scholarly journals Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

2014 ◽  
Vol 27 (3) ◽  
pp. 196-206 ◽  
Author(s):  
Vivianne G. A. A. Vleeshouwers ◽  
Richard P. Oliver
Keyword(s):  
Fungicide Resistance ◽  
Plant Pathogens ◽  
Functional Characterization ◽  
Resistance Breeding ◽  
World Population ◽  
Breeding Programs ◽  
Genome Wide ◽  
Disease Resistance Breeding ◽  
Pathogen Populations ◽  
New Strategies

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. “Effectoromics” has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

scholarly journals The Age of Effectors: Genome-Based Discovery and Applications

2016 ◽  
Vol 106 (10) ◽  
pp. 1206-1212 ◽  
Author(s):  
Hesham A. Y. Gibriel ◽  
Bart P. H. J. Thomma ◽  
Michael F. Seidl
Keyword(s):  
Plant Pathogen ◽  
Plant Pathogens ◽  
Gene Annotation ◽  
Functional Characterization ◽  
Resistance Breeding ◽  
Infection Process ◽  
Microbial Pathogens ◽  
Global Food Security ◽  
Pathogen Effector ◽  
Pathogen Populations

Microbial pathogens cause devastating diseases on economically and ecologically important plant species, threatening global food security, and causing billions of dollars of losses annually. During the infection process, pathogens secrete so-called effectors that support host colonization, often by deregulating host immune responses. Over the last decades, much of the research on molecular plant-microbe interactions has focused on the identification and functional characterization of such effectors. The increasing availability of sequenced plant pathogen genomes has enabled genomics-based discovery of effector candidates. Nevertheless, identification of full plant pathogen effector repertoires is often hampered by erroneous gene annotation and the localization effector genes in genomic regions that are notoriously difficult to assemble. Here, we argue that recent advances in genome sequencing technologies, genome assembly, gene annotation, as well as effector identification methods hold promise to disclose complete and correct effector repertoires. This allows to exploit complete effector repertoires, and knowledge of their diversity within pathogen populations, to develop durable and sustainable resistance breeding strategies, disease control, and management of plant pathogens.

scholarly journals At Least Two Origins of Fungicide Resistance in Grapevine Downy Mildew Populations

2007 ◽  
Vol 73 (16) ◽  
pp. 5162-5172 ◽  
Author(s):  
Wei-Jen Chen ◽  
François Delmotte ◽  
Sylvie Richard Cervera ◽  
Lisette Douence ◽  
Charles Greif ◽  
...  
Keyword(s):  
Plant Pathogen ◽  
Fungicide Resistance ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Plasmopara Viticola ◽  
Isolated Populations ◽  
Grapevine Downy Mildew ◽  
First Case ◽  
Wide Range ◽  
Pathogen Populations

ABSTRACT Quinone outside inhibiting (QoI) fungicides represent one of the most widely used groups of fungicides used to control agriculturally important fungal pathogens. They inhibit the cytochrome bc 1 complex of mitochondrial respiration. Soon after their introduction onto the market in 1996, QoI fungicide-resistant isolates were detected in field plant pathogen populations of a large range of species. However, there is still little understanding of the processes driving the development of QoI fungicide resistance in plant pathogens. In particular, it is unknown whether fungicide resistance occurs independently in isolated populations or if it appears once and then spreads globally by migration. Here, we provide the first case study of the evolutionary processes that lead to the emergence of QoI fungicide resistance in the plant pathogen Plasmopara viticola. Sequence analysis of the complete cytochrome b gene showed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Phylogenetic analysis of a large mitochondrial DNA fragment including the cytochrome b gene (2,281 bp) across a wide range of European P. viticola isolates allowed the detection of four major haplotypes belonging to two distinct clades, each of which contains a different QoI fungicide resistance allele. This is the first demonstration that a selected substitution conferring resistance to a fungicide has occurred several times in a plant-pathogen system. Finally, a high population structure was found when the frequency of QoI fungicide resistance haplotypes was assessed in 17 French vineyards, indicating that pathogen populations might be under strong directional selection for local adaptation to fungicide pressure.

scholarly journals Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261461
Author(s):  
Girma Mengistu ◽  
Hussein Shimelis ◽  
Ermias Assefa ◽  
Dagnachew Lule
Keyword(s):  
Sorghum Bicolor ◽  
Resistance Breeding ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Breeding Programs ◽  
Anthracnose Resistance ◽  
Progress Curve ◽  
Genome Wide ◽  
Population Structure Analysis

In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.

scholarly journals Selection of Host Differentials for Elucidating Pathogenic Variation in Magnaporthe grisea Populations Adapted to Finger Millet (Eleusine coracana)

Plant Disease ◽  
2015 ◽  
Vol 99 (12) ◽  
pp. 1784-1789 ◽  
Author(s):  
Talluri Kiran Babu ◽  
Rajan Sharma ◽  
R. P. Thakur ◽  
Hari D. Upadhyaya ◽  
P. Narayan Reddy ◽  
...  
Keyword(s):  
Andhra Pradesh ◽  
Magnaporthe Grisea ◽  
Finger Millet ◽  
Blast Resistance ◽  
Resistance Breeding ◽  
Breeding Programs ◽  
Pathogenic Variation ◽  
Differential Set ◽  
Disease Resistance Breeding ◽  
Selection Of

Blast, caused by Pyricularia grisea (teleomorph: Magnaporthe grisea), is the most devastating disease of finger millet affecting production, utilization, and trade in Africa and Southeast Asia. An attempt was made to select a set of putative host differentials that can be used to determine virulence diversity in finger-millet-infecting populations of M. grisea. Thus, a differential set comprising eight germplasm accessions selected from finger millet core collection (IE 2911, IE 2957, IE 3392, IE 4497, IE 5091, IE 6240, IE 6337, and IE 7079) and a resistant (‘GPU 28’) and a susceptible (‘VR 708’) variety was developed. This differential set was used to study pathogenic variation in 25 isolates of M. grisea collected from Karnataka, Telangana, and Andhra Pradesh states in India. Based on the reaction (virulent = score ≥4 and avirulent = score ≤3 on a 1-to-9 scale) on host differentials, nine pathotypes were identified among 25 M. grisea isolates. Pathotype 9, represented by isolate Pg23 from Vizianagaram, was the most virulent because it could infect all of the host differentials except GPU 28. This study will be helpful in devising strategies for monitoring virulence change in M. grisea populations, and for identification of blast resistance in finger millet for use in disease resistance breeding programs.

scholarly journals Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
John T. Dobbs ◽  
Mee-Sook Kim ◽  
Nicklos S. Dudley ◽  
Ned B. Klopfenstein ◽  
Aileen Yeh ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Early Detection ◽  
Fusarium Oxysporum ◽  
Resistance Breeding ◽  
Wilt Disease ◽  
Disease Development ◽  
Whole Genome ◽  
Breeding Programs ◽  
Disease Resistance Breeding ◽  
Highly Virulent

Abstract Background Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. Results This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. Conclusions These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.

scholarly journals The Ficus erecta genome to identify the Ceratocystis canker resistance gene for breeding programs in common fig (F. carica)

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Hiroshi Yakushiji ◽  
Ryotaro Nishimura ◽  
Takeshige Morita ◽  
Shota Jikumaru ◽  
...  
Keyword(s):  
Single Molecule ◽  
Resistance Breeding ◽  
Nucleotide Polymorphisms ◽  
Donor Genome ◽  
Breeding Programs ◽  
Common Fig ◽  
Genome Wide ◽  
Resistance Trait ◽  
Whole Genome Resequencing ◽  
Recurrent Backcrossing

AbstractFicus erecta, a wild relative of common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programs. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig; however, this is time consuming and labor-intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programs. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51,806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site associated DNA sequencing. Subsequent linkage analysis and whole genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled selection of female lines that possessed resistance and effective elimination of donor genome from progeny. The genome resources provided in this study will accelerate and enhance disease resistance breeding programs in fig.

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