scholarly journals Complex adaptive architecture of quantitative resistance erosion in a plant fungal pathogen

2021 ◽  
Author(s):  
Thomas Dumartinet ◽  
Sébastien Ravel ◽  
Véronique Roussel ◽  
Luis Pérez Vicente ◽  
Jaime Aguayo ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Quantitative Resistance ◽  
Parallel Evolution ◽  
Genetic Resistance ◽  
Biological Data ◽  
Caribbean Region ◽  
Adaptive Architecture ◽  
Complex Adaptive ◽  
Pathogen Populations ◽  
Genomic Regions

Plant pathogens often adapt to plant genetic resistance so characterization of the architecture under-lying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host se-lection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation be-tween haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly varia-ble across all the population pairs studied. These results suggest complex adaptive architecture un-derlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were highlighted in genomic regions combining annotation analysis with available biological data.

scholarly journals Convergent Adaptation to Quantitative Host Resistance in a Major Plant Pathogen

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jean Carlier ◽  
François Bonnot ◽  
Véronique Roussel ◽  
Sébastien Ravel ◽  
Reina Teresa Martinez ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Genetic Basis ◽  
Plant Pathogens ◽  
Quantitative Resistance ◽  
Biological Data ◽  
Content Type ◽  
A Genome ◽  
Genomic Regions ◽  
Plant Pathogen Interactions ◽  
Pseudocercospora Fijiensis

ABSTRACT Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance. IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.

scholarly journals Specific Resistance of Barley to Powdery Mildew, Its Use and Beyond: A Concise Critical Review

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 971 ◽  
Author(s):  
Antonín Dreiseitl
Keyword(s):  
Powdery Mildew ◽  
Resistance Genes ◽  
Plant Pathogens ◽  
Specific Resistance ◽  
Wide Spectrum ◽  
Quantitative Resistance ◽  
Spring Barley ◽  
Durable Resistance ◽  
Genetic Resistance ◽  
Barley Cultivars

Powdery mildew caused by the airborne ascomycete fungus Blumeria graminis f. sp. hordei (Bgh) is one of most common diseases of barley (Hordeum vulgare). This, as with many other plant pathogens, can be efficiently controlled by inexpensive and environmentally-friendly genetic resistance. General requirements for resistance to the pathogens are effectiveness and durability. Resistance of barley to Bgh has been studied intensively, and this review describes recent research and summarizes the specific resistance genes found in barley varieties since the last conspectus. Bgh is extraordinarily adaptable, and some commonly recommended strategies for using genetic resistance, including pyramiding of specific genes, may not be effective because they can only contribute to a limited extent to obtain sufficient resistance durability of widely-grown cultivars. In spring barley, breeding the nonspecific mlo gene is a valuable source of durable resistance. Pyramiding of nonspecific quantitative resistance genes or using introgressions derived from bulbous barley (Hordeum bulbosum) are promising ways for breeding future winter barley cultivars. The utilization of a wide spectrum of nonhost resistances can also be adopted once practical methods have been developed.

scholarly journals Qualitative and Quantitative Resistance against Early Blight Introgressed in Potato

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 892
Author(s):  
Pieter J. Wolters ◽  
Doret Wouters ◽  
Emil J. Kromhout ◽  
Dirk Jan Huigen ◽  
Richard G. F. Visser ◽  
...  
Keyword(s):  
Early Blight ◽  
Plant Pathogens ◽  
Quantitative Resistance ◽  
Genetic Resistance ◽  
Natural Resistance ◽  
Endosperm Balance Number ◽  
Gene Model ◽  
Wild Potato Species ◽  
Alternaria Species ◽  
Blight Disease

Early blight is a disease of potato that is caused by Alternaria species, notably A. solani. The disease is usually controlled with fungicides. However, A. solani is developing resistance against fungicides, and potato cultivars with genetic resistance to early blight are currently not available. Here, we identify two wild potato species, which are both crossable with cultivated potato (Solanum tuberosum), that show promising resistance against early blight disease. The cross between resistant S. berthaultii and a susceptible diploid S. tuberosum gave rise to a population in which resistance was inherited quantitatively. S. commersonii subsp. malmeanum was also crossed with diploid S. tuberosum, despite a differing endosperm balance number. This cross resulted in triploid progeny in which resistance was inherited dominantly. This is somewhat surprising, as resistance against necrotrophic plant pathogens is usually a quantitative trait or inherited recessively according to the inverse-gene-for-gene model. Hybrids with high levels of resistance to early blight are present among progeny from S. berthaultii as well as S. commersonii subsp. malmeanum, which is an important step towards the development of a cultivar with natural resistance to early blight.

scholarly journals Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

2020 ◽  
Vol 22 (1) ◽  
pp. 313
Author(s):  
Aldrin Y. Cantila ◽  
Nur Shuhadah Mohd Saad ◽  
Junrey C. Amas ◽  
David Edwards ◽  
Jacqueline Batley
Keyword(s):  
Brassica Napus ◽  
Genetic Factors ◽  
Quantitative Resistance ◽  
Genetic Resistance ◽  
Leptosphaeria Maculans ◽  
Gene Interaction ◽  
R Gene ◽  
R Genes ◽  
Blackleg Resistance ◽  
Avr Gene

Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.

Potential New Herbicides – Phytotoxins from Plant Pathogens

1988 ◽  
Vol 2 (4) ◽  
pp. 519-524 ◽  
Author(s):  
Doug Kenfield ◽  
Greg Bunkers ◽  
Gary A. Strobel ◽  
Fumio Sugawara
Keyword(s):  
Organic Synthesis ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Biological Activities ◽  
Biological Data

A rationale for the study of phytotoxins from fungal pathogens of plants is presented. Structural chemistries and biological data are given for numerous, recently discovered phytotoxins in such diverse chemical classes as polyketides, terpenoids, diketopiperazines, and isocoumarins. The biological activities of these compounds range from broadly toxic (curvulin) to host specific (maculosin-1). Phytotoxicology offers a viable supplement to organic synthesis as a means of developing and implementing new, biorational, and economical herbicides.

Advances in breeding techniques for durable Septoria tritici blotch (STB) resistance in cereals

2021 ◽  
pp. 303-356
Author(s):  
Harsh Raman ◽  
Keyword(s):  
Quantitative Resistance ◽  
Durable Resistance ◽  
Genetic Resistance ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Zymoseptoria Tritici ◽  
Winter Cereal ◽  
Cereal Breeding ◽  
Qualitative Resistance ◽  
Breeding Techniques

Septoria tritici blotch (STB), caused by the hemibiotrophic fungus Zymoseptoria tritici, is one of the most important foliar diseases of winter cereal crops. Recent advances are helping to understand the genetic basis and architecture of resistance to STB. To date, at least 22 genes for qualitative resistance and over 200 quantitative trait loci (QTL) for quantitative resistance have been identified in cereals. This knowledge is enabling cereal breeding programs to develop varieties with more durable resistance to STB. This chapter reviews recent research on genetic resistance loci and breeding strategies based on both conventional and biotechnology-based breeding approaches (molecular marker/genomic-assisted breeding, genetic transformation, and gene-editing) to achieve achieving durable resistance to STB infection and minimise grain yield losses.

scholarly journals Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

2014 ◽  
Vol 281 (1783) ◽  
pp. 20140012 ◽  
Author(s):  
Devon E. Pearse ◽  
Michael R. Miller ◽  
Alicia Abadía-Cardoso ◽  
John Carlos Garza
Keyword(s):  
Life History ◽  
Rainbow Trout ◽  
Parallel Evolution ◽  
Genomic Region ◽  
Life History Strategies ◽  
Strong Linkage Disequilibrium ◽  
Rapid Adaptation ◽  
Life History Variation ◽  
Standing Variation ◽  
Genomic Regions

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L.

Genome ◽  
2012 ◽  
Vol 55 (2) ◽  
pp. 152-163 ◽  
Author(s):  
Mirko Barbieri ◽  
Thierry C. Marcel ◽  
Rients E. Niks ◽  
Enrico Francia ◽  
Marianna Pasquariello ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Rust Fungus ◽  
Brachypodium Distachyon ◽  
Transgressive Segregation ◽  
Snp Markers ◽  
Growth Stages ◽  
Resistance Qtls ◽  
Ssr And Snp Markers ◽  
Model Grass ◽  
Genomic Regions

The potential of the model grass Brachypodium distachyon L. (Brachypodium) for studying grass–pathogen interactions is still underexploited. We aimed to identify genomic regions in Brachypodium associated with quantitative resistance to the false brome rust fungus Puccinia brachypodii . The inbred lines Bd3-1 and Bd1-1, differing in their level of resistance to P. brachypodii, were crossed to develop an F2 population. This was evaluated for reaction to a virulent isolate of P. brachypodii at both the seedling and advanced growth stages. To validate the results obtained on the F2, resistance was quantified in F2-derived F3 families in two experiments. Disease evaluations showed quantitative and transgressive segregation for resistance. A new AFLP-based Brachypodium linkage map consisting of 203 loci and spanning 812 cM was developed and anchored to the genome sequence with SSR and SNP markers. Three false brome rust resistance QTLs were identified on chromosomes 2, 3, and 4, and they were detected across experiments. This study is the first quantitative trait analysis in Brachypodium. Resistance to P. brachypodii was governed by a few QTLs: two acting at the seedling stage and one acting at both seedling and advanced growth stages. The results obtained offer perspectives to elucidate the molecular basis of quantitative resistance to rust fungi.

scholarly journals Comparative Genomics and Functional Studies of Wheat BED-NLR Loci

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1406
Author(s):  
Clemence Marchal ◽  
Georg Haberer ◽  
Manuel Spannagl ◽  
Cristobal Uauy ◽  
Keyword(s):  
Cell Death ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Functional Studies ◽  
Network Analyses ◽  
Binding Factor ◽  
Localization Signal ◽  
Integrated Domains ◽  
Genomic Regions

Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and ‘MHD’ variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.

scholarly journals Dissecting Genetic Resistance to Fire Blight in Three Pear Populations

2020 ◽  
Vol 110 (7) ◽  
pp. 1305-1311 ◽  
Author(s):  
Jason D. Zurn ◽  
John L. Norelli ◽  
Sara Montanari ◽  
Richard Bell ◽  
Nahla V. Bassil
Keyword(s):  
Fire Blight ◽  
Genetic Resistance ◽  
Bacterial Pathogen ◽  
The United States ◽  
Future Research ◽  
Chromosome 2 ◽  
Resistance Qtls ◽  
Persistent Problem ◽  
El Dorado ◽  
Genomic Regions

Fire blight, caused by the bacterial pathogen Erwinia amylovora, is a persistent problem for pear (Pyrus spp.) growers in the United States. Growing resistant cultivars is one of the best options for managing fire blight. The cultivars Potomac and Old Home and the selection NJA2R59T69 display resistance to fire blight. As such, three mapping populations (El Dorado × Potomac, Old Home × Bartlett, and NJA2R59T69 × Bartlett) were developed to identify genomic regions associated with resistance to fire blight. Progeny were phenotyped during 2017 and 2018 by inoculating multiple actively growing shoots of field-grown seedling trees with E. amylovora isolate E153n via the cut-leaf method. Genotyping was conducted using the recently developed Axiom Pear 70 K Genotyping Array and chromosomal linkage groups were created for each population. An integrated two-way pseudo-testcross approach was used to map quantitative trait loci (QTLs). Resistance QTLs were identified on chromosome 2 for each population. The QTLs identified in the El Dorado × Potomac and Old Home × Bartlett populations are in the same region as QTLs that were previously identified in Harrow Sweet and Moonglow. The QTL in NJA2R59T69 mapped proximally to the previously identified QTLs and originated from an unknown Asian or occidental source. Future research will focus on further characterizing the resistance regions and developing tools for DNA-informed breeding.

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