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21. Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population

Author

Keurentjes, Joost J.B., Bentsink, Leonie, Alonso-Blanco, Carlos, Hanhart, Corrie J., Blankestijn-De Vries, Hetty, Effgen, Sigi, Vreugdenhil, Dick, and Koornneef, Maarten

Subjects
Arabidopsis thaliana -- Genetic aspects, Quantitative trait loci -- Research, Chromosome mapping -- Methods, Biological sciences
Abstract

In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.

Published
2007

22. New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci

Author

El-Lithy, Mohamed E., Bentsink, Leonie, Hanhart, Corrie J., Ruys, Gerda J., Rovito, Daniela, Broekhof, Jose L.M., van der Poel, Hein J.A., van Eijk, Michiel J.T., Vreugdenhil, Dick, and Koornneef, Maarten

Subjects
Arabidopsis -- Research, Quantitative trait loci -- Research, Biological sciences
Abstract

The SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Let as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Lerhas an allele different from one, two, or three of the other accessions.

Published
2006

24. Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landsberg erecta and Shakdara, using a new recombinant inbred line population (1)

Author

Clerkx, Emile J.M., El-Lithy, Mohamed E., Vierling, Elizabeth, Ruys, Gerda J., Blankestijn-De Vries, Hetty, Groot, Steven P.C., Vreugdenhil, Dick, and Koornneef, Maarten

Subjects
Quantitative trait loci -- Usage, Germination -- Research, Arabidopsis -- Genetic aspects, Arabidopsis -- Growth, Company growth, Biological sciences, Science and technology
Published
2004

33. Preface

Author

Vreugdenhil, Dick, primary, Bradshaw, John, additional, Gebhardt, Christiane, additional, Govers, Francine, additional, MacKerron, Donald K.L., additional, Taylor, Mark A., additional, and Ross, Heather A., additional

Published
2007
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34. List of contributors

Author

Allen, Eric J., primary, Börnke, Frederik A.J., additional, Bradshaw, John E., additional, Bryan, Glen J., additional, Bucher, Marcel, additional, Conner, A.J., additional, De Boer, Solke H., additional, De Temmerman, Ludwig, additional, Donnelly, Danielle J., additional, Firman, David M., additional, Gavrilenko, Tatjana, additional, Gebhardt, Christiane, additional, Govers, Francine, additional, Hammond, John P., additional, Hannapel, David J., additional, Haverkort, Anton J., additional, Hofius, Daniel, additional, Jacobs, Mirjam M.J., additional, Jansky, Shelley H., additional, Kirkman, Michael A., additional, Kossmann, Jens, additional, Lagnaoui, Abdelaziz, additional, Lulai, Edward C., additional, MacKerron, D.K.L., additional, Marshall, Bruce, additional, McDougall, Gordon J., additional, McGregor, Iain, additional, Millam, Steve, additional, Mugniéry, Didier, additional, Patel, R.M., additional, Phillips, Mark S., additional, Prasher, S.O., additional, Radcliffe, Edward B., additional, Ross, Heather A., additional, Sharma, Sanjeev Kumar, additional, Simko, Ivan, additional, Sowokinos, Joe R., additional, Spooner, David M., additional, Stephenson, Sarah A., additional, Stewart, Derek, additional, Storey, Michael, additional, Struik, Paul C., additional, Suttle, Jeffrey C., additional, Taylor, Mark A., additional, Termorshuizen, Aad J., additional, Valkonen, Jari P.T., additional, van den Berg, Ronald G., additional, van der Wolf, Jan M., additional, van Eck, Herman J., additional, van Loon, Cees D., additional, Vandermeiren, Karine, additional, van Oijen, Marcel, additional, Vos, Jan, additional, Vreugdenhil, Dick, additional, Wheatley, Ron E., additional, White, Philip J., additional, and Zhang, Kefeng, additional

Published
2007
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37. Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping

Author

Thoen, Manus P M, Davila Olivas, Nelson H., Kloth, Karen J., Coolen, Silvia, Huang, Ping Ping, Aarts, Mark G M, Bac-Molenaar, Johanna A., Bakker, Jaap, Bouwmeester, Harro J., Broekgaarden, Colette, Bucher, Johan, Busscher-Lange, Jacqueline, Cheng, Xi, Fradin, Emilie F., Jongsma, Maarten A., Julkowska, Magdalena M., Keurentjes, Joost J B, Ligterink, Wilco, Pieterse, Corné M J, Ruyter-Spira, Carolien, Smant, Geert, Testerink, Christa, Usadel, Björn, van Loon, Joop J A, van Pelt, Johan A., van Schaik, Casper C., van Wees, Saskia C M, Visser, Richard G F, Voorrips, Roeland, Vosman, Ben, Vreugdenhil, Dick, Warmerdam, Sonja, Wiegers, Gerrie L., van Heerwaarden, Joost, Kruijer, Willem, van Eeuwijk, Fred A., Dicke, Marcel, Sub Plant-Microbe Interactions, Dynamics of Innovation Systems, Sub Plant-Microbe Interactions, Dynamics of Innovation Systems, Plant Hormone Biology (SILS, FNWI), Plant Cell Biology (SILS, FNWI), and Plant Physiology (SILS, FNWI)

Subjects
0106 biological sciences, 0301 basic medicine, genome‐wide association mapping, Physiology, Arabidopsis, Inheritance Patterns, Genome-wide association study, Plant Science, 01 natural sciences, Wiskundige en Statistische Methoden - Biometris, Laboratorium voor Plantenveredeling, Plant Growth Regulators, Laboratorium voor Plantenfysiologie, Laboratory of Entomology, PBR Groei & Ontwikkeling, Abiotic component, Genetics, PBR Kwantitatieve aspecten, Full Paper, Entomology & Disease Management, Chromosome Mapping, food and beverages, Full Papers, PBR Breeding for growth and development, PE&RC, Phenotype, ddc:580, Biometris, Plant Production Systems, BIOS Applied Metabolic Systems, Laboratory of Plant Physiology, DNA, Bacterial, PBR Non host and insect resistance, abiotic stress, genome-wide association mapping, Quantitative Trait Loci, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Genes, Plant, PBR Quantitative aspects of Plant Breeding, 03 medical and health sciences, biotic stress, Stress, Physiological, Groep Koornneef, BIOS Plant Development Systems, Mathematical and Statistical Methods - Biometris, Laboratorium voor Nematologie, Genetic Association Studies, Models, Genetic, Abiotic stress, Research, Reproducibility of Results, Robustness (evolution), Biotic stress, Laboratorium voor Entomologie, genetic architecture, Genetic architecture, Plant Breeding, 030104 developmental biology, Plantaardige Productiesystemen, Mutation, multiple stresses, EPS, Laboratory of Nematology, PBR Non host en Insectenresistentie, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

The new phytologist 213(3), 1346-1362 (2017). doi:10.1111/nph.14220, Published by Wiley-Blackwell, Oxford [u.a.]

Published
2017

44. Phytochrome a protects tomato plants from injuries induced by continuous light

Author

Velez-Ramirez, Aaron I., Vreugdenhil, Dick, Millenaar, Frank F., van Ieperen, Wim, Velez-Ramirez, Aaron I., Vreugdenhil, Dick, Millenaar, Frank F., and van Ieperen, Wim

Abstract

Plants perceive and transduce information about light quantity, quality, direction and photoperiod via several photoreceptors and use it to adjust their growth and development. A role for photoreceptors has been hypothesized in the injuries that tomato plants develop when exposed to continuous light as the light spectral distribution influences the injury severity. Up to now, however, only indirect clues suggested that phytochromes (PHY), red/far-red photoreceptors, are involved in the continuous-light-induced injuries in tomato. In this study, therefore, we exposed mutant and transgenic tomato plants lacking or over-expressing phytochromes to continuous light, with and without far-red light enrichment. The results show that PHYA over-expression confers complete tolerance to continuous light regardless the light spectrum. Under continuous light with low far-red content, PHYB1 and PHYB2 diminished and enhanced the injury, respectively, yet the effects were small. These results confirm that phytochrome signaling networks are involved in the induction of injury under continuous light. HIGHLIGHTS-PHYA over-expression confers tolerance to continuous light regardless the light spectrum.-In the absence of far-red light, PHYB1 slightly diminishes the continuous light-induced injury.-Continuous light down-regulates photosynthesis genes in sensitive tomato lines.

Published
2019

45. Quantitative trait loci analysis of hormone levels in Arabidopsis roots

Author

Lee, Sangseok, Sergeeva, Lidiya I., Vreugdenhil, Dick, Lee, Sangseok, Sergeeva, Lidiya I., and Vreugdenhil, Dick

Abstract

Quantitative trait loci (QTL) analyses for five groups of hormones, including cytokinins in Arabidopsis roots were performed using recombinant inbred lines (Ler×Cvi). Significant QTLs were detected for cytokinins, jasmonic acid and salicylic acid. Separate analysis of two sub-populations, viz., vegetative and flowering plants revealed that many of the QTLs were development-specific. Using near-isogenic lines, several significant QTLs were confirmed; three co-localized QTL regions were responsible for determining several cytokinin metabolites. Using a knock-out plant, a functional role of zeatin N-glucosyltransferase gene (UGT76C2) underlying a large-effect QTL for levels of tZ-N-glucosides and tZRMP was evaluated in the metabolism of cytokinins. Pleotropic effects of this gene were found for cytokinin levels in both roots and leaves, but significant changes of morphological traits were observed only in roots. Hormone QTL analysis reveals development-specific and organ-dependent aspects of the regulation of plant hormone content and metabolism.

Published
2019

48. Natural variation of hormone levels in Arabidopsis roots and correlations with complex root architecture

Author

Lee, Sangseok, I. Sergeeva, Lidiya, and Vreugdenhil, Dick

Subjects
Ecotype, Principal Component Analysis, Time Factors, High‐Impact Article, Indoleacetic Acids, High‐Impact Articles, Arabidopsis, Genetic Variation, Plant Roots, Cell and Developmental Biology, Phenotype, Quantitative Trait, Heritable, Hydroponics, Plant Growth Regulators, Image Processing, Computer-Assisted, Life Science, Laboratorium voor Plantenfysiologie, EPS, Laboratory of Plant Physiology
Abstract

Studies on natural variation are an important tool to unravel the genetic basis of quantitative traits in plants. Despite the significant roles of phytohormones in plant development, including root architecture, hardly any studies have been done to investigate natural variation in endogenous hormone levels in plants. Therefore, in the present study a range of hormones were quantified in root extracts of thirteen Arabidopsis thaliana accessions using a ultra performance liquid chromatography triple quadrupole mass spectrometer. Root system architecture of the set of accessions was quantified, using a new parameter (mature root unit) for complex root systems, and correlated with the phytohormone data. Significant variations in phytohormone levels among the accessions were detected, but were remarkably small, namely less than three‐fold difference between extremes. For cytokinins, relatively larger variations were found for ribosides and glucosides, as compared to the free bases. For root phenotyping, length‐related traits—lateral root length and total root length—showed larger variations than lateral root number‐related ones. For root architecture, antagonistic interactions between hormones, for example, indole‐3‐acetic acid to trans‐zeatin were detected in correlation analysis. These findings provide conclusive evidence for the presence of natural variation in phytohormone levels in Arabidopsis roots, suggesting that quantitative genetic analyses are feasible.

Published
2018

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