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Genetics and Epigenetics of Biotic Stress Response in Plants
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Genetics and Epigenetics of Biotic Stress Response in Plants

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

Deadline for manuscript submissions: closed (20 April 2021) | Viewed by 58294

Special Issue Editors

Prof. Dr. Rosa Rao

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Guest Editor
Università degli Studi di Napoli Federico II, Dipartimento di Agraria, Napoles, Italy
Prof. Dr. Giandomenico Corrado

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Guest Editor
Università degli Studi di Napoli Federico II, Naples, Italy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biotic stress causes significant agricultural losses in spite of the constant progress in fighting adverse organisms. Currently, there is an unmet need for more eco-efficient and effective strategies to increase plant resistance to stress. In agriculture, increases in resource efficiency, environmental performance, and food primary production need to be supported by basic science and translational research. The implementation of improved or novel approaches are strongly dependent on the advancement of knowledge on the plant interaction with biotic stressors. This information is the bases towards an environmentally safer agriculture and ultimately, the foundation of a science-driven bio-based economy.

The forthcoming Special Issue aims to provide an overview of recent topics on plant genetics and epigenetics in plant–biotic stress response, with emphasis on fundamental or applied studies that aim to decipher the dynamic molecular responses of plants as they adapt and respond to other living organisms (beneficial and antagonistic). Priority will be also given to works that elucidate the changes in plant growth, development, and yield induced by a stress, or that report on the molecular basis of the plastic phenotypic response of the plants to the environment. Moreover, studies on the genetic and epigenetic regulatory networks that underpin plant response to single or combined stresses, including abiotic stress, are also welcome. Topics also include the phenotypic and molecular evaluation of plant germplasm in relation to biotic stress, the detection and validation of genes or genomic regions involved in plant–stress interaction, and (pre-)breeding efforts to increase tolerance or resistance, also using biotechnological and genomic approaches.

Prof. Rosa Rao
Prof. Giandomenico Corrado
Guest Editors

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Keywords

  • gene expression
  • transcription
  • network models
  • antagonists
  • beneficial organisms
  • insects
  • fungi
  • bacteria
  • viruses
  • DNA methylation
  • smallRNA
  • genomics
  • transcriptomics
  • epigenomics
  • biotechnology
  • genome editing

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Published Papers (10 papers)

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Research

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22 pages, 5981 KiB  
Article
Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice
by Ruchi Bansal, Nitika Rana, Akshay Singh, Pallavi Dhiman, Rushil Mandlik, Humira Sonah, Rupesh Deshmukh and Tilak Raj Sharma
Genes 2020, 11(12), 1412; https://doi.org/10.3390/genes11121412 - 26 Nov 2020
Cited by 6 | Viewed by 3344
Abstract
Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies [...] Read more.
Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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24 pages, 4823 KiB  
Article
Knockout of Pi21 by CRISPR/Cas9 and iTRAQ-Based Proteomic Analysis of Mutants Revealed New Insights into M. oryzae Resistance in Elite Rice Line
by Gul Nawaz, Babar Usman, Haowen Peng, Neng Zhao, Ruizhi Yuan, Yaoguang Liu and Rongbai Li
Genes 2020, 11(7), 735; https://doi.org/10.3390/genes11070735 - 2 Jul 2020
Cited by 54 | Viewed by 8086
Abstract
Rice blast (Magnaporthe oryzae) is a devastating disease affecting rice production globally. The development of cultivars with host resistance has been proved to be the best strategy for disease management. Several rice-resistance genes (R) have been recognized which induce resistance to [...] Read more.
Rice blast (Magnaporthe oryzae) is a devastating disease affecting rice production globally. The development of cultivars with host resistance has been proved to be the best strategy for disease management. Several rice-resistance genes (R) have been recognized which induce resistance to blast in rice but R gene-mediated mechanisms resulting in defense response still need to be elucidated. Here, mutant lines generated through CRISPR/Cas9 based targeted mutagenesis to investigate the role of Pi21 against blast resistance and 17 mutant plants were obtained in T0 generation with the mutation rate of 66% including 26% bi-allelic, 22% homozygous, 12% heterozygous, and 3% chimeric and 17 T-DNA-free lines in T1 generation. The homozygous mutant lines revealed enhanced resistance to blast without affecting the major agronomic traits. Furthermore, comparative proteome profiling was adopted to study the succeeding proteomic regulations, using iTRAQ-based proteomic analysis. We identified 372 DEPs, among them 149 up and 223 were down-regulated, respectively. GO analysis revealed that the proteins related to response to stimulus, photosynthesis, carbohydrate metabolic process, and small molecule metabolic process were up-regulated. The most of DEPs were involved in metabolic, ribosomal, secondary metabolites biosynthesis, and carbon metabolism pathways. 40S ribosomal protein S15 (P31674), 50S ribosomal protein L4, L5, L6 (Q10NM5, Q9ZST0, Q10L93), 30S ribosomal protein S5, S9 (Q6YU81, Q850W6, Q9XJ28), and succinate dehydrogenase (Q9S827) were hub-proteins. The expression level of genes related to defense mechanism, involved in signaling pathways of jasmonic acid (JA), salicylic acid (SA), and ethylene metabolisms were up-regulated in mutant line after the inoculation of the physiological races of M. oryzae as compared to WT. Our results revealed the fundamental value of genome editing and expand knowledge about fungal infection avoidance in rice. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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18 pages, 602 KiB  
Article
Identification of QTLs for Resistance to Fusarium Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035
by Alejandro Castro Aviles, Stephen Alan Harrison, Kelly Joseph Arceneaux, Gina Brown-Guidera, Richard Esten Mason and Niranjan Baisakh
Genes 2020, 11(6), 699; https://doi.org/10.3390/genes11060699 - 25 Jun 2020
Cited by 14 | Viewed by 3626
Abstract
Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high [...] Read more.
Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high inoculum pressure from corn stubble contribute to frequent FHB epidemics in the southern United States. The soft red winter wheat variety AGS 2060 is moderately susceptible (as opposed to susceptible) to FHB and regularly found in pedigrees of resistant breeding lines. AGS 2060 does not carry any known resistance genes or quantitative trait loci (QTL). A QTL mapping study was conducted to determine the location and genetic effect of its resistance using a doubled haploid mapping population produced from a cross between wheat varieties AGS 2060 and AGS 2035 (FHB susceptible). The population was genotyped using the Illumina iSelect single nucleotide polymorphism (SNP) array for wheat and phenotyped in Baton Rouge and Winnsboro, Louisiana and Newport, Arkansas in 2018 and 2019. The effect of genotype was significant for Fusarium damaged kernels (FDK) and deoxynivalenol (DON) content across all locations and years, indicating genetic variation in the population. The study detected 13 QTLs (one each on chromosome 1A, 1B, 1D, 2A, 2B, 6A, 6B, 7A, and 7B, and two each on 5A and 5B) responsible for the reduction of FDK and/or DON. Of these, nine QTLs for FHB resistance were identified in Winnsboro, Louisiana, in 2019. QTLs on chromosomes 2A and 7A could be valuable sources of resistance to both DON and FDK over several environments and were likely the best candidates for use in marker-assisted selection. Consistently expressed QTLs on chromosomes 5A, 6B, and 7A were potentially newly identified sources of resistance to FHB in soft red winter wheat. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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16 pages, 1767 KiB  
Article
Genotyping by Sequencing Revealed QTL Hotspots for Trichome-Based Plant Defense in Gossypium hirsutum
by Haris Ahmed, Mian Faisal Nazir, Zhoe Pan, Wenfang Gong, Muhammad Shahid Iqbal, Shoupu He and Xiongming Du
Genes 2020, 11(4), 368; https://doi.org/10.3390/genes11040368 - 28 Mar 2020
Cited by 13 | Viewed by 5254
Abstract
Cotton possesses certain physical features, including leaf and stem trichomes that help plants deter damage caused by insect pests, and to some extent, from abiotic factors as well. Among those features, trichomes (pubescence) hold a special place as a first line of defense [...] Read more.
Cotton possesses certain physical features, including leaf and stem trichomes that help plants deter damage caused by insect pests, and to some extent, from abiotic factors as well. Among those features, trichomes (pubescence) hold a special place as a first line of defense and a managemental tool against sucking insect pests of cotton. Different insect pests of cotton (whiteflies, aphids, jassids, and boll weevil) severely damage the yield and quality of the crop. Likewise, whiteflies, aphids, jassids, and other insect pests are considered as potential carriers for cotton leaf curl viruses and other diseases. Genotyping by sequencing (GBS) study was conducted to understand and explore the genomic regions governing hairy (Pubescence) leaves and stem phenotypes. A total of 224 individuals developed from an intraspecific cross (densely haired cotton (Liaoyang duomao mian) × hairless cotton (Zong 128)) and characterized phenotypically for leaf and stem pubescence in different environments. Here we identify and report significant QTLs (quantitative trait loci) associated with leaf and stem pubescence, and the response of plant under pest (aphid) infestation. Further, we identified putative genes colocalized on chromosome A06 governing mechanism for trichome development and host–pest interaction. Our study provides a comprehensive insight into genetic architecture that can be employed to improve molecular marker-assisted breeding programs aimed at developing biotic (insect pests) resilient cotton cultivars. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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24 pages, 4175 KiB  
Article
Ectopic Expression of AhGLK1b (GOLDEN2-like Transcription Factor) in Arabidopsis Confers Dual Resistance to Fungal and Bacterial Pathogens
by Niaz Ali, Hua Chen, Chong Zhang, Shahid Ali Khan, Mamadou Gandeka, Dongyang Xie and Weijian Zhuang
Genes 2020, 11(3), 343; https://doi.org/10.3390/genes11030343 - 24 Mar 2020
Cited by 23 | Viewed by 5717
Abstract
GOLDEN2-LIKE (GLK) is a member of the myeloblastosis (MYB) family transcription factor and it plays an important role in the regulation of plastid development and stress tolerance. In this study, a gene named AhGLK1b was identified from a cultivated peanut showing down-regulation in [...] Read more.
GOLDEN2-LIKE (GLK) is a member of the myeloblastosis (MYB) family transcription factor and it plays an important role in the regulation of plastid development and stress tolerance. In this study, a gene named AhGLK1b was identified from a cultivated peanut showing down-regulation in response to low calcium with a complete open reading frame (ORF) of 1212 bp. The AhGLK1b has 99.26% and 96.28% sequence similarities with its orthologs in Arachis ipaensis and A. duranensis, respectively. In the peanut, the AhGLK1b was localized in the nucleus and demonstrated the highest expression in the leaf, followed by the embryo. Furthermore, the expression of AhGLK1b was induced significantly in response to a bacterial pathogen, Ralstonia solanacearum infection. Ectopic expression of AhGLK1b in Arabidopsis showed stronger resistance against important phytopathogenic fungi S. sclerotiorum. It also exhibited high resistance to infection of the bacterial pathogen Pst DC3000. AhGLK1b-expressing Arabidopsis induced defense-related genes including PR10 and Phox/Bem 1 (PBI), which are involved in multiple disease resistance. Taken together, the results suggest that AhGLK1b might be useful in providing dual resistance to fungal and bacterial pathogens as well as tolerance to abiotic stresses. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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20 pages, 2046 KiB  
Article
Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.)
by Hyo Chul Kim, Kyung-Hee Kim, Kitae Song, Jae Yoon Kim and Byung-Moo Lee
Genes 2020, 11(2), 191; https://doi.org/10.3390/genes11020191 - 11 Feb 2020
Cited by 19 | Viewed by 4506
Abstract
Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed [...] Read more.
Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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17 pages, 4671 KiB  
Article
RNA Sequencing Reveals That Both Abiotic and Biotic Stress-Responsive Genes are Induced during Expression of Steroidal Glycoalkaloid in Potato Tuber Subjected to Light Exposure
by Weina Zhang, Cunwu Zuo, Zhongjian Chen, Yichen Kang and Shuhao Qin
Genes 2019, 10(11), 920; https://doi.org/10.3390/genes10110920 - 11 Nov 2019
Cited by 15 | Viewed by 4889
Abstract
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and [...] Read more.
Steroidal glycoalkaloids (SGAs), which are widely produced by potato, even in other Solanaceae plants, are a class of potentially toxic compounds, but are beneficial to host resistance. However, changes of the other metabolic process along with SGA accumulation are still poorly understood and researched. Based on RNA sequencing (RNA-seq) and bioinformatics analysis, the global gene expression profiles of potato variety Helan 15 (Favorita) was investigated at four-time points during light exposure. The data was further verified by using quantitative Real-time PCR (qRT-PCR). When compared to the control group, 1288, 1592, 1737, and 1870 differentially expressed genes (DEGs) were detected at 6 h, 24 h, 48 h, and 8 d, respectively. The results of both RNAseq and qRT-PCR showed that SGA biosynthetic genes were up-regulated in the potato tuber under light exposure. Functional enrichment analysis revealed that genes related to PS light reaction and Protein degradation were significantly enriched in most time points of light exposure. Additionally, enriched Bins included Receptor kinases, Secondary metabolic process in flavonoids, Abiotic stress, and Biotic stress in the early stage of light exposure, but PS Calvin cycle, RNA regulation of transcription, and UDP glucosyl and glucoronyl transferases in the later stage. Most of the DEGs involved in PS light reaction and Abiotic stress were up-regulated at all four time points, whereas DEGs that participated in biotic stresses were mainly up-regulated at the later stage (48 h and 8 d). Cis-element prediction and co-expression assay were used to confirm the expressional correlation between genes that are responsible for SGA biosynthesis and disease resistance. In conclusion, the expressions of genes involved in PS light reaction, Abiotic stress, and Biotic stress were obviously aroused during the accumulation of SGAs induced by light exposure. Moreover, an increased defense response might contribute to the potato resistance to the infection by phytopathogenic microorganisms. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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15 pages, 8692 KiB  
Article
The CaAP2/ERF064 Regulates Dual Functions in Pepper: Plant Cell Death and Resistance to Phytophthora capsici
by Jing-Hao Jin, Huai-Xia Zhang, Muhammad Ali, Ai-Min Wei, De-Xu Luo and Zhen-Hui Gong
Genes 2019, 10(7), 541; https://doi.org/10.3390/genes10070541 - 17 Jul 2019
Cited by 23 | Viewed by 4415
Abstract
Phytophthora blight is one of the most destructive diseases of pepper (Capsicum annuum L.) globally. The APETALA2/Ethylene Responsive Factors (AP2/ERF) genes play a crucial role in plant response to biotic stresses but, to date, have not been studied in the [...] Read more.
Phytophthora blight is one of the most destructive diseases of pepper (Capsicum annuum L.) globally. The APETALA2/Ethylene Responsive Factors (AP2/ERF) genes play a crucial role in plant response to biotic stresses but, to date, have not been studied in the context of Phytophthora resistance in pepper. Here, we documented potential roles for the pepper CaAP2/ERF064 gene in inducing cell death and conferring resistance to Phytophthora capsici (P. capsici) infection. Results revealed that the N-terminal, AP2 domain, and C-terminal of CaAP2/ERF064 protein is responsible for triggering cell death in Nicotiana benthamiana (N. benthamiana). Moreover, the transcription of CaAP2/ERF064 in plant is synergistically regulated by the Methyl-Jasmonate (MeJA) and ethephon (ET) signaling pathway. CaAP2/ERF064 was found to regulate the expression of CaBPR1, which is a pathogenesis-related (PR) gene of pepper. Furthermore, the silencing of CaAP2/ERF064 compromised the pepper plant resistance to P. capsici by reducing the transcript level of defense-related genes CaBPR1, CaPO2, and CaSAR82, while the ectopic expression of CaAP2/ERF064 in N. benthamiana plant elevated the expression level of NbPR1b and enhanced resistance to P. capsici. These results suggest that CaAP2/ERF064 could positively regulate the defense response against P. capsici by modulating the transcription of PR genes in the plant. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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23 pages, 6066 KiB  
Article
DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing
by Yuyan Sun, Min Fan and Yanjun He
Genes 2019, 10(5), 344; https://doi.org/10.3390/genes10050344 - 7 May 2019
Cited by 32 | Viewed by 5019
Abstract
DNA methylation is an important epigenetic mark associated with plant immunity, but little is known about its roles in viral infection of watermelon. We carried out whole-genome bisulfite sequencing of watermelon leaves at 0 h (ck), 48 h, and 25 days post-inoculation with [...] Read more.
DNA methylation is an important epigenetic mark associated with plant immunity, but little is known about its roles in viral infection of watermelon. We carried out whole-genome bisulfite sequencing of watermelon leaves at 0 h (ck), 48 h, and 25 days post-inoculation with Cucumber green mottle mosaic virus (CGMMV). The number of differentially methylated regions (DMRs) increased during CGMMV infection and 2788 DMR-associated genes (DMGs) were screened out among three libraries. Most DMRs and DMGs were obtained under the CHH context. These DMGs were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of secondary biosynthesis and metabolism, plant–pathogen interactions, Toll-like receptor signaling, and ABC transporters. Additionally, DMGs encoding PR1a, CaMs, calcium-binding protein, RIN4, BAK1, WRKYs, RBOHs, STKs, and RLPs/RLKs were involved in the watermelon–CGMMV interaction and signaling. The association between DNA methylation and gene expression was analyzed by RNA-seq and no clear relationship was detected. Moreover, downregulation of genes in the RdDM pathway suggested the reduced RdDM-directed CHH methylation plays an important role in antiviral defense in watermelon. Our findings provide genome-wide DNA methylation profiles of watermelon and will aid in revealing the molecular mechanism in response to CGMMV infection at the methylation level. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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Review

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19 pages, 1931 KiB  
Review
Tomato Natural Resistance Genes in Controlling the Root-Knot Nematode
by Ahmed H. El-Sappah, Islam M. M., Hamada H. El-awady, Shi Yan, Shiming Qi, Jingyi Liu, Guo-ting Cheng and Yan Liang
Genes 2019, 10(11), 925; https://doi.org/10.3390/genes10110925 - 14 Nov 2019
Cited by 83 | Viewed by 11990
Abstract
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to [...] Read more.
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to the RKN have already been identified as Mi-1, Mi-2, Mi-3, Mi-4, Mi-5, Mi-6, Mi-7, Mi-8, Mi-9, and Mi-HT. Only five of these genes have been mapped. The major problem is that their resistance breaks down at high temperatures. Some of these genes still work at high temperatures. In this paper, the mechanism and characteristics of these natural resistance genes are summarized. Other difficulties in using these genes in the resistance and how to improve them are also mentioned. Full article
(This article belongs to the Special Issue Genetics and Epigenetics of Biotic Stress Response in Plants)
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