references.bib

@article{Mendel1866,
  author        = {Mendel, Gregor},
  title         = {Experiments in Plant Hybridization (English translation)},
  journal       = {Verhandlungen des Naturforschenden Vereines in Br{\"u}nn},
  year          = {1866},
  volume        = {4},
  pages         = {3--47},
  original-date = {1866},
  note          = {Translation based on Druery and Bateson (1901)},
  howpublished  = {\url{http://www.esp.org/foundations/genetics/classical/gm-65.pdf}},
  language      = {English}
}

@ARTICLE{Komatsu2024,
  title     = "{CoRRE} Trait Data: A dataset of 17 categorical and continuous
               traits for 4079 grassland species worldwide",
  author    = "Komatsu, Kimberly J and Avolio, Meghan L and Padullés Cubino,
               Josep and Schrodt, Franziska and Auge, Harald and Cavender-Bares,
               Jeannine and Clark, Adam T and Flores-Moreno, Habacuc and Grman,
               Emily and Harpole, W Stanley and Kattge, Jens and Kimmel, Kaitlin
               and Koerner, Sally E and Korell, Lotte and Langley, J Adam and
               Münkemüller, Tamara and Ohlert, Timothy and Onstein, Renske E and
               Roscher, Christiane and Soudzilovskaia, Nadejda A and Taylor,
               Benton N and Tedersoo, Leho and Terry, Rosalie S and Wilcox,
               Kevin",
  journal   = "Scientific Data",
  publisher = "Springer Science and Business Media LLC",
  volume    =  11,
  number    =  1,
  pages     =  795,
  abstract  = "In our changing world, understanding plant community responses to
               global change drivers is critical for predicting future ecosystem
               composition and function. Plant functional traits promise to be a
               key predictive tool for many ecosystems, including grasslands;
               however, their use requires both complete plant community and
               functional trait data. Yet, representation of these data in
               global databases is sparse, particularly beyond a handful of most
               used traits and common species. Here we present the CoRRE Trait
               Data, spanning 17 traits (9 categorical, 8 continuous)
               anticipated to predict species' responses to global change for
               4,079 vascular plant species across 173 plant families present in
               390 grassland experiments from around the world. The dataset
               contains complete categorical trait records for all 4,079 plant
               species obtained from a comprehensive literature search, as well
               as nearly complete coverage (99.97\%) of imputed continuous trait
               values for a subset of 2,927 plant species. These data will shed
               light on mechanisms underlying population, community, and
               ecosystem responses to global change in grasslands worldwide.",
  month     =  jul,
  year      =  2024,
  doi       = "10.1038/s41597-024-03637-x",
  pmc       = "PMC11258227",
  pmid      =  39025901,
  issn      = "2052-4463,2052-4463",
  language  = "en"
}

@article{alonso2016,
  title={1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana},
  author={Alonso-Blanco, Carlos and Andrade, Jorge and Becker, Claude and Bemm, Felix and Bergelson, Joy and Borgwardt, Karsten M and Cao, Jun and Chae, Eunyoung and Dezwaan, Todd M and Ding, Wei and others},
  journal={Cell},
  volume={166},
  number={2},
  pages={481--491},
  year={2016},
  publisher={Elsevier}
}

@article{korte2013,
  title={The advantages and limitations of trait analysis with GWAS: a review},
  author={Korte, Arthur and Farlow, Ashley},
  journal={Plant methods},
  volume={9},
  number={1},
  pages={29},
  year={2013},
  publisher={Springer}
}


@Manual{statgengwas,
  title = {statgenGWAS: Genome Wide Association Studies},
  author = {Bart-Jan {van Rossum} and Willem Kruijer},
  year = {2025},
  note = {R package version 1.0.12},
  url = {https://biometris.github.io/statgenGWAS/index.html},
}

@article{Warmerdam2018,
   author = {Warmerdam, S. and Sterken, M.G. and Van Schaik, C. and Lozano-Torres, J. and Dicke, M. and Kammenga, J.E. and Goverse, A. and Bakker, J. and Smant, G.},
   title = {Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana},
   journal = {New Phytol},
   volume = {218},
   number = {2},
   pages = {724-737},
   note = {Warmerdam, Sonja
Sterken, Mark G
van Schaik, Casper
Oortwijn, Marian E P
Sukarta, Octavina C A
Lozano-Torres, Jose L
Dicke, Marcel
Helder, Johannes
Kammenga, Jan E
Goverse, Aska
Bakker, Jaap
Smant, Geert
eng
Research Support, Non-U.S. Gov't
England
2018/02/23
New Phytol. 2018 Apr;218(2):724-737. doi: 10.1111/nph.15034. Epub 2018 Feb 22.},
   abstract = {Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F-box family protein may function as (co-)regulators of susceptibility to M. incognita in Arabidopsis. Our data suggest that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.},
   keywords = {Animals
Arabidopsis/*genetics/*parasitology
*Chromosome Mapping
Chromosomes, Plant/genetics
Gene Expression Regulation, Plant
*Genetic Predisposition to Disease
*Genome-Wide Association Study
Mutation/genetics
Plant Diseases/genetics/*parasitology
Plant Roots/genetics/*parasitology
Polymorphism, Single Nucleotide/genetics
Quantitative Trait Loci/genetics
Reproduction
Tylenchoidea/*physiology
Arabidopsis thaliana
Meloidogyne incognita
F-box protein
allelic variation
brassinosteroid signalling
genome-wide association
susceptibility},
   ISSN = {1469-8137 (Electronic)
0028-646X (Print)
0028-646X (Linking)},
   DOI = {10.1111/nph.15034},
   url = {https://www.ncbi.nlm.nih.gov/pubmed/29468687},
   year = {2018},
   type = {Journal Article}
}

@article{Jones2013,
author = {Jones, John T. and Haegeman, Annelies and Danchin, Etienne G. J. and Gaur, Hari S. and Helder, Johannes and Jones, Michael G. K. and Kikuchi, Taisei and Manzanilla-López, Rosa and Palomares-Rius, Juan E. and Wesemael, Wim M. L. and Perry, Roland N.},
title = {Top 10 plant-parasitic nematodes in molecular plant pathology},
journal = {Molecular Plant Pathology},
volume = {14},
number = {9},
pages = {946-961},
doi = {https://doi.org/10.1111/mpp.12057},
url = {https://bsppjournals.onlinelibrary.wiley.com/doi/abs/10.1111/mpp.12057},
eprint = {https://bsppjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/mpp.12057},
abstract = {Summary The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a ‘top 10’ list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.},
year = {2013}
}

@article{Willig2023,
    author = {Willig, J. and Sonneveld, D. and Van Steenbrugge, J.J.M. and Deurhof, L. and Van Schaik, C.C. and Teklu, M.G. and Goverse, A. and Lozano-Torres, J.L. and Smant, G. and Sterken, M.G.},
    title = "{From root to shoot; Quantifying nematode tolerance in Arabidopsis thaliana by high-throughput phenotyping of plant development}",
    journal = {Journal of Experimental Botany},
    pages = {erad266},
    year = {2023},
    month = {07},
    abstract = "{Nematode migration, feeding site formation, withdrawal of plant assimilates, and activation of plant defence responses have a significant impact on plant growth and development. Plants display intraspecific variation in tolerance limits for root-feeding nematodes. Although disease tolerance has been recognised as a distinct trait in biotic interactions of mainly crops, we lack mechanistic insights. Progress is hampered by difficulties in quantification and laborious screening methods. We turned to the model plant Arabidopsis thaliana, since it offers extensive resources to study the molecular and cellular mechanisms underlying nematode-plant interactions. Through imaging of tolerance-related parameters the green canopy area was identified as an accessible and robust measure for assessing damage due to cyst nematode infection. Subsequently, a high-throughput phenotyping platform simultaneously measuring the green canopy area growth of 960 A. thaliana plants was developed. This platform can accurately measure cyst- and root-knot nematode tolerance limits in A. thaliana through classical modelling of tolerance limits. Furthermore, real-time monitoring provided data for a novel view of tolerance, identifying a compensatory growth response. These findings show that our phenotyping platform will enable further studies into a mechanistic understanding of tolerance to below-ground biotic stress.}",
    issn = {0022-0957},
    doi = {10.1093/jxb/erad266},
    url = {https://doi.org/10.1093/jxb/erad266},
    eprint = {https://academic.oup.com/jxb/advance-article-pdf/doi/10.1093/jxb/erad266/50854660/erad266.pdf},
}

@article{Schaveling2026,
author = {Schaveling, A.S. and Te Molder, D.M. and Heeres, P. and Van Steenbrugge, J.J.M. and Van de Ruitenbeek, S.J.S. and Van Schaik, C.C. and Van den Elsen, S. and Smant, G. and Sterken, M.G.},
title = {The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus},
journal = {New Phytologist},
volume = {n/a},
number = {n/a},
pages = {},
keywords = {effector, Globodera pallida, GpaVvrn, potato, resistance, standing variation, virulence},
doi = {https://doi.org/10.1111/nph.70886},
url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.70886},
eprint = {https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70886},
abstract = {Summary Globodera pallida poses a major threat to potato production, with management strategies primarily relying on genetic resistance. However, increasing virulence in field populations across Western Europe raises major concerns for G. pallida control. To investigate the evolutionary mechanisms driving this rise in virulence, we propagated 13 field populations on 30 commercial potato varieties. Our findings indicate that the genetic basis of resistance in potatoes is small, with the major resistance conferred by GpaV from Solanum vernei. The wide application of GpaVvrn has led to continuous selection on standing genetic variation in G. pallida. To map virulence, we propagated two field populations on a GpaVvrn-resistant variety for five generations. High-coverage whole-genome sequencing of each generation revealed that GpaVvrn-mediated selection acted on a single locus of a newly assembled G. pallida Rookmaker reference genome. Examination of this virulence-associated locus identified Gp-pat-1 as a candidate gene. Silencing Gp-pat-1 increased virulence on a GpaVvrn-resistant variety but had no effect on nematode virulence on a susceptible variety, classifying Gp-pat-1 as an avirulence gene. Our findings show that GpaVvrn-mediated negative selection on Gp-pat-1 is driving the emergence of virulence and improves our understanding of resistance breakdown and the evolutionary dynamics of nematode adaptation in the field.}
}

@article {Schaveling2025,
author = {Schaveling, A.S. and Van Rijt, L. and Do, Y. and Soffree, N. and Langendoen, D. and Room, H. and Bertran, A.M. and Raven, M. and Van Kessel, S.P. and Van Heese, E.Y.J. and Van de Ruitenbeek, S.J.S. and van Schaik, C.C. and Kiewnick, S. and Smant, G. and Sterken, M.G.},
title = {Globodera pallida virulence on major potato resistance has a common genetic basis across Western Europe},
elocation-id = {2025.12.22.695896},
year = {2025},
doi = {10.64898/2025.12.22.695896},
publisher = {Cold Spring Harbor Laboratory},
abstract = {The potato cyst nematode Globodera pallida poses a major threat to potato production in Western Europe. Current management strategies largely depend on the use of potato varieties carrying the genetic resistance GpaVvrn. However, reports from multiple West-European countries indicate a steady rise in virulence against GpaVvrn-containing potato varieties, raising serious concerns about G. pallida control. Although recent studies have resolved the genetic basis of virulence in two Dutch G. pallida populations, it remains unclear how conserved this genetic adaptation is in populations from different regions. To investigate this, we first selected eight Dutch G. pallida populations on the GpaVvrn-containing potato variety Seresta and confirmed a previously identified virulence locus. Second, by analysing the allele frequencies of four virulence-associated SNPs in Dutch, British, and French GpaVvrn-selected G. pallida populations, we found that the same allele is consistently selected by GpaVvrn across Western Europe. Third, we analysed the propagation of eight G. pallida populations on 26 GpaVvrn-containing potato varieties and showed that a population{\textquoteright}s allele frequency of a single SNP (T173N) accurately reflects its reproduction on GpaVvrn. Fourth, we developed an allele-specific quantitative PCR (AS-qPCR) assay to determine a population{\textquoteright}s alternative allele frequency (AAF) of T173N and showed that AS-qPCR-based AAFs reliably indicate virulence levels on GpaVvrn in Dutch and German G. pallida populations. Together, these findings suggest that a common allele is consistently selected by GpaVvrn in populations from different regions across Western Europe. The AS-qPCR assay developed in this study provides a practical tool to estimate G. pallida virulence on GpaVvrn in the field, enabling field-tailored and sustainable resistance management strategies for farmers.Competing Interest StatementThis research was executed as part of a public/private partnership project funded by the Dutch government including co-financing from several public and private organisations. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. After the AS-qPCR results were unblinded, one of the private partners involved in the validation, HLB, began considering offering the assay as a service to growers.Dutch Ministry of Agriculture, Nature and Food Quality and Topsector T\&U, KV1604-022/TU-16004, LWV22225/TU202202Dutch Research Council, https://ror.org/04jsz6e67, 17282, 21240German agency for renewable resources, FKZ 2222NR093B},
URL = {https://www.biorxiv.org/content/early/2025/12/23/2025.12.22.695896},
eprint = {https://www.biorxiv.org/content/early/2025/12/23/2025.12.22.695896.full.pdf},
journal = {bioRxiv}
}

@article{Yanai2020,
  title={A hypothesis is a liability},
  author={Yanai, Itai and Lercher, Martin},
  journal={Genome biology},
  volume={21},
  number={1},
  pages={231},
  year={2020},
  publisher={Springer},
  doi={10.1186/s13059-020-02133-w}
}

@article{Yanai2019,
  title={Night science},
  author={Yanai, Itai and Lercher, Martin},
  journal={Genome Biology},
  volume={20},
  number={1},
  pages={179},
  year={2019},
  publisher={Springer},
  doi={10.1186/s13059-019-1800-6}
}

@article{Felin2021,
  title={The data-hypothesis relationship},
  author={Felin, Teppo and Koenderink, Jan and Krueger, Joachim I and Noble, Denis and Ellis, George FR},
  journal={Genome Biology},
  volume={22},
  number={1},
  pages={57},
  year={2021},
  publisher={Springer},
  doi={10.1186/s13059-021-02276-4}
}

@BOOK{Wickham2019,
  title     = "Advanced {R}",
  author    = "Wickham, Hadley",
  publisher = "Chapman and Hall/CRC",
  month     =  may,
  year      =  2019,
  doi       = "10.1201/9781351201315",
  isbn      =  9781351201315
}

@ARTICLE{Baggerly2009,
  title         = "Deriving chemosensitivity from cell lines: Forensic
                   bioinformatics and reproducible research in high-throughput
                   biology",
  author        = "Baggerly, Keith A and Coombes, Kevin R",
  journal       = "The Annals of Applied Statistics",
  number        =  4,
  pages         = "1309--1334",
  abstract      = "High-throughput biological assays such as microarrays let us
                   ask very detailed questions about how diseases operate, and
                   promise to let us personalize therapy. Data processing,
                   however, is often not described well enough to allow for
                   exact reproduction of the results, leading to exercises in
                   ``forensic bioinformatics'' where aspects of raw data and
                   reported results are used to infer what methods must have
                   been employed. Unfortunately, poor documentation can shift
                   from an inconvenience to an active danger when it obscures
                   not just methods but errors. In this report we examine
                   several related papers purporting to use microarray-based
                   signatures of drug sensitivity derived from cell lines to
                   predict patient response. Patients in clinical trials are
                   currently being allocated to treatment arms on the basis of
                   these results. However, we show in five case studies that the
                   results incorporate several simple errors that may be putting
                   patients at risk. One theme that emerges is that the most
                   common errors are simple (e.g., row or column offsets);
                   conversely, it is our experience that the most simple errors
                   are common. We then discuss steps we are taking to avoid such
                   errors in our own investigations.",
  month         =  dec,
  year          =  2009,
  archivePrefix = "arXiv",
  eprint        = "1010.1092",
  eprintclass   = "stat.AP"
}

@ARTICLE{Benedetti2018,
  title     = "Biomass from microalgae: the potential of domestication towards
               sustainable biofactories",
  author    = "Benedetti, Manuel and Vecchi, Valeria and Barera, Simone and
               Dall'Osto, Luca",
  journal   = "Microbial Cell Factories",
  publisher = "Springer Science and Business Media LLC",
  volume    =  17,
  number    =  1,
  pages     =  173,
  abstract  = "Interest in bulk biomass from microalgae, for the extraction of
               high-value nutraceuticals, bio-products, animal feed and as a
               source of renewable fuels, is high. Advantages of microalgal vs.
               plant biomass production include higher yield, use of non-arable
               land, recovery of nutrients from wastewater, efficient carbon
               capture and faster development of new domesticated strains.
               Moreover, adaptation to a wide range of environmental conditions
               evolved a great genetic diversity within this polyphyletic group,
               making microalgae a rich source of interesting and useful
               metabolites. Microalgae have the potential to satisfy many global
               demands; however, realization of this potential requires a
               decrease of the current production costs. Average productivity of
               the most common industrial strains is far lower than maximal
               theoretical estimations, suggesting that identification of
               factors limiting biomass yield and removing bottlenecks are
               pivotal in domestication strategies aimed to make algal-derived
               bio-products profitable on the industrial scale. In particular,
               the light-to-biomass conversion efficiency represents a major
               constraint to finally fill the gap between theoretical and
               industrial productivity. In this respect, recent results suggest
               that significant yield enhancement is feasible. Full realization
               of this potential requires further advances in cultivation
               techniques, together with genetic manipulation of both algal
               physiology and metabolic networks, to maximize the efficiency
               with which solar energy is converted into biomass and
               bio-products. In this review, we draft the molecular events of
               photosynthesis which regulate the conversion of light into
               biomass, and discuss how these can be targeted to enhance
               productivity through mutagenesis, strain selection or genetic
               engineering. We outline major successes reached, and promising
               strategies to achieving significant contributions to future
               microalgae-based biotechnology.",
  month     =  nov,
  year      =  2018,
  keywords  = "Bio-based products; Biomass; Light-use efficiency; Microalgae;
               Molecular genetic; Photobioreactor; Photosynthesis; Strain
               domestication",
  doi       = "10.1186/s12934-018-1019-3",
  pmc       = "PMC6230293",
  pmid      =  30414618,
  issn      = "1475-2859",
  language  = "en"
}