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Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 July 2022) | Viewed by 20483

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Special Issue Editors

Dr. Anna M. Mastrangelo

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Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics, 24126 Bergamo, Italy
Interests: transcriptional and post-transcriptional regulation mechanisms; genetic analysis of quantitative traits related to grain yield and quality of cereals; functional analysis of abiotic stress regulated genes
Special Issues, Collections and Topics in MDPI journals

Dr. Elisabetta Mazzucotelli

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Research Centre for Genomics and Bioinformatics, Council for Agricultural and Economics Research (CREA), via San Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Fungal pathogens pose great challenges to crop production worldwide, with strong impacts on yield, quality, and safety. Especially in the context of current climate changes, new virulent races are emerging, which are overcoming established resistance genes in common cultivars. Moreover, they are spreading in areas in which they were not present before. Crop treatments with fungicides are not completely effective in protecting plants from pathogen attacks and raises serious concerns in terms of environmental pollution and agriculture sustainability. It is, therefore, of outstanding importance to develop new tools to strongly reduce the negative impacts of fungal diseases on crop production.

The purpose of this Special Issue is to present to the scientific community tools and methods to limit the damaging effects of fungal pathogens on crop production, taking a multidisciplinary approach. Manuscripts describing the genetic analysis of plant resistance to pathogens are welcome. New advances in crop genomics and breeding, along with the availability of the genome sequences for many cereal species, have opened up new opportunities for breeding, which were considered unthinkable only a few years ago, using new approaches to improve plant resistance. The impacts of fungal pathogens on crop production can also be limited through the correct use of agronomic practices. Manuscripts focused on these aspects are also welcomed in this Special Issue. Lastly, studies on epidemiology, especially in relation to the cultivars adopted by farmers, are very useful in understanding the diffusion and evolution of species and in adopting suitable solutions, including the choice of cultivars carrying specific R genes, in order to limit their impacts on crop production. Manuscripts are welcomed focusing on any of these aspects, which should report new information or novel viewpoints.

In addition, for manuscripts related to durum wheat genomics and breeding with a corresponding author or first author from developing and emerging countries, the Wheat Initiative through the Expert Working Group Durum Wheat Genomics and Breeding is offering an Open Access Grant. Application details can be found here on the website of the EWG Durum: https://www.wheatinitiative.org/durum

Dr. Anna M. Mastrangelo
Dr. Elisabetta Mazzucotelli
Guest Editors

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Keywords

crop fungal pathogens
functional genomics
resistance breeding
crop management

Published Papers (9 papers)

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Editorial

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3 pages, 185 KiB

Open AccessEditorial

Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management

by Elisabetta Mazzucotelli and Anna Maria Mastrangelo

Genes 2023, 14(9), 1758; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14091758 - 04 Sep 2023

Viewed by 702

Abstract

This Special Issue comprises a collection of eight peer-reviewed articles centered around the plant–pathogen interaction with the aim of proposing strategies that enhance plant resistance to pathogens and limit the damage to crop production, utilizing a multidisciplinary approach [...] Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

Research

Jump to: Editorial

17 pages, 870 KiB

Open AccessArticle

QTL Mapping of Stem Rust Resistance in Populations of Durum Wheat

by Daniela Marone, Elisabetta Mazzucotelli, Oadi Matny, Francesca Desiderio, Giuseppe Sciara, Marco Maccaferri, Ilaria Marcotuli, Agata Gadaleta, Brian Steffenson and Anna Maria Mastrangelo

Genes 2022, 13(10), 1793; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13101793 - 04 Oct 2022

Cited by 4 | Viewed by 1859

Abstract

Stem rinfectionust, caused by the fungus Puccinia graminis f. sp. tritici (Pgt), is one of the most devastating fungal diseases of durum and common wheat worldwide. The identification of sources of resistance and the validation of QTLs identified through genome-wide association studies is of paramount importance for reducing the losses caused by this disease to wheat grain yield and quality. Four segregating populations whose parents showed contrasting reactions to some Pgt races were assessed in the present study, and 14 QTLs were identified on chromosomes 3A, 4A, 6A, and 6B, with some regions in common between different segregating populations. Several QTLs were mapped to chromosomal regions coincident with previously mapped stem rust resistance loci; however, their reaction to different Pgt races suggest that novel genes or alleles could be present on chromosomes 3A and 6B. Putative candidate genes with a disease-related functional annotation have been identified in the QTL regions based on information available from the reference genome of durum cv. ‘Svevo’. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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13 pages, 3813 KiB

Open AccessArticle

Ethylene Plays a Dual Role during Infection by Plasmodiophora brassicae of Arabidopsis thaliana

by Kai Wang, Yiji Shi, Qingbin Sun, Mingjiao Lu, Lin Zheng, Bakirov Aldiyar, Chengyu Yu, Fengqun Yu, Aixia Xu and Zhen Huang

Genes 2022, 13(8), 1299; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13081299 - 22 Jul 2022

Cited by 2 | Viewed by 1510

Abstract

Plasmodiophora brassicae infection leads to hypertrophy of host roots and subsequent formation of galls, causing huge economic losses to agricultural producers of Cruciferae plants. Ethylene (ET) has been reported to play a vital role against necrotrophic pathogens in the classic immunity system. More clues suggested that the defense to pathogens in roots may be different from the acrial. The ET pathway may play a positive role in the infection of P. brassicae, as shown by recent transcriptome profiling. However, the molecular basis of ET remains poorly understood. In this study, we investigated the potential role of ethylene against P. brassicae infection in an ein3/eil1 double-mutant of Arabidopsis thaliana (A. thaliana). After infection, ein3/eil1 (Disease Index/DI: 93) showed more susceptibility compared with wild type (DI: 75). Then, we inoculated A. thaliana Columbia-0 (Col-0) with P. brassicae by 1-aminocyclopropane-1-carboxylic acid (ACC) and pyrazinamide (PZA), respectively. It was found that the symptoms of infected roots with ACC were more serious than those with PZA at 20 dpi (day post infection). However, the DI were almost the same in different treatments at 30 dpi. WRKY75 can be directly regulated by ET and was upregulated at 7 dpi with ACC, as shown by qRT-PCR. The wrky75-c mutant of A. thaliana (DI: 93.75) was more susceptible than the wild type in Arabidopsis. Thus, our work reveals the dual roles of ET in infection of P. brassicae and provides evidence of ET in root defense against pathogens. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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9 pages, 614 KiB

Open AccessArticle

Discovery of the New Leaf Rust Resistance Gene Lr82 in Wheat: Molecular Mapping and Marker Development

by Harbans S. Bariana, Prashanth Babu, Kerrie L. Forrest, Robert F. Park and Urmil K. Bansal

Genes 2022, 13(6), 964; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13060964 - 27 May 2022

Cited by 13 | Viewed by 2263

Abstract

Breeding for leaf rust resistance has been successful worldwide and is underpinned by the discovery and characterisation of genetically diverse sources of resistance. An English scientist, Arthur Watkins, collected pre-Green Revolution wheat genotypes from 33 locations worldwide in the early part of the 20th Century and this collection is now referred to as the ‘Watkins Collection’. A common wheat genotype, Aus27352 from Yugoslavia, showed resistance to currently predominating Australian pathotypes of the wheat leaf rust pathogen. We crossed Aus27352 with a leaf rust susceptible wheat selection Avocet S and a recombinant inbred line (RIL) F₆ population of 200 lines was generated. Initial screening at F₃ generation showed monogenic segregation for seedling response to leaf rust in Aus27352. These results were confirmed by screening the Aus27352/Avocet S RIL population. The underlying locus was temporarily named LrAW2. Bulked segregant analysis using the 90K Infinium SNP array located LrAW2 in the long arm of chromosome 2B. Tests with molecular markers linked to two leaf rust resistance genes, Lr50 and Lr58, previously located in chromosome 2B, indicated the uniqueness of LrAW2 and it was formally designated Lr82. Kompetitive allele-specific polymerase chain reaction assays were developed for Lr82-linked SNPs. KASP_22131 mapped 0.8 cM proximal to Lr82 and KASP_11333 was placed 1.2 cM distal to this locus. KASP_22131 showed 91% polymorphism among a set of 89 Australian wheat cultivars. We recommend the use of KASP_22131 for marker assisted pyramiding of Lr82 in breeding programs following polymorphism check on parents. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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20 pages, 4312 KiB

Open AccessArticle

Phenotyping Mediterranean Durum Wheat Landraces for Resistance to Zymoseptoria tritici in Tunisia

by Sarrah Ben M’Barek, Marwa Laribi, Hajer Kouki, Dalma Castillo, Chayma Araar, Meriem Nefzaoui, Karim Ammar, Carolina Saint-Pierre and Amor Hassine Yahyaoui

Genes 2022, 13(2), 355; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020355 - 16 Feb 2022

Cited by 9 | Viewed by 2893

Abstract

Durum wheat landraces have huge potential for the identification of genetic factors valuable for improving resistance to biotic stresses. Tunisia is known as a hot spot for Septoria tritici blotch disease (STB), caused by the fungus Zymoseptoria tritici (Z. tritici). In this context, a collection of 3166 Mediterranean durum wheat landraces were evaluated at the seedling and adult stages for STB resistance in the 2016–2017 cropping season under field conditions in Kodia (Tunisia). Unadapted/susceptible accessions were eliminated to reach the final set of 1059 accessions; this was termed the Med-collection, which comprised accessions from 13 countries and was also screened in the 2018–2019 cropping season. The Med-collection showed high frequency of resistance reactions, among which over 50% showed an immune reaction (HR) at both seedling and adult growth stages. Interestingly, 92% of HR and R accessions maintained their resistance levels across the two years, confirming the highly significant correlation found between seedling- and adult-stage reactions. Plant Height was found to have a negative significant effect on adult-stage resistance, suggesting that either this trait can influence disease severity, or that it can be due to environmental/epidemiological factors. Accessions from Italy showed the highest variability, while those from Portugal, Spain and Tunisia showed the highest levels of resistance at both growth stages, suggesting that the latter accessions may harbor novel QTLs effective for STB resistance. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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20 pages, 3855 KiB

Open AccessFeature PaperArticle

Characterization of Mediterranean Durum Wheat for Resistance to Pyrenophora tritici-repentis

by Marwa Laribi, Amor Hassine Yahyaoui, Wided Abdedayem, Hajer Kouki, Khaled Sassi and Sarrah Ben M’Barek

Genes 2022, 13(2), 336; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020336 - 11 Feb 2022

Cited by 3 | Viewed by 1857

Abstract

Tan spot (TS), caused by the fugus Pyrenophora tritici-repentis (Ptr), has gained significant importance in the last few years, thereby representing a threat to wheat production in all major wheat-growing regions, including Tunisia. In this context, we evaluated a Mediterranean collection of 549 durum wheat accessions under field conditions for resistance to Ptr over two cropping seasons in Jendouba (Tunisia), a hot spot for Ptr. The relative disease severities showed significant phenotypic variation from resistance to susceptibility. The correlation between disease scores over the two trials was significant, as 50% of the accessions maintained good levels of resistance (resistant–moderately resistant). Seedling and adult-stage reactions were significantly correlated. The ANOVA analysis revealed that the genotype term is highly significant at the adult stage, thus emphasizing the high genetic variability of the tested accessions. Reaction-type comparison among and between countries revealed a high diversity of TS resistance. Plant height (PH) was negatively correlated to disease scores, indicating that PH might either have a significant effect on TS severity or that it can be a potential disease escape trait. The evaluation of this collection allowed for the identification of potential diverse resistance sources to Ptr that can be incorporated in breeding programs. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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28 pages, 1422 KiB

Open AccessArticle

Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map

by Camilla Langlands-Perry, Murielle Cuenin, Christophe Bergez, Safa Ben Krima, Sandrine Gélisse, Pierre Sourdille, Romain Valade and Thierry C. Marcel

Genes 2022, 13(1), 100; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010100 - 31 Dec 2021

Cited by 12 | Viewed by 3202

Abstract

Quantitative resistance is considered more durable than qualitative resistance as it does not involve major resistance genes that can be easily overcome by pathogen populations, but rather a combination of genes with a lower individual effect. This durability means that quantitative resistance could be an interesting tool for breeding crops that would not systematically require phytosanitary products. Quantitative resistance has yet to reveal all of its intricacies. Here, we delve into the case of the wheat/Septoria tritici blotch (STB) pathosystem. Using a population resulting from a cross between French cultivar Renan, generally resistant to STB, and Chinese Spring, a cultivar susceptible to the disease, we built an ultra-dense genetic map that carries 148,820 single nucleotide polymorphism (SNP) markers. Phenotyping the interaction was done with two different Zymoseptoria tritici strains with contrasted pathogenicities on Renan. A linkage analysis led to the detection of three quantitative trait loci (QTL) related to resistance in Renan. These QTL, on chromosomes 7B, 1D, and 5D, present with an interesting diversity as that on 7B was detected with both fungal strains, while those on 1D and 5D were strain-specific. The resistance on 7B was located in the region of Stb8 and the resistance on 1D colocalized with Stb19. However, the resistance on 5D was new, so further designated Stb20q. Several wall-associated kinases (WAK), nucleotide-binding and leucine-rich repeats (NB-LRR) type, and kinase domain carrying genes were present in the QTL regions, and some of them were expressed during the infection. These results advocate for a role of Stb genes in quantitative resistance and for resistance in the wheat/STB pathosystem being as a whole quantitative and polygenic. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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23 pages, 5204 KiB

Open AccessArticle

Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection

by Gyan P. Mishra, Muraleedhar S. Aski, Tejas Bosamia, Shiksha Chaurasia, Dwijesh Chandra Mishra, Jyotika Bhati, Atul Kumar, Shaily Javeria, Kuldeep Tripathi, Manju Kohli, Ranjeet Ranjan Kumar, Amit Kumar Singh, Jyoti Devi, Shiv Kumar and Harsh Kumar Dikshit

Genes 2022, 13(1), 90; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010090 - 29 Dec 2021

Cited by 12 | Viewed by 3039

Abstract

Dry root rot (Rhizoctonia bataticola) is an important disease of lentils (Lens culinaris Medik.).To gain an insight into the molecular aspects of host-pathogen interactions, the RNA-seq approach was used in lentils following inoculation with R.bataticola. The RNA-Seq has generated >450 million high-quality reads (HQRs) and nearly 96.97% were properly aligned to the reference genome. Very high similarity in FPKM (fragments per kilobase of exon per million mapped fragments) values (R > 0.9) among biological replicates showed the consistency of the RNA-Seq results. The study revealed various DEGs (differentially expressed genes) that were associated with changes in phenolic compounds, transcription factors (TFs), antioxidants, receptor kinases, hormone signals which corresponded to the cell wall modification enzymes, defense-related metabolites, and jasmonic acid (JA)/ethylene (ET) pathways. Gene ontology (GO) categorization also showed similar kinds of significantly enriched similar GO terms. Interestingly, of the total unigenes (42,606), 12,648 got assembled and showed significant hit with Rhizoctonia species. String analysis also revealed the role of various disease responsive proteins viz., LRR family proteins, LRR-RLKs, protein kinases, etc. in the host-pathogen interaction. Insilico validation analysis was performed using Genevestigator^® and DEGs belonging to six major defense-response groups viz., defense-related enzymes, disease responsive genes, hormones, kinases, PR (pathogenesis related) proteins, and TFs were validated. For the first time some key miRNA targets viz. miR156, miR159, miR167, miR169, and miR482 were identified from the studied transcriptome, which may have some vital role in Rhizoctonia-based responses in lentils. The study has revealed the molecular mechanisms of the lentil/R.bataticola interactions and also provided a theoretical approach for the development of lentil genotypes resistant to R.bataticola. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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13 pages, 2801 KiB

Open AccessArticle

Population Genetic Structures of Puccinia striiformis f. sp. tritici in the Gansu-Ningxia Region and Hubei Province, China

by Cuicui Wang, Bingbing Jiang, Junmin Liang, Leifu Li, Yilin Gu, Jintang Li, Yong Luo and Zhanhong Ma

Genes 2021, 12(11), 1712; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111712 - 27 Oct 2021

Cited by 6 | Viewed by 1736

Abstract

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a destructive wheat disease in China. The Gansu–Ningxia region (GN) is a key area for pathogen over-summering in China, and northwestern Hubei (HB) is an important region for pathogen over-wintering, serving as a source of inoculum in spring epidemic regions. The spatiotemporal population genetic structure of Pst in HB and the pathogen population exchanges between GN and HB are important for estimating the risk of interregional epidemics. Here, 567 isolates from GN and HB were sampled from fall 2016 to spring 2018 and were genotyped using simple sequence repeat markers. The genotypic and genetic diversity of Pst subpopulations in HB varied among seasons and locations. Greater genetic diversification levels were found in the spring compared with fall populations using principal coordinate analysis and Bayesian assignments. In total, there were 17 common genotypes among the 208 determined, as shown by a small overlap of genotypes in the principal coordinate analysis and dissimilar Bayesian assignments in both regions, which revealed the limited genotype exchange between the populations of GN and HB. Full article

(This article belongs to the Special Issue Coping with Fungal Diseases in Crops: New Advances in Genomics, Breeding and Management)

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