological traits. The physiological maturity criteria also illustrated the physiological trade-offs that existed between the selected traits and underlined the subtle complexities in classifying maturity type. This study highlighted the capabilities of different maturity type criteria in discriminating between different maturity classes among the large set of genotypes. Our new approach involving key physiological traits could be beneficial in offering physiology-based criteria to re-define maturity type. An improved criterion based on important physiological traits would allow relating the maturity to crop phenology and physiology. These new criteria may be amenable to further genetic analysis and could help in designing strategies for potato ideotype breeding for genotypes with specific maturity types.
    Full-text · Article · Jun 2013 · European Potato Journal
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    ABSTRACT: Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1-3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60-80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
    Full-text · Article · May 2013 · PLoS ONE
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    ABSTRACT: Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.
    Full-text · Article · Mar 2013 · Nature
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    ABSTRACT: After the publication of the article 'A hybrid BAC physical map of potato: a framework forsequencing a heterozygous genome [BMC Genomics 2011, 12:594]' the submitting authorwas notified that the contributions of LWP and LdL were quite substantial. To properly showtheir contribution to the manuscript, they have been taken out of the acknowlegdementssection and are now added to the authors list. LWP performed the BAC AFLP fingerprinting.LdL performed BAC pool AFLP reactions and BAC pool AFLP fingerprinting. Also, thesubmitting author was notified that patents and patent applications for technologies used inthis publication should have been included in the acknowledgements section. Therefore, thisarticle presents corrections to authors list, to the authors' contributions section, and to theacknowledgements section. Also, we declare the existence competing interests. We apologizefor any inconveniences these omissions may have caused.
    Full-text · Article · Aug 2012 · BMC Genomics
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    ABSTRACT: List of AFLP anchor points. A list of AFLP marker anchor locations in BACs of the AFLP physical map.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Figure S2. Example of the integration of the AFLP and WGP physical maps of potato. Contigs from the WGP physical map (red frames above) are matched with contigs from the AFLP physical map (blue frames below) on the basis of BAC clones that are present in both maps, as partially indicated by green connecting lines. AFLP contig #37 is connecting the four WGP contigs, and WGP contig #3076 connects the two AFLP contigs. Clone order is largely the same in both maps, but small deviations can be noticed. Parts of AFLP contig #37 are anchored to the two different haplotypes of chromosome 12 by AFLP markers that are in repulsion in the genetic map: blue squares indicate clones anchored to genetic haplotype {0} and pink squares mark clones from genetic haplotype {1}.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Integrated hybrid AFLP and WGP physical map. A table with all BACs incorporated in the potato AFLP and WGP physical maps, with their FPC contig numbers and contig alignment coordinates. Includes the contig group numbers of the hybrid physical map, which show the overlaps between contigs of both physical maps.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
    Full-text · Article · Dec 2011 · BMC Genomics
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    ABSTRACT: AFLP marker size conversions. list of AFLP marker mobilities in radioactive mapping gels versus capillary BAC fingerprint gels.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Additional AFLP marker information. Full names and genetic map information of AFLP markers in the AFLP physical map.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Figure S1. Example of BAC alignment with WGP sequence tags in the WGP physical map. Pseudo mobility values (ID numbers) were assigned to the 46 sequence tags of clone RH003F10 (left), which was then aligned into WGP physical map contig #3520 (right) on the basis of shared sequence tags with overlapping BAC clones. The consensus band map (CB map) shows the position of the sequence tags (red box) of BAC RH003F10 (highlighted in blue) relative to the neighboring clones. Plus signs indicate in which BAC clones the tags are present. On the basis of the BAC overlaps, a partial ordering of the sequence tags has taken place across the contig and a sequence scaffold is created that can be used for alignment of genomic sequences.
    Preview · Dataset · Dec 2011
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    ABSTRACT: Background / Purpose: Polyploid species, such as the autotetraploid crop potato, can have four highly diverse genomes, and a large number of highly diverse haplotypes can be found across the gene pool. Main conclusion: Our results demonstrate that in-solution hybridization enrichment of indexed polyploid DNA samples is a viable and cost-effective approach for performing large-scale resequencing and genotyping studies using high-throughput sequencing technologies. This approach: captured 95% of the 800 target gene sequences identified DNA variants at a high accuracy detected individual zygosity (allele copy-number) for 83 potato cultivars
    Full-text · Conference Paper · Oct 2011
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    ABSTRACT: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
    Full-text · Article · Jul 2011 · Nature
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    ABSTRACT: Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect, analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006, one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18years. Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced. The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients of trait variation were highly correlated (r = 0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be used in a genome-wide association study. Issues related to data management and definition of traits are discussed. KeywordsGenotype-by-environment interaction–Heritabilities–Mixed models–Potato
    Full-text · Article · Jun 2011 · Potato Research

Publication Stats

3k Citations
281.52 Total Impact Points

Institutions

  • 1995-2015
    • Wageningen University
      • • Department of Nematology
      • • Department of Plant Breeding
      Wageningen, Gelderland, Netherlands
  • 2013
    • Wageningen UR
      • Department of Plant Sciences
      Wageningen, Gelderland, Netherlands
  • 2008
    • University of California, Davis
      • Department of Plant Sciences
      Davis, California, United States