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Functional Characterization of Two RNA Methyltransferase Genes METTL3 and METTL14 Uncovers the Roles of m 6A in Mediating Adaptation of Plutella xylostella to Host Plants. Int J Mol Sci 2022; 23:ijms231710013. [PMID: 36077410 PMCID: PMC9456542 DOI: 10.3390/ijms231710013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the major epigenetic modifications in eukaryotes. Although increasing functions of m6A have been identified in insects, its role in Plutella xylostella L. for host plant adaptation remains unclear. In the current study, we show that the m6A content of P. xylostella was relatively low in different developmental stages and tissues, with no significant differences. Two RNA methyltransferase genes, PxMETTL3 (methyltransferase-like 3) and PxMETTL14 (methyltransferase-like 14), were identified and characterized. PxMETTL3 could be transcribed into two transcripts, and PxMETTL14 had only one transcript; both of these genes were highly expressed in egg and adult stages and reproductive tissues. The CRISPR/Cas9-mediated knockout of PxMETTL3 (ΔPxMETTL3-2) or PxMETTL14 (ΔPxMETTL14-14) confirmed their function in m6A installation into RNA. Furthermore, upon transfer from an artificial diet to the host plant, the mutant strains were affected in terms of larval and pupal weight or adult emergence rate, while the wildtype (WT) strain did not exhibit any difference. In addition, the fecundity and egg hatching rate of the WT strain decreased significantly, whereas only the ΔPxMETTL14-14 mutant strain displayed significantly decreased fecundity. There seemed to be a tradeoff between the stress adaptation and reproduction in P. xylostella mediated by m6A modification. During host transfer, the expression of PxMETTL14 was consistent with the change in m6A content, which implied that PxMETTL14 could respond to host plant defense effectively, and may regulate m6A content. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed transcripts with changes in m6A levels revealed that the potential functions of m6A-related genes may be involved in steroid biosynthesis for larval performance and metabolic pathways for adult reproduction. Overall, our work reveals an epigenetic regulation mechanism for the rapid adaptation of P. xylostella to variations in the host environment.
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Xie Y, Nachappa P, Nalam VJ, Pearce S. Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus 2 ( Wsm2) in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:928949. [PMID: 35845691 PMCID: PMC9285007 DOI: 10.3389/fpls.2022.928949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed Wsm2 as a major locus conferring WSMV resistance in wheat. The Wsm2 flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that Wsm2 lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety "Snowmass", which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in "Snowmass" compared to "Antero," a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in "Snowmass," three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.
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Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Punya Nachappa
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Vamsi J. Nalam
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
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Emebiri L, Hildebrand S, Tan MK, Juliana P, Singh PK, Fuentes-Davila G, Singh RP. Pre-emptive Breeding Against Karnal Bunt Infection in Common Wheat: Combining Genomic and Agronomic Information to Identify Suitable Parents. FRONTIERS IN PLANT SCIENCE 2021; 12:675859. [PMID: 34394138 PMCID: PMC8358121 DOI: 10.3389/fpls.2021.675859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Wheat (Triticum aestivum L.) is the most widely grown cereal crop in the world and is staple food to half the world's population. The current world population is expected to reach 9.8 billion people by 2050, but food production is not expected to keep pace with demand in developing countries. Significant opportunities exist for traditional grain exporters to produce and export greater amounts of wheat to fill the gap. Karnal bunt, however, is a major threat, due to its use as a non-tariff trade barrier by several wheat-importing countries. The cultivation of resistant varieties remains the most cost-effective approach to manage the disease, but in countries that are free of the disease, genetic improvement is difficult due to quarantine restrictions. Here we report a study on pre-emptive breeding designed to identify linked molecular markers, evaluate the prospects of genomic selection as a tool, and prioritise wheat genotypes suitable for use as parents. In a genome-wide association (GWAS) study, we identified six DArTseq markers significantly linked to Karnal bunt resistance, which explained between 7.6 and 29.5% of the observed phenotypic variation. The accuracy of genomic prediction was estimated to vary between 0.53 and 0.56, depending on whether it is based solely on the identified Quantitative trait loci (QTL) markers or the use of genome-wide markers. As genotypes used as parents would be required to possess good yield and phenology, further research was conducted to assess the agronomic value of Karnal bunt resistant germplasm from the International Maize and Wheat Improvement Center (CIMMYT). We identified an ideal genotype, ZVS13_385, which possessed similar agronomic attributes to the highly successful Australian wheat variety, Mace. It is phenotypically resistant to Karnal bunt infection (<1% infection) and carried all the favourable alleles detected for resistance in this study. The identification of a genotype combining Karnal bunt resistance with adaptive agronomic traits overcomes the concerns of breeders regarding yield penalty in the absence of the disease.
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Affiliation(s)
- Livinus Emebiri
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, NSW, Australia
| | - Shane Hildebrand
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Mui-Keng Tan
- NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Philomin Juliana
- International Maize and Wheat Improvement Center, Mexico City, Mexico
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center, Mexico City, Mexico
| | | | - Ravi P. Singh
- International Maize and Wheat Improvement Center, Mexico City, Mexico
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A central circadian oscillator confers defense heterosis in hybrids without growth vigor costs. Nat Commun 2021; 12:2317. [PMID: 33875651 PMCID: PMC8055661 DOI: 10.1038/s41467-021-22268-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/05/2021] [Indexed: 11/10/2022] Open
Abstract
Plant immunity frequently incurs growth penalties, which known as the trade-off between immunity and growth. Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits but rarely for disease resistance. Here, we report that the central circadian oscillator, CCA1, confers heterosis for bacterial defense in hybrids without growth vigor costs, and it even significantly enhances the growth heterosis of hybrids under pathogen infection. The genetic perturbation of CCA1 abrogated heterosis for both defense and growth in hybrids. Upon pathogen attack, the expression of CCA1 in F1 hybrids is precisely modulated at different time points during the day by its rhythmic histone modifications. Before dawn of the first infection day, epigenetic activation of CCA1 promotes an elevation of salicylic acid accumulation in hybrids, enabling heterosis for defense. During the middle of every infection day, diurnal epigenetic repression of CCA1 leads to rhythmically increased chlorophyll synthesis and starch metabolism in hybrids, effectively eliminating the immunity-growth heterosis trade-offs in hybrids. There is frequently a trade-off between plant immunity and growth. Here the authors show that the epigenetic control of CCA1, encoding a core component of the circadian oscillator, simultaneously promotes heterosis for both defense and growth in hybrids under pathogen invasion.
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Wang J, Long X, Chern M, Chen X. Understanding the molecular mechanisms of trade-offs between plant growth and immunity. SCIENCE CHINA-LIFE SCIENCES 2020; 64:234-241. [PMID: 32710363 DOI: 10.1007/s11427-020-1719-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/05/2020] [Indexed: 12/24/2022]
Abstract
Trade-offs between plant growth and immunity are a well-known phenomenon in plants that are meant to ensure the best use of limited resources. Recently, many advances have been achieved on molecular regulations of the trade-offs between plant growth and immunity. Here, we provide an overview on molecular understanding of these trade-offs including those regulated at the transcriptional level or post-transcriptional level by transcriptional factors, microRNAs, and post-translational modifications of proteins, respectively The understanding on the molecular regulation of these trade-offs will provide new strategies to breed crops with high yield and enhanced resistance to disease.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China
| | - Xiaoyu Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, California, 95616, USA
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China.
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Skoracka A, Rector BG, Hein GL. The Interface Between Wheat and the Wheat Curl Mite, Aceria tosichella, the Primary Vector of Globally Important Viral Diseases. FRONTIERS IN PLANT SCIENCE 2018; 9:1098. [PMID: 30100916 PMCID: PMC6072864 DOI: 10.3389/fpls.2018.01098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 07/09/2018] [Indexed: 05/08/2023]
Abstract
Wheat production and sustainability are steadily threatened by pests and pathogens in both wealthy and developing countries. This review is focused on the wheat curl mite (WCM), Aceria tosichella, and its relationship with wheat. WCM is a major pest of wheat and other cereals and a vector of at least four damaging plant viruses (Wheat streak mosaic virus, High plains wheat mosaic virus, Brome streak mosaic virus, and Triticum mosaic virus). The WCM-virus pathosystem causes considerable yield losses worldwide and its severity increases significantly when mixed-virus infections occur. Chemical control strategies are largely ineffective because WCM occupies secluded niches on the plant, e.g., leaf sheaths or curled leaves in the whorl. The challenge of effectively managing this pest-virus complex is exacerbated by the existence of divergent WCM lineages that differ in host-colonization and virus-transmission abilities. We highlight research progress in mite ecology and virus epidemiology that affect management and development of cereal cultivars with WCM- and virus-resistance genes. We also address the challenge of avoiding both agronomically deleterious side effects and selection for field populations of WCM that can overcome these resistance genes. This report integrates the current state of knowledge of WCM-virus-plant interactions and addresses knowledge gaps regarding the mechanisms driving WCM infestation, viral epidemics, and plant responses. We discuss the potential application of molecular methods (e.g., transcriptomics, epigenetics, and whole-genome sequencing) to understand the chemical and cellular interface between the wheat plant and WCM-virus complexes.
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Affiliation(s)
- Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Brian G. Rector
- Great Basin Rangelands Research Unit, United States Department of Agriculture – Agricultural Research Service, Reno, NV, United States
| | - Gary L. Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, United States
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Zhang G, Hua Z. Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation. PeerJ 2018; 6:e4678. [PMID: 29707435 PMCID: PMC5918131 DOI: 10.7717/peerj.4678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/09/2018] [Indexed: 02/01/2023] Open
Abstract
Wheat streak mosaic virus (WSMV) causes streak mosaic disease in wheat (Triticum aestivum L.) and has been an important constraint limiting wheat production in many regions around the world. Wsm2 is the only resistance gene discovered in wheat genome and has been located in a short genomic region of its chromosome 3B. However, the sequence nature and the biological function of Wsm2 remain unknown due to the difficulty of genetic manipulation in wheat. In this study, we tested WSMV infectivity among wheat and its two closely related grass species, rice (Oryza sativa) and Brachypodium distachyon. Based on the phenotypic result and previous genomic studies, we developed a novel bioinformatics pipeline for interpreting a potential biological function of Wsm2 and its ancestor locus in wheat. In the WSMV resistance tests, we found that rice has a WMSV resistance gene while Brachypodium does not, which allowed us to hypothesize the presence of a Wsm2 ortholog in rice. Our OrthoMCL analysis of protein coding genes on wheat chromosome 3B and its syntenic chromosomes in rice and Brachypodium discovered 4,035 OrthoMCL groups as preliminary candidates of Wsm2 orthologs. Given that Wsm2 is likely duplicated through an intrachromosomal illegitimate recombination and that Wsm2 is dominant, we inferred that this new WSMV-resistance gene acquired an activation domain, lost an inhibition domain, or gained high expression compared to its ancestor locus. Through comparison, we identified that 67, 16, and 10 out of 4,035 OrthoMCL orthologous groups contain a rice member with 25% shorter or longer in length, or 10 fold more expression, respectively, than those from wheat and Brachypodium. Taken together, we predicted a total of 93 good candidates for a Wsm2 ancestor locus. All of these 93 candidates are not tightly linked with Wsm2, indicative of the role of illegitimate recombination in the birth of Wsm2. Further sequence analysis suggests that the protein products of Wsm2 may combat WSMV disease through a molecular mechanism involving protein degradation and/or membrane trafficking. The 93 putative Wsm2 ancestor loci discovered in this study could serve as good candidates for future genetic isolation of the true Wsm2 locus.
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Affiliation(s)
- Guorong Zhang
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, United States of America
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States of America.,Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH, United States of America
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Li W, Hu W, Fang C, Chen L, Zhuang W, Katin‐Grazzini L, McAvoy RJ, Guillard K, Li Y. An AGAMOUS intron-driven cytotoxin leads to flowerless tobacco and produces no detrimental effects on vegetative growth of either tobacco or poplar. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2276-2287. [PMID: 27168170 PMCID: PMC5103258 DOI: 10.1111/pbi.12581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 05/22/2023]
Abstract
Flowerless trait is highly desirable for poplar because it can prevent pollen- and seed-mediated transgene flow. We have isolated the second intron of PTAG2, an AGAMOUS (AG) orthologue from Populus trichocarpa. By fusing this intron sequence to a minimal 35S promoter sequence, we created two artificial promoters, fPTAG2I (forward orientation of the PTAG2 intron sequence) and rPTAG2I (reverse orientation of the PTAG2 intron sequence). In tobacco, expression of the β-glucuronidase gene (uidA) demonstrates that the fPTAG2I promoter is non-floral-specific, while the rPTAG2I promoter is active in floral buds but with no detectable vegetative activity. Under glasshouse conditions, transgenic tobacco plants expressing the Diphtheria toxin A (DT-A) gene driven by the rPTAG2I promoter produced three floral ablation phenotypes: flowerless, neuter (stamenless and carpel-less) and carpel-less. Further, the vegetative growth of these transgenic lines was similar to that of the wild-type plants. In field trials during 2014 and 2015, the flowerless transgenic tobacco stably maintained its flowerless phenotype, and also produced more shoot and root biomass when compared to wild-type plants. In poplar, the rPTAG2I::GUS gene exhibited no detectable activity in vegetative organs. Under field conditions over two growing seasons (2014 to the end of 2015), vegetative growth of the rPTAG2I::DT-A transgenic poplar plants was similar to that of the wild-type plants. Our results demonstrate that the rPTAG2I artificial promoter has no detectable activities in vegetative tissues and organs, and the rPTAG2I::DT-A gene may be useful for producing flowerless poplar that retains normal vegetative growth.
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Affiliation(s)
- Wei Li
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Wei Hu
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Chu Fang
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Longzheng Chen
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
- Institute of Vegetable CropsJiangsu Academy of Agricultural SciencesNanjingChina
| | - Weibing Zhuang
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
| | - Lorenzo Katin‐Grazzini
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Richard J. McAvoy
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Karl Guillard
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
| | - Yi Li
- Department of Plant Science and Landscape ArchitectureUniversity of ConnecticutStorrsCTUSA
- College of Horticulture and State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
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