scholarly journals Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance

2020 ◽  
Vol 287 (1941) ◽  
pp. 20202723
Author(s):  
Parvinderdeep S. Kahlon ◽  
Shallet Mindih Seta ◽  
Gesche Zander ◽  
Daniela Scheikl ◽  
Ralph Hückelhoven ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Major Gene ◽  
Pathogen Resistance ◽  
Natural Resistance ◽  
Small Scale ◽  
Pathogen Recognition ◽  
Geographical Differences ◽  
Natural Plant ◽  
Wild Tomato ◽  
Solanum Chilense

Natural plant populations encounter strong pathogen pressure and defence-associated genes are known to be under selection dependent on the pressure by the pathogens. Here, we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum , a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene-mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance ( Hcr ) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene-mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.

scholarly journals Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance

2020 ◽  
Author(s):  
Parvinderdeep S. Kahlon ◽  
Shallet Mindih Seta ◽  
Gesche Zander ◽  
Daniela Scheikl ◽  
Ralph Hückelhoven ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Pathogenic Fungus ◽  
Major Gene ◽  
Pathogen Resistance ◽  
Climatic Conditions ◽  
Natural Resistance ◽  
Plant Populations ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Solanum Chilense

AbstractNatural plant populations encounter strong pathogen pressure and defense-associated genes are known to be under different selection pressure dependent on the pressure by the pathogens. Here we use wild tomato Solanum chilense populations to investigate natural resistance against Cladosporium fulvum, a well-known pathogenic fungus of domesticated tomatoes. We show that populations of S. chilense differ in resistance against the pathogen. Next, we explored the underlying molecular processes in a species wide-context. Then, focusing on recognition of the two prominent avirulence factors secreted by C. fulvum (Avr4 and Avr9) in central and northern populations of S. chilense we observed high complexity in the cognate homologues of Cladosporium resistance (Hcr9) locus underlying the recognition of these effectors. Presence of canonical genomic regions coding for Cf-4 and Cf-9, two major dominant resistance genes in the Hcr9 locus recognizing Avr4 and Avr9, respectively, does not meet prediction from Avr response phenotypes. We find both genes in varying fractions of the plant populations and we show possible co-existence of two functionally active resistance genes, previously thought to be allelic. Additionally, we observed the complete local absence of recognition of additional Avr proteins of C. fulvum. In the southern populations we attribute this to changes in the coregulatory network. As a result of loss of pathogen pressure or adaptation to extreme climatic conditions. This may ultimately explain the observed pathogen susceptibility in the southern populations. This work puts major gene mediated disease resistance in an ecological context.

scholarly journals Periodic catastrophes over human evolutionary history are necessary to explain the forager population paradox

2019 ◽  
Vol 116 (26) ◽  
pp. 12758-12766 ◽  
Author(s):  
Michael D. Gurven ◽  
Raziel J. Davison
Keyword(s):  
Evolutionary History ◽  
Homo Sapiens ◽  
Vital Rate ◽  
Small Scale ◽  
Human Populations ◽  
Wild Chimpanzee ◽  
Population Fluctuations ◽  
Vital Rates ◽  
Zero Population Growth ◽  
Major Adjustment

The rapid growth of contemporary human foragers and steady decline of chimpanzees represent puzzling population paradoxes, as any species must exhibit near-stationary growth over much of their evolutionary history. We evaluate the conditions favoring zero population growth (ZPG) among 10 small-scale subsistence human populations and five wild chimpanzee groups according to four demographic scenarios: altered mean vital rates (i.e., fertility and mortality), vital rate stochasticity, vital rate covariance, and periodic catastrophes. Among most human populations, changing mean fertility or survivorship alone requires unprecedented alterations. Stochastic variance and covariance would similarly require major adjustment to achieve ZPG in most populations. Crashes could maintain ZPG in slow-growing populations but must be frequent and severe in fast-growing populations—more extreme than observed in the ethnographic record. A combination of vital rate alteration with catastrophes is the most realistic solution to the forager population paradox. ZPG in declining chimpanzees is more readily obtainable through reducing mortality and altering covariance. While some human populations may have hovered near ZPG under harsher conditions (e.g., violence or food shortage), modernHomo sapienswere equipped with the potential to rapidly colonize new habitats and likely experienced population fluctuations and local extinctions over evolutionary history.

scholarly journals Natural Variation in the Pto Pathogen Resistance Gene Within Species of Wild Tomato (Lycopersicon). I. Functional Analysis of Pto Alleles

Genetics ◽  
2005 ◽  
Vol 171 (1) ◽  
pp. 345-357 ◽  
Author(s):  
Laura E. Rose ◽  
Charles H. Langley ◽  
Adriana J. Bernal ◽  
Richard W. Michelmore
Keyword(s):  
Functional Analysis ◽  
Resistance Gene ◽  
Natural Variation ◽  
Pathogen Resistance ◽  
Wild Tomato

scholarly journals Natural resistance-associated macrophage protein 1 gene polymorphisms in thalassemia patients with tuberculosis infection

2016 ◽  
Vol 56 (2) ◽  
pp. 84 ◽  
Author(s):  
Mohammad Ghozali ◽  
Sari Puspa Dewi ◽  
Reni Ghrahani ◽  
Ani Melani Maskoen ◽  
Lelani Reniarti ◽  
...  
Keyword(s):  
Genetic Polymorphisms ◽  
Gene Polymorphisms ◽  
Serum Iron ◽  
Binding Capacity ◽  
Iron Status ◽  
Major Gene ◽  
Natural Resistance ◽  
Cross Sectional ◽  
Metal Transporter ◽  
Macrophage Protein

that needs regular blood transfusions leading to accumulation of iron in the cells. This iron overload level in macrophage might cause intracellular bacteria, particularly Mycobacterium tuberculosis (MTB) to multiply. Polymorphisms in natural resistance-associated macrophage protein 1 (NRAMP1), a metal transporter across the phagosome membrane, play important role in regulating iron, which is also needed by MTB. Increased iron in thalassemia patients may have an increased potential risk for TB.Objective To compare natural resistance-associated macrophage protein 1 (NRAMP1) gene polymorphisms (INT4, D543N, and 3’UTR) in thalassemia patients with and without tuberculosis (TB) infection.Methods A cross-sectional measurement of NRAMP1 genetic polymorphisms was performed in pediatric thalassemia patients with TB (n=40) and without TB (n=50). Iron status including serum iron, total iron-binding capacity (TIBC), and ferritin, was compared between the two groups. The NRAMP1 genetic polymorphisms were analysed using polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP). Allelic and genotypic distributions of each polymorphism were assessed for possible associations with TB infection.Results Mean serum iron and TIBC in thalassemia patients with TB were higher compared to thalassemia patients without TB (mean serum: 166.26 vs. 134.92 μmol/L, respectively; P=0.026) and (mean TIBC: 236.78 vs. 195.84 μmol/L, respectively; P=0.029). In thalassemia patients with TB, we observed significantly higher frequency of the C allele in INT4 (10% vs. 2%, respectively; OR=5.44; 95%CI 1.1 to 26.4; P=0.02) and the TGTG deletion allele (78.8% vs. 51%, respectively; OR=3.56; 95%CI 1.83 to 6.9; P=0.0002) in 3’UTR polymorphisms than in thalassemia patients without TB. There were no significant differences in distributions of the A allele between TB and non-TB groups (16.3% vs. 15%, respectively; P=0.84) or the GA genotype (32.5% vs. 30%, respectively; P=0.79) in D543N.Conclusion The NRAMP1 polymorphisms are known to be associated with major gene susceptibility to TB, and in our thalassemia patients this association is even more pronounced.

scholarly journals Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1745
Author(s):  
Leonardo I. Pereyra-Bistraín ◽  
Cesaré Ovando-Vázquez ◽  
Alejandra Rougon-Cardoso ◽  
Ángel G. Alpuche-Solís
Keyword(s):  
Defense Mechanism ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Natural Resistance ◽  
Human Consumption ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species

Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to Cmm. Here, we contrasted the transcriptomes of the resistant wild tomato species Solanum arcanum LA2157 and the susceptible species Solanum lycopersicum cv. Ailsa Craig, during the first 24 h of challenge with Cmm. We used three analyses approaches which demonstrated to be complementary: mapping to S. lycopersicum reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in S. arcanum during Cmm interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although S. lycopersicum showed enriched functional groups related to defense, S. arcanum displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against Cmm, and the development of new control methods.

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.

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