scholarly journals The wild tomato species Solanum chilense shows local variation in pathogen resistance between geographically distinct populations

2016 ◽  
Author(s):  
Remco Stam ◽  
Daniela Scheikl ◽  
Aurélien Tellier
Keyword(s):  
Disease Resistance ◽  
Alternaria Solani ◽  
Local Variation ◽  
Pathogen Resistance ◽  
Genetic Traits ◽  
Phenotypic Differences ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense ◽  
Demographic Patterns

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens, however evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity is very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

scholarly journals The wild tomato species Solanum chilense shows local variation in pathogen resistance between geographically distinct populations

2016 ◽  
Author(s):  
Remco Stam ◽  
Daniela Scheikl ◽  
Aurélien Tellier
Keyword(s):  
Disease Resistance ◽  
Alternaria Solani ◽  
Local Variation ◽  
Pathogen Resistance ◽  
Genetic Traits ◽  
Phenotypic Differences ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Solanum Chilense ◽  
Demographic Patterns

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens, however evolution of resistance traits is yet poorly understood. For some species, like Solanum chilense, both differences in habitat and within species genetic diversity is very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations of S. chilense. We investigate the phenotypic differences in disease resistance within S. chilense against three common tomato pathogens (Alternaria solani, Phytophthora infestans and a Fusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that within S. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

scholarly journals The wild tomato speciesSolanum chilenseshows variation in pathogen resistance between geographically distinct populations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2910 ◽  
Author(s):  
Remco Stam ◽  
Daniela Scheikl ◽  
Aurélien Tellier
Keyword(s):  
Disease Resistance ◽  
Alternaria Solani ◽  
Pathogen Resistance ◽  
Genetic Traits ◽  
Phenotypic Differences ◽  
Resistance Variation ◽  
Evolution Of Resistance ◽  
Solanum Chilense ◽  
Fusarium Sp ◽  
Demographic Patterns

Wild tomatoes are a valuable source of disease resistance germplasm for tomato (Solanum lycopersicum) breeders. Many species are known to possess a certain degree of resistance against certain pathogens; however, evolution of resistance traits is yet poorly understood. For some species, likeSolanum chilense, both differences in habitat and within species genetic diversity are very large. Here we aim to investigate the occurrence of spatially heterogeneous coevolutionary pressures between populations ofS. chilense. We investigate the phenotypic differences in disease resistance withinS. chilenseagainst three common tomato pathogens (Alternaria solani,Phytophthora infestansand aFusarium sp.) and confirm high degrees of variability in resistance properties between selected populations. Using generalised linear mixed models, we show that disease resistance does not follow the known demographic patterns of the species. Models with up to five available climatic and geographic variables are required to best describe resistance differences, confirming the complexity of factors involved in local resistance variation. We confirm that withinS. chilense, resistance properties against various pathogens show a mosaic pattern and do not follow environmental patterns, indicating the strength of local pathogen pressures. Our study can form the basis for further investigations of the genetic traits involved.

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 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 Signatures of natural selection in abiotic stress-responsive genes of Solanum chilense

2018 ◽  
Vol 5 (1) ◽  
pp. 171198 ◽  
Author(s):  
Katharina B. Böndel ◽  
Tetyana Nosenko ◽  
Wolfgang Stephan
Keyword(s):  
Abiotic Stress ◽  
Natural Selection ◽  
Local Adaptation ◽  
Stress Factors ◽  
Abiotic Stress Response ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
Abiotic Stress Factors ◽  
Solanum Chilense ◽  
Stress Responsive Genes

Environmental conditions are strong selective forces, which may influence adaptation and speciation. The wild tomato species Solanum chilense , native to South America, is exposed to a range of abiotic stress factors. To identify signatures of natural selection and local adaptation, we analysed 16 genes involved in the abiotic stress response and compared the results to a set of reference genes in 23 populations across the entire species range. The abiotic stress-responsive genes are characterized by elevated nonsynonymous nucleotide diversity and divergence. We detected signatures of positive selection in several abiotic stress-responsive genes on both the population and species levels. Local adaptation to abiotic stresses is particularly apparent at the boundary of the species distribution in populations from coastal low-altitude and mountainous high-altitude regions.

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
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