Biology subjects

Sterken, M. G.

Publications and source records attributed to Sterken, M. G..

At least 19 recordsLinked to original sources

bioRxiv2026

Interspecific adaptations in root system architecture define host tolerance of Arabidopsis to biotic stresses by root feeding nematodes

Belowground, plants are exposed to a wide range of biotic stresses that vary in severity and nature, including tissue damage, disruption of vascular connectivity, and depletion of assimilates. How plants adapt their root systems to cope with different types of belowground biotic stresses is not well known. In this paper we compare above- and belowground plant adaptations to three nematode species with distinct tissue migration and feeding behaviours to study mechanisms underlying tolerance to different types of biotic stresses. We monitored both green canopy growth and changes in root system architecture of Arabidopsis inoculated with Pratylenchus penetrans, Heterodera schachtii, and Meloidogyne incognita. This revealed three distinct phases in aboveground plant responses: (i) initial growth inhibition associated with host invasion and tissue damage, (ii) persistent growth reduction associated with nematode sedentarism, and (iii) late growth stimulus in more advanced stages of infection. Specific adaptations in the root systems further revealed fundamentally different stress coping strategies. Tissue damage and intermittent feeding by P. penetrans in the root cortex did not induce significant changes in root system architecture. Tissue damage to the root cortex and prolonged feeding on host vascular cells by H. schachtii induced secondary root formation compensating for primary root growth inhibition. Prolonged feeding on host vascular cell by M. incognita alone did not induce secondary root formation, but was accompanied by typical local tissue swelling instead. Our data suggest that local secondary root formation and tissue swelling are two distinct compensatory mechanisms underlying tolerance to sedentarism by root-feeding nematodes. HighlightHow plants utilize root system plasticity to cope with different types of biotic stresses by root feeding nematodes remains largely unknown. Here, we report on specific adaptive growth responses in Arabidopsis roots to three nematode species, Pratylenchus penetrans, Heterodera schachtii, and Meloidogyne incognita, with fundamentally different strategies for host invasion, subsequent migration through host tissue, and feeding on host cells.

plant biology↗

bioRxiv2025

Globodera pallida virulence on major potato resistance has a common genetic basis across Western Europe

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 populations 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 populations 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.

genetics↗

bioRxiv2025

Plant parasitic cyst nematodes respond to viral infection through RNA interference

Plant-parasitic nematodes (PPN) cause yield losses to multiple important crop species and counteractive measures are only partially successful. Recently the first viruses that infect PPN were discovered, presenting new research opportunities to understand and halt PPN. A critical step in this process is to identify how PPN respond to viruses. Here, two PPN species, the potato cyst nematode Globodera rostochiensis and the beet cyst nematode Heterodera schachtii, were used to study PPN-virus interactions. Viral discovery based on bioinformatic analyses indicated three putative viral genomes present in G. rostochiensis (a Toti-like, Xinzhou-like, and Picorna-like virus) and five putative viral genomes in H. schachtii (a Bunya-like, Tobamo-like, Picorna-like, and two Nyami-like viruses). A genome composition analysis and RT-PCR data confirmed that these viruses infect the nematodes and not their host plants. Subsequently, antiviral RNAi activity was detected in both H. schachtii and G. rostochiensis using small RNA sequencing. For G. rostochiensis two distinct genotypes were investigated. These strongly differed in their RNAi response: Ro5-line 22 produced roughly 40 times more antiviral viRNAs than Ro1-line 19. Our measurement of an active antiviral response represents the first indication of antiviral activity in PPN. Author summaryPlant-parasitic nematodes (PPN) are key agricultural pests and although some PPN viruses have been discovered recently, it is still unknown if and how PPN respond to viral infection. Here we find three viruses in the potato cyst nematode (Globodera rostochiensis) and five viruses in the beet cyst nematode (Heterodera schachtii). Of these viruses, six are newly discovered. Genome and molecular analyses confirm that all found viruses specifically infect nematodes and not their host plants. By measuring small RNA profiles, it was confirmed that PPN react to viral infection by means of RNAi, except for a weak response against two negatively stranded Nyami-like viruses. Moreover, distinct RNAi profiles were found for two potato cyst nematode lines, giving the first insight into which genes might be involved in RNAi in PPN. Together, this research provides the first proof of an active antiviral response in PPN. Thereby this finding opens new opportunities for biological control and gene editing tools.

molecular biology↗

bioRxiv2025

Natural variation suggests candidate genes underlying Caenorhabditis elegans susceptibility to diverse toxicants

Genetic differences among individuals shape how they respond to environmental toxicants, but the identification and validation of the genes responsible for this variation is difficult, particularly in humans. Consequently, our limited knowledge of the genes that influence susceptibility constrains our ability to accurately predict the risks posed by environmental toxicants. To identify genes underlying natural differences in toxicant susceptibilities, we measured the effects of 23 environmental toxicants on larval development across 195 genetically diverse Caenorhabditis elegans strains using a high-throughput imaging platform. We then combined these response data with whole-genome sequences to perform genome-wide association mappings, identifying 40 genomic regions where genetic variants are correlated with susceptibility differences. Many of these regions are enriched for genes involved in biological processes previously linked with toxicant responses, supporting the potential contributions of these genes to natural variation in susceptibility. Using a set of heuristics, we identified 94 candidate susceptibility genes, offering targets for experimental validation that could ultimately inform toxicant risk prediction and regulatory assessment by linking genetic variation to differences in susceptibility. Impact StatementAnalysis of natural genetic variation among 195 wild C. elegans strains identified 94 candidate genes putatively linked to differences in susceptibility to 23 environmental toxicants. These findings can inform the discovery of conserved susceptibility genes and the development of biomarkers that improve chemical risk assessment by accounting for genetic differences among humans.

pharmacology and toxicology↗

bioRxiv2025

Environmental sex determination in the cyst nematode Globodera pallida defaults to male development

Environmental sex determination (ESD) enables organisms to adjust their sexual fate in response to external cues. Fluctuating sex ratios have long suggested the presence of ESD in populations of plant-parasitic nematodes. We show that in the potato cyst nematode Globodera pallida sex is regulated by nutritional cues. By manipulating sucrose availability to the host plant, we could steer the sex determination of G. pallida. Whereas high-sucrose medium promotes female development, low-sucrose medium promotes male development. Transcriptome analyses on the early stages of parasitism reveal that female development requires extensive transcriptional activation and post-transcriptional regulation. We identify Gp-lin-29, a transcription factor homologous to lin-29 in Caenorhabditis elegans, as a potential regulator of ESD. Small RNA sequencing uncovered the male-biased expression of Gp-let-7, a putative repressor of Gp-lin-29, and the female-biased expression of four miRNAs, including Gp-miR-100, located at the same genomic locus as Gp-let-7. Target prediction and enrichment analyses suggest that these female-biased miRNAs actively suppress male developmental programs. Together, our findings support a model in which G. pallida juveniles follow a default male developmental trajectory unless redirected by favourable environmental cues to become female. This study provides mechanistic insight into ESD in cyst nematodes and positions G. pallida as a tractable system for exploring epigenetic regulation of developmental plasticity.

developmental biology↗

bioRxiv2025

The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus

Globodera pallida poses a major threat to potato production, with management strategies primarily relying on genetic resistance. However, reports from multiple locations in Western Europe indicate a steady increase in virulence levels among field populations, raising major concerns about G. pallida control. The evolutionary mechanisms driving this rise in virulence are poorly understood. To investigate this, we analysed the propagation of thirteen recently isolated field populations on thirty commercial potato varieties over four independent PCN resistance tests. Our findings indicate that (1) the genetic basis of resistance in potatoes is small, with the major resistance conferred by GpaV from Solanum vernei, and (2) the wide application of GpaVvrn has led to continuous selection on standing genetic variation in G. pallida field populations. To map virulence, we propagated two field populations on a GpaVvrn-resistant variety for four consecutive 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 G. pallida virulence on a GpaVvrn-resistant potato variety but had no effect on nematode virulence on a susceptible variety. Thereby classifying Gp-pat-1 as an avirulence gene and confirming its role in the breakdown of GpaVvrn-resistance. These findings demonstrate that negative selection on the Gp-pat-1 avirulence allele by GpaVvrn-mediated resistance is driving the emergence of virulence in the G. pallida field populations used in our selection experiments. Our results therefore strongly suggest that selection on Gp-pat-1 is likely underlying the current outbreak of GpaVvrn-resistance breaking populations. Our results provide a foundation for the development of molecular diagnostic tools to monitor virulence in field populations, to enhance understanding of resistance breakdown, and to inform the sustainable deployment of resistances in the field. SIGNIFICANCE STATEMENTIn Western Europe, management of the potato cyst nematode Globodera pallida primarily relies on genetic resistances in potato plants. However, resistance-breaking populations are emerging across Western Europe. Here, we identify a single resistance locus shared by all tested resistant potato varieties. We also identify a corresponding virulence locus on a newly assembled G. pallida reference genome and identify a gene within this locus that contributes to virulence. Our findings provide critical insights into the selective pressure acting on this plant-parasitic nematode, the emergence of virulence over time, and the molecular mechanism underlying resistance breakdown. These results provide much needed insights into a highly adapted soil-borne plant-pathogen.

genetics↗

bioRxiv2025

A Chromosome-scale Reference Genome of Meloidogyne hapla reveals localized recombination hotspots enriched with Effector Proteins

Root-knot nematodes (Meloidogyne spp.) are among the most destructive agricultural pests that cause significant yield losses across a wide range of crops. Meloidogyne hapla, a diploid species, is a valuable model for studying root-knot nematodes due to its parasitic diversity, small genome, and a reproductive strategy that facilitates genetic analysis. Here, we present a high-quality chromosome-scale assembly of M. hapla, generated using multiple sequencing platforms-PacBio HiFi, ONT, Illumina and HiC. The 59 Mb assembly comprises 16 chromosome-length scaffolds, notably lacking canonical telomeric repeats. Instead, we identified a tandem 16-mer repeat mainly present at scaffold ends, suggesting an alternative system for chromosome-end maintenance. Genetic linkage analysis of F2 populations derived from crosses between M. hapla strains validated the assembly but also revealed anomalies indicating chromosome structure differences between parental isolates such as fissions, fusions, and rearrangements. This analysis also revealed sharply delineated zones of high recombination on most chromosome arms. We also identified 1,258 genes encoding putative secreted proteins (PSP), which should be enriched in genes involved in host interaction and pathogenicity. Most of the PSP genes had orthologs in other plant parasitic nematode species, and the majority were pioneers, lacking known functional domains. Notably, we found that PSPs are significantly enriched in high-recombination zones, possibly facilitating their rapid evolution. Overall, our study provides new insights into the genome structure of diploid root-knot nematodes and highlights the interplay between genome architecture, recombination, and parasitism. These findings raise new questions about how genetic and genomic adaptations drive the success of rootknot nematodes as plant parasites.

plant biology↗

bioRxiv2023

WOX11-mediated cell size control in Arabidopsis attenuates fecundity of endoparasitic cyst nematodes

O_LICyst nematodes establish permanent feeding structures called syncytia inside host root vasculature, disrupting the flow of water and minerals. In response, plants form WOX11-mediated adventitious lateral roots at nematode infection sites. WOX11-adventitious lateral rooting modulates tolerance to nematode infections, however, whether this also benefits nematode parasitism remains unknown. C_LIO_LIHere, we report on bioassays using a 35S::WOX11-SRDX transcriptional repressor mutant to investigate whether WOX11-adventitious lateral rooting promotes syncytium development and thereby female fecundity. Moreover, we chemically inhibited cellulose biosynthesis to verify if WOX11 directly modulates cell wall plasticity in syncytia. Finally, we performed histochemical analyses to test if WOX11 mediates syncytial cell wall plasticity via reactive oxygen species (ROS). C_LIO_LIRepression of WOX11-mediated transcription specifically enhanced the radial expansion of syncytial elements, increasing both syncytium size and female offspring. The enhanced syncytial hypertrophy observed in the 35S::WOX11-SRDX mutant could be phenocopied by chemical inhibition of cellulose biosynthesis and was associated with elevated levels of ROS at nematode infection sites. C_LIO_LIWe therefore conclude that WOX11 restricts radial expansion of nematode feeding structures and female fecundity, likely by modulating ROS-mediated cell wall plasticity mechanisms. Remarkably, this novel role of WOX11 in plant cell size control is independent of WOX11-adventitious rooting underlying disease tolerance. C_LI

plant biology↗

bioRxiv2023

eQTL mapping in transgenic alpha-synuclein carrying Caenorhabditis elegans recombinant inbred line

Protein aggregation of -synuclein (S) is a genetic and neuropathological hallmark of Parkinsons disease (PD). Studies in the model nematode Caenorhabditis elegans suggested that variation of S aggregation depends on the genetic background. However, which genes and genetic modifiers underlie individual differences in S pathology remains unknown. To study the genotypic-phenotypic relationship of S aggregation, we constructed a Recombinant Inbred Line (RIL) panel derived from a cross between genetically divergent strains C. elegans NL5901 and SCH4856, both harboring the human S gene. As a first step to discover genetic modifiers 70 S-RILs were measured for whole-genome gene expression and expression quantitative locus analysis (eQTL) were mapped. We detected multiple eQTL hot-spots, many of which were located on Chromosome V. To confirm a causal locus, we developed Introgression Lines (ILs) that contain SCH4856 introgressions on Chromosome V in an NL5901 background. We detected 74 genes with an interactive effect between S and the genetic background, including the human p38 MAPK homologue pmk-1 that has previously been associated with PD. Together, we present a unique S-RIL panel for defining effects of natural genetic variation on S pathology, which contributes to finding genetic modifiers of PD.

genomics↗

bioRxiv2023

WOX11-mediated adventitious lateral root formation modulates tolerance of Arabidopsis to cyst nematode infections

The transcription factor WUSCHEL-RELATED HOMEOBOX 11 (WOX11) in Arabidopsis initiates the formation of adventitious lateral roots upon mechanical injury in primary roots. Root-invading nematodes also induce de novo root organogenesis leading to excessive root branching, but it is not known if this symptom of disease involves mediation by WOX11 and if it benefits the plant. Here, we show with targeted transcriptional repression and reporter gene analyses in Arabidopsis that the beet cyst nematode Heterodera schachtii activates WOX11-adventitious lateral rooting from primary roots close to infection sites. The activation of WOX11 in nematode-infected roots occurs downstream of jasmonic acid-dependent damage signaling via ETHYLENE RESPONSIVE FACTOR109, linking adventitious lateral root formation to nematode damage to host tissues. By measuring different root system components, we found that WOX11-mediated formation of adventitious lateral roots compensates for nematode-induced inhibition of primary root growth. Our observations further demonstrate that WOX11-mediated rooting reduces the impact of nematode infections on aboveground plant development and growth. Altogether, we conclude that the transcriptional regulation by WOX11 modulates root system plasticity under biotic stress, which is one of the key mechanisms underlying tolerance of Arabidopsis to cyst nematode infections.

plant biology↗

bioRxiv2023

The effect of developmental variation on expression QTLs in a multi parental C. elegans population

Regulation of gene expression plays a crucial role in the development and adaptation of organisms to changing environments. A population-based procedure used to investigate the genetic regulation of gene expression is eQTL mapping. Typically, the age of the population used for eQTL mapping at the time of sampling is strictly controlled. This is necessary because the developmental process causes changes in gene expression, complicating the interpretation of eQTL mapping experiments. However, organisms can differ in their "developmental age", even if they are of the same chronological age. As a result, eQTL patterns are affected by uncontrolled developmental variation in gene expression. The model organism C. elegans is particularly suited for studying the effect of developmental variation on eQTL mapping patterns. In a span of days C. elegans transitions from embryo through four larval stages to adult while undergoing massive changes to its transcriptome. Here we use C. elegans to investigate the effect of developmental age variation on eQTL patterns and an available normalization procedure. We used dynamical eQTL mapping, which includes developmental age as a cofactor, to separate the variation in development from genotypic variation and explain variation in gene expression levels. We compare classical single marker eQTL mapping and dynamical eQTL mapping using RNA-seq data of [~]200 multi-parental recombinant inbred lines of C. elegans. The results show that many eQTLs are actually caused by developmental variation, that most trans-bands are associated with developmental age and that dynamical eQTL mapping detects additional eQTLs not found with classical eQTL mapping.

genetics↗

bioRxiv2023

From root to shoot; Quantifying nematode tolerance in Arabidopsis thaliana by high-throughput phenotyping of plant development

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. HighlightThe mechanisms of tolerance to root-parasitic nematodes remain unknown. We developed a high-throughput phenotyping system that enables unravelling the underlying mechanisms of tolerance to nematodes.

plant biology↗

bioRxiv2022

Two sides to every coin: complementary introgression line populations in Caenorhabditis elegans

Quantitative genetics seeks to understand the role of allelic variation in trait differences. Introgression lines (ILs) contain a single genetic locus introgressed into another genetic background, and are one of the most powerful quantitative trait locus (QTL) mapping designs. However, albeit useful for QTL discovery, this homogenous background confounds genetic interactions. Here, we created an IL population with N2 segments in a CB4856 background (ILCB4856), reciprocal to an N2 background with CB4856 introgressions population (ILN2). The ILCB4856 panel comprises a population of 145 strains with sequencing confirmed N2 introgressions in a CB4856 background. A core set of 87 strains covering the entire genome was selected. We present three experiments demonstrating the power of the reciprocal IL panels. First, we performed QTL mapping identifying new regions associated with lifespan. Second, the existence of opposite-effect loci regulating heat-stress survival is demonstrated. Third, by combining ILN2 and ILCB4856 strains, an interacting expression QTL was uncovered. In conclusion, the reciprocal IL panels are a unique and ready-to-use resource to identify, resolve, and refine complex trait architectures in C. elegans.

genetics↗

bioRxiv2022

Root architecture plasticity in response to endoparasitic cyst nematodes is mediated by damage signaling

O_LIPlant root architecture plasticity in response to biotic stresses has not been thoroughly investigated. Infection by the endoparasitic cyst nematodes induces root architectural changes that involve the formation of secondary roots at infection sites. However, the molecular mechanisms regulating secondary root formation in response to cyst nematode infection remain largely unknown. C_LIO_LIWe first assessed whether secondary roots form in a nematode-density dependent manner by challenging wild type Arabidopsis plants with increasing numbers of cyst nematodes (Heterodera schachtii). Next, by using jasmonate-related reporter lines and knock-out mutants, we tested if tissue damage by nematodes triggers secondary root formation. Finally, we verified whether damage-induced secondary root formation depends on local auxin biosynthesis at nematode infection sites. C_LIO_LIIntracellular host invasion by H. schachtii triggers a transient local increase in jasmonates, which activates the expression of ERF109 in a COI1-dependent manner. Knock-out mutations in COI1 and ERF109 disrupt the nematode-density dependent increase of secondary roots observed in wildtype plants. Furthermore, ERF109 regulates secondary root formation upon H. schachtii infection via local auxin biosynthesis. C_LIO_LIHost invasion by H. schachtii triggers secondary root formation via the damage-induced jasmonate-dependent ERF109 pathway. This points at a novel mechanism underlying plant root plasticity in response to biotic stress. C_LI

plant biology↗

bioRxiv2021

Comparative genomics among three cyst nematode species reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs

Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are an essential handle for PCN control. However, the poor delineation of G. pallida pathotypes hampers the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCN after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ( DOG boxes) were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Re-sequencing of PCN populations with deviant virulence characteristics will allow for the linking of these characteristics with the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.

genomics↗

bioRxiv2021

The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B.

Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.

genetics↗

bioRxiv2021

The genetic architecture underlying body-size traits plasticity over different temperatures and developmental stages in Caenorhabditis elegans

Most ectotherms obey the temperature-size rule, meaning they grow larger in a colder environment. This raises the question of how the interplay between genes and temperature affect the body size of ectotherms. Despite the growing body of literature on the physiological life-history and molecular genetic mechanism underlying the temperature-size rule, the overall genetic architecture orchestrating this complex phenotype is not yet fully understood. One approach to identify genetic regulators of complex phenotypes is Quantitative Trait Locus (QTL) mapping. Here, we explore the genetic architecture of body size phenotypes, and plasticity of body-size phenotypes in different temperatures using Caenorhabditis elegans as a model ectotherm. We used 40 recombinant inbred lines (RILs) derived from N2 and CB4856, which were reared at four different temperatures (16{degrees}C, 20{degrees}C, 24{degrees}C, and 26{degrees}C) and measured at two developmental stages (L4 and adult). The animals were measured for body length, width at vulva, body volume, length/width ratio, and seven other body-size traits. The genetically diverse RILs varied in their body-size phenotypes with heritabilities ranging from 0.0 to 0.99. We detected 18 QTL underlying the body-size traits across all treatment combinations, with the majority clustering on Chromosome X. We hypothesize that the Chromosome X QTL could result from a known pleiotropic regulator - npr-1 - known to affect the body size of C. elegans through behavioral changes. We also found five plasticity QTL of body-size which three of them colocalized with some body-size QTL at certain temperature. In conclusion, our findings shed more light on multiple loci affecting body size plasticity and the possibility of co-regulation of traits and traits plasticity by the same loci under different environment.

genetics↗

bioRxiv2021

Plasticity of maternal environment dependent expression-QTLs of tomato seeds

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depends on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to measure gene expression of seeds of a tomato RIL population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments; i.e. on high phosphorus or low nitrogen. The obtained SNPs were subsequently used to construct a high-density genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

plant biology↗