Esther van der Knaap

Esther van der Knaap
University of Georgia | UGA · Center for Applied Genetic Technologies, Horticulture

PhD

About

185
Publications
95,152
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
10,519
Citations
Additional affiliations
March 2001 - present
The Ohio State University
Position
  • Professor (Associate)
Description
  • Plant genetics and genomics, Plant development, Plant domestication, Crop improvement.

Publications

Publications (185)
Article
Full-text available
Blossom-end rot (BER) is a devastating physiological disorder affecting vegetable production worldwide. Extensive research into the physiological aspects of the disorder has demonstrated that the underlying causes of BER are associated with perturbed calcium (Ca ²⁺ ) homeostasis and irregular watering conditions in predominantly cultivated accessio...
Article
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accession...
Article
Premise: Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (> 60 landraces) are common; additionally wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role...
Article
Full-text available
CRISPR/Cas-mediated genome editing is a powerful approach to accelerate yield enhancement to feed growing populations. Most applications focus on “negative regulators” by targeting coding regions and promoters to create nulls or weak loss-of-function alleles. However, many agriculturally important traits are conferred by gain-of-function alleles. T...
Article
A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to...
Preprint
Full-text available
Tomato domestication history has been revealed to be a highly complex story. A major contributor to this complexity is an evolutionary intermediate group ( Solanum lycopersicum var. cerasiforme (Alef.) Voss; SLC) between the domesticated tomato ( Solanum lycopersicum var. lycopersicum L.; SLL) and its wild relative ( Solanum pimpinellifolium L.; SP...
Article
Full-text available
Within large-fruited germplasm, fruit size is influenced by flat and globe shapes. Whereas flat fruits are smaller and retain better marketability, globe fruits are larger and more prone to cuticle disorders. Commercial hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fr...
Preprint
Full-text available
Understanding the evolution of deleterious mutations through domestication has fascinated evolutionary biologists and breeders alike. Some domesticated organisms have been reported to accumulate deleterious mutations, i.e. radical amino acid changes, through their domestication history (“cost of domestication”). However, more recent evidence paints...
Article
Full-text available
Key Message Six novel fruit weight QTLs were identified in tomato using multiple bi-parental populations developed from ancestral accessions. Beneficial alleles at these loci arose in semi-domesticated subpopulations and were likely left behind. This study paves the way to introgress these alleles into breeding programs. Abstract The size and weig...
Preprint
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, through comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions, we...
Article
Full-text available
Key message Blossom-End Rot is Quantitatively Inherited and Maps to Four Loci in Tomato . Abstract Blossom-end rot (BER) is a devastating physiological disorder that affects tomato and other vegetables, resulting in significant crop losses. To date, most studies on BER have focused on the environmental factors that affect calcium translocation to...
Preprint
Full-text available
A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian cultures domesticated species of interest by introducing complex genetic modifications. For tomato, two species, and for one of them two botanical varieties: are thought to...
Article
Full-text available
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5 , A...
Article
Full-text available
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some na...
Preprint
Full-text available
Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Thus, specific breeding programs to incorporate these natural defences, that are common within...
Article
Full-text available
The size of plant organs such as fruit and seed are crucial yield components. Tomato KLUH underlies the QTL fw3.2 that is an important regulator of fruit and seed weight. However, the mechanism by which the expression levels of KLUH affects organ size is poorly understood. Here, we found that higher expression of SlKLUH increased cell proliferation...
Article
Patterns of indeterminate and determinate growth specify plant architecture and influence crop productivity. In cotton (Gossypium hirsutum), SINGLE FLOWER TRUSS (SFT) stimulates the transition to flowering and determinate growth while its closely related antagonist SELF-PRUNING (SP) maintains meristems in indeterminate states to favor vegetative gr...
Article
Aberrant regulation of metabolic kinases by altered redox homeostasis substantially contributes to aging and various diseases, such as diabetes. We found that the catalytic activity of a conserved family of fructosamine-3-kinases (FN3Ks), which are evolutionarily related to eukaryotic protein kinases, is regulated by redox-sensitive cysteine residu...
Article
Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-sca...
Article
Full-text available
A collection of 163 accessions, including Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme and Solanum lycopersicum var. lycopersicum, was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication: Andean regions of Peru and Ecuador and Mesoamerica. The collection is enriched...
Article
Full-text available
Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulat...
Preprint
Aberrant regulation of metabolic kinases by altered redox homeostasis is a major contributing factor in aging and disease such as diabetes. However, the biochemical mechanisms by which metabolic kinases are regulated under oxidative stress is poorly understood. In this study, we demonstrate that the catalytic activity of a conserved family of Fruct...
Article
Full-text available
The process of plant domestication is often protracted, involving under-explored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. (SP) to a semi-domesticated...
Article
Full-text available
The process of plant domestication is often protracted, involving under-explored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. (SP) to a semi-domesticated...
Article
The shape of produce is an important agronomic trait. The knowledge of the cellular regulation of organ shapes can be implemented in the improvement of a variety of crops. The plant-specific Ovate Family Proteins (OFPs) regulate organ shape in Arabidopsis and many crops including rice, tomato, and melon. Although OFPs were previously described as t...
Article
Full-text available
Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries...
Article
Full-text available
Improving yield by increasing the size of produce is an important selection criterion during the domestication of fruit and vegetable crops. Genes controlling meristem organization and organ formation work in concert to regulate the size of reproductive organs. In tomato, lc and fas control locule number, which often leads to enlarged fruits compar...
Article
Full-text available
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and inten...
Article
Elongated tomato fruit shape is the result of the action of the fruit shape genes possibly in coordination with the phytohormone auxin. To investigate the possible link between auxin and the fruit shape genes, a series of auxin (2,4-D) treatments were performed on the wild-type and the fruit shape near-isogenic lines (NILs) in Solanum pimpinellifol...
Article
Full-text available
Host-associated differentiation (HAD) has played a major role in insect diversification at both macroevolutionary and microevolutionary scales. This evolutionary process has been reported in insects associated with wild and domesticated plant species. In particular, domesticated species harbor large genetic and phenotypic diversity associated with...
Article
Full-text available
Plant organ shape is determined by the spatial-temporal expression of genes that control the direction and rate of cell division and expansion, as well as the mechanical constraints provided by the rigid cell walls and surrounding cells. Despite the importance of organ morphology during the plant life cycle, the interplay of patterning genes with t...
Article
Full-text available
Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family P...
Article
Full-text available
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. ann...
Article
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how br...
Article
Angiosperms produce seeds as their progeny enclosed in maternally-derived structures called fruits. Evolutionarily, fruits have contributed enormously to the success of the Angiosperms phylum by providing protection and nutrition to the developing seeds, while ensuring the efficient dispersal upon maturity. Fruits vary massively in both size and sh...
Article
Full-text available
Increases in fruit weight of cultivated vegetables and fruits accompanied the domestication of these crops. Here we report on the positional cloning of a quantitative trait locus (QTL) controlling fruit weight in tomato. The derived allele of Cell Size Regulator (CSR-D) increases fruit weight predominantly through enlargement of the pericarp areas....
Data
Expression of CSR in fruit tissues. (A) Expression of CSR in developing fruit tissues from anthesis to ripe fruit. (B) Expression of CSR in developing pericarp tissues after fruit set. (PDF)
Data
CSR co-expression analysis. (A) fw11.3-D NIL gene expression cluster analysis. CSR-D and its co-expressed genes are included in cluster 11. (B) fw11.3-WT NIL gene expresssion cluster analysis. CSR-WT and its co-expressed genes are included in cluster 1. Normalized RPKM were used. Horizontal axis represents the following tissues and stages: 7Col (1)...
Data
Fruit weight data from CSR transgenic and non-transgenic lines. (XLSX)
Data
Phenotypic characterizations of the fw11.3 NILs. (XLSX)
Data
Association mapping core collection and genotypes for fw11.3 region. (XLSX)
Data
Expression of CSR and CSR-like genes. (XLSX)
Data
Flow cytometry of tomato pericarp nuclei. The single nuclei gating (upper) and nuclei ploidy histogram (lower) is shown for each genotype. In the upper graphs, the P1 box was manually set prior to counting the single nuclei that showed different ploidy levels (non-red dots). Colors were automatically generated by the flow cytometry BD FACSDIVATM so...
Data
Progeny test of the selected recombinants in the fw11.3 region. (XLSX)
Data