scholarly journals Quantitative resistance differences between and within natural populations of Solanum chilense against the oomycete pathogen Phytophthora infestans

2021 ◽  
Author(s):  
Parvinderdeep Kahlon ◽  
Melissa Verin ◽  
Ralph Hückelhoven ◽  
Remco Stam
Keyword(s):  
Phytophthora Infestans ◽  
Phenotypic Diversity ◽  
Quantitative Resistance ◽  
Natural Populations ◽  
Infection Frequency ◽  
Plant Genotype ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense

The wild tomato species Solanum chilense is divided in geographically and genetically distinct populations that show signs of defense gene selection and differential phenotypes when challenged with several phytopathogens, including the oomycete causal agent of late blight Phytophthora infestans. To better understand the phenotypic diversity of this disease resistance in S. chilense and to assess the effect of plant genotype vs. pathogen isolate, respectively, we evaluated infection frequency in a systematic approach and with large sample sizes. We studied 85 genetically distinct individuals representing nine geographically separated populations of S. chilense. This showed that differences in quantitative resistance properties can be observed between but also within populations at the level of individual plants. Data also did not reveal clear indications for complete immunity in any of the genotypes. We further evaluated the resistance of a subset of the plants against P. infestans isolates with diverse virulence properties. This confirmed that the relative differences in resistance phenotypes between individuals were mainly determined by the plant genotype under consideration with modest effects of pathogen isolate used in the study. Thus, our report suggest that quantitative resistance against P. infestans in natural populations of a wild tomato species S. chilense is likely not the result of specific adaptations of hosts to the pathogen but of basal defence responses that depend on the host genotype and are pathogen isolate-unspecific.

scholarly journals The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

2019 ◽  
Author(s):  
Remco Stam ◽  
Tetyana Nosenko ◽  
Anja C. Hörger ◽  
Wolfgang Stephan ◽  
Michael Seidel ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Comparative Genomics ◽  
Reference Genome ◽  
Biotic And Abiotic Stress ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense ◽  
Tomato Breeding ◽  
Gene Models

ABSTRACTBackgroundWild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.FindingsWe generated ∼134 Gb of DNA and 157 Gb of RNA sequence data of S chilense, which yielded a draft genome with an estimated length of 914 Mb in total encoding 25,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNA-seq data derived from leaf tissue samples. A benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% BUSCO genes, which is in the current range of high-quality genomes for non-inbred plants. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We revealed the existence of unique gene families of NLRs to S. chilense. Comparative genomics analyses of S. chilense, cultivated tomato S. lycopersicum and its wild relative S. pennellii revealed similar levels of highly syntenic gene clusters between the three species.ConclusionsWe generated the first genome and transcriptome sequence assembly for the wild tomato species Solanum chilense and demonstrated its value in comparative genomics analyses. We make these genomes available for the scientific community as an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility, and for tomato breeding.

scholarly journals The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species

2019 ◽  
Vol 9 (12) ◽  
pp. 3933-3941 ◽  
Author(s):  
Remco Stam ◽  
Tetyana Nosenko ◽  
Anja C. Hörger ◽  
Wolfgang Stephan ◽  
Michael Seidel ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense

scholarly journals Migration through a major Andean ecogeographic disruption as a driver of genotypic and phenotypic diversity in a wild tomato species

2020 ◽  
Author(s):  
Jacob B. Landis ◽  
Christopher M. Miller ◽  
Amanda K. Broz ◽  
Alexandra A. Bennett ◽  
Noelia Carrasquilla-Garcia ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Isolation By Distance ◽  
Population Level ◽  
Fixation Index ◽  
Isolated Populations ◽  
Major Barrier ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
And Migration

AbstractThe large number of species on our planet arises from the phenotypic variation and reproductive isolation occurring at the population level. In this study, we sought to understand the origins of such population-level variation in defensive acylsugar chemistry and mating systems in Solanum habrochaites – a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-Associated-Digestion Sequencing (RAD-seq) of 50 S. habrochaites accessions, we identified eight population clusters generated via isolation and hybridization dynamics of 4-6 ancestral populations. Estimation of heterozygosity, fixation index, isolation by distance, and migration probabilities, allowed identification of multiple barriers to gene flow leading to the establishment of extant populations. One major barrier is the Amotape-Huancabamba Zone (AHZ) – a geographical feature in the Andes with high endemism, where the mountainous range breaks up into isolated microhabitats. The AHZ was associated with emergence of alleles for novel reproductive and acylsugar phenotypes. These alleles led to the evolution of self-compatibility in the northern populations, where alleles for novel defense-related enzyme variants were also found to be fixed. We identified geographical distance as a major force causing population differentiation in the central/southern part of the range, where S. habrochaites was also inferred to have originated. Findings presented here highlight the role of the diverse ecogeography of Peru and Ecuador in generating new, reproductively isolated populations, and enhance our understanding of the microevolutionary processes that lay a path to speciation.

scholarly journals Intraspecific diversity observed in the wild tomato species Solanum chilense in initial immune responses towards a glucan elicitor.

2021 ◽  
Author(s):  
Parvinderdeep S. Kahlon ◽  
Andrea Förner ◽  
Michael Muser ◽  
Mhaned Oubounyt ◽  
Michael Gigl ◽  
...  
Keyword(s):  
Immune Responses ◽  
Resistance Phenotype ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Multiple Components ◽  
In The Wild ◽  
Defence Responses ◽  
Solanum Chilense ◽  
High Diversity

Natural plant populations are highly polymorphic and often show intraspecific quantitative, variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on the perception of conserved pathogen-associated molecular patterns (PAMPs). To dissect and understand such variation, we evaluated the diversity of responses induced by laminarin (representing a general glucan elicitor of plant immune responses) in the wild tomato species Solanum chilense. We confirm considerable overlap of the plant's global transcriptional responses to laminarin and to the oomycete pathogen Phytophthora infestans. We further measured key components of basal defence responses such as reactive oxygen species (ROS) production and levels of diverse phytohormones and their derivatives upon elicitation with laminarin in 83 plants originating from nine natural populations of S. chilense from distinct geographic origin. We found high diversity in these components at basal and elicitor-induced levels. We generated generalised linear mixed models (GLMMs) with these components to explain the observed resistance phenotype against P. infestans in the plants and found that additive effects of multiple components best explain resistance at the species level. For individual components, we observed the strongest positive correlation between the resistance phenotype and ethylene (ET) production upon laminarin elicitation. The strength of this correlation differed between individual populations. Chemical inhibition of ET production in individuals from a population, in which ET production was associated with resistance, provoked more severe disease symptoms. Our findings reveal high diversity in the strength of induced defence responses within a species and in the basal levels of other stress-related phytohormones. We show the involvement of multiple components with a quantitatively different contribution of individual components to resistance in geographically separated populations of S. chilense against P. infestans.

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