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Wang Y, Chen B, Cheng C, Fu B, Qi M, Du H, Geng S, Zhang X. Comparative Transcriptomics Analysis Reveals the Differences in Transcription between Resistant and Susceptible Pepper ( Capsicum annuum L.) Varieties in Response to Anthracnose. PLANTS (BASEL, SWITZERLAND) 2024; 13:527. [PMID: 38498545 PMCID: PMC10892400 DOI: 10.3390/plants13040527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/20/2024]
Abstract
Pepper (Capsicum annuum L.) is a herbaceous plant species in the family Solanaceae. Capsicum anthracnose is caused by the genus Colletotrichum. spp., which decreases pepper production by about 50% each year due to anthracnose. In this study, we evaluated the resistance of red ripe fruits from 17 pepper varieties against anthracnose fungus Colletotrichum capsici. We assessed the size of the lesion diameter and conducted significance analysis to identify the resistant variety of B158 and susceptible variety of B161. We selected a resistant cultivar B158 and a susceptible cultivar B161 of pepper and used a transcription to investigate the molecular mechanisms underlying the plant's resistance to C. capsici, of which little is known. The inoculated fruit from these two varieties were used for the comparative transcription analysis, which revealed the anthracnose-induced differential transcription in the resistant and susceptible pepper samples. In the environment of an anthrax infection, we found that there were more differentially expressed genes in resistant varieties compared to susceptible varieties. Moreover, the response to stimulus and stress ability was stronger in the KANG. The transcription analysis revealed the activation of plant hormone signaling pathways, phenylpropanoid synthesis, and metabolic processes in the defense response of peppers against anthracnose. In addition, ARR-B, AP2-EREBP, bHLH, WRKY, and NAC are associated with disease resistance to anthracnose. Notably, WRKY and NAC were found to have a potentially positive regulatory role in the defense response against anthracnose. These findings contribute to a more comprehensive understanding of the resistance mechanisms of red pepper fruit to anthracnose infection, providing valuable molecular insights for further research on the resistance mechanisms and genetic regulations during this developmental stage of pepper.
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Affiliation(s)
- Yixin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
| | - Chunyuan Cheng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
| | - Bingkun Fu
- College of Horticultural, China Agricultural University, Beijing 100097, China; (B.F.); (M.Q.)
| | - Meixia Qi
- College of Horticultural, China Agricultural University, Beijing 100097, China; (B.F.); (M.Q.)
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (Y.W.); (B.C.); (C.C.); (H.D.); (S.G.)
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Wang Y, Xu C, Gao Y, Ma Y, Zhang X, Zhang L, Di H, Ma J, Dong L, Zeng X, Zhang N, Xu J, Li Y, Gao C, Wang Z, Zhou Y. Physiological Mechanisms Underlying Tassel Symptom Formation in Maize Infected with Sporisorium reilianum. PLANTS (BASEL, SWITZERLAND) 2024; 13:238. [PMID: 38256790 PMCID: PMC10820020 DOI: 10.3390/plants13020238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Head smut is a soil-borne fungal disease caused by Sporisorium reilianum that infects maize tassels and ears. This disease poses a tremendous threat to global maize production. A previous study found markedly different and stably heritable tassel symptoms in some maize inbred lines with Sipingtou blood after infection with S. reilianum. In the present study, 55 maize inbred lines with Sipingtou blood were inoculated with S. reilianum and classified into three tassel symptom types (A, B, and C). Three maize inbred lines representing these classes (Huangzao4, Jing7, and Chang7-2, respectively) were used as test materials to investigate the physiological mechanisms of tassel formation in infected plants. Changes in enzyme activity, hormone content, and protein expression were analyzed in all three lines after infection and in control plants. The activities of peroxidase (POD), superoxide dismutase (SOD), and phenylalanine-ammonia-lyase (PAL) were increased in the three typical inbred lines after inoculation. POD and SOD activities showed similar trends between lines, with the increase percentage peaking at the V12 stage (POD: 57.06%, 63.19%, and 70.28% increases in Huangzao4, Jing7, and Chang7-2, respectively; SOD: 27.01%, 29.62%, and 47.07% in Huangzao4, Jing7, and Chang7-2, respectively. These were all higher than in the disease-resistant inbred line Mo17 at the same growth stage); this stage was found to be key in tassel symptom formation. Levels of gibberellic acid (GA3), indole-3-acetic acid (IAA), and abscisic acid (ABA) were also altered in the three typical maize inbred lines after inoculation, with changes in GA3 and IAA contents tightly correlated with tassel symptoms after S. reilianum infection. The differentially expressed proteins A5H8G4, P09233, and Q8VXG7 were associated with changes in enzyme activity, whereas P49353, P13689, and P10979 were associated with changes in hormone contents. Fungal infection caused reactive oxygen species (ROS) and nitric oxide (NO) bursts in the three typical inbred lines. This ROS accumulation caused biofilm disruption and altered host signaling pathways, whereas NO signaling triggered strong secondary metabolic responses in the host and altered the activities of defense-related enzymes. These factors together resulted in the formation of varying tassel symptoms. Thus, interactions between S. reilianum and susceptible maize materials were influenced by a variety of signals, enzymes, hormones, and metabolic cycles, encompassing a very complex regulatory network. This study preliminarily identified the physiological mechanisms leading to differences in tassel symptoms, deepening our understanding of S. reilianum-maize interactions.
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Affiliation(s)
- Yuhe Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chuzhen Xu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yansong Gao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yanhua Ma
- Institute of Forage and Grass land Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Xiaoming Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Jinxin Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Ling Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Naifu Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Jiawei Xu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yujuan Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Chao Gao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China
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Liu M, Wang L, Yu Q, Song J, Zhu L, Jia KH, Qin X. The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01062-6. [PMID: 38108929 DOI: 10.1007/s11120-023-01062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.
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Affiliation(s)
- Menghua Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Longxin Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Qianqian Yu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jialin Song
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
- Shandong University of Arts, Jinan, China
| | - Lixia Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
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Dehbi I, Achemrk O, Ezzouggari R, El Jarroudi M, Mokrini F, Legrifi I, Belabess Z, Laasli SE, Mazouz H, Lahlali R. Beneficial Microorganisms as Bioprotectants against Foliar Diseases of Cereals: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:4162. [PMID: 38140489 PMCID: PMC10747484 DOI: 10.3390/plants12244162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Cereal production plays a major role in both animal and human diets throughout the world. However, cereal crops are vulnerable to attacks by fungal pathogens on the foliage, disrupting their biological cycle and photosynthesis, which can reduce yields by 15-20% or even 60%. Consumers are concerned about the excessive use of synthetic pesticides given their harmful effects on human health and the environment. As a result, the search for alternative solutions to protect crops has attracted the interest of scientists around the world. Among these solutions, biological control using beneficial microorganisms has taken on considerable importance, and several biological control agents (BCAs) have been studied, including species belonging to the genera Bacillus, Pseudomonas, Streptomyces, Trichoderma, Cladosporium, and Epicoccum, most of which include plants of growth-promoting rhizobacteria (PGPRs). Bacillus has proved to be a broad-spectrum agent against these leaf cereal diseases. Interaction between plant and beneficial agents occurs as direct mycoparasitism or hyperparasitism by a mixed pathway via the secretion of lytic enzymes, growth enzymes, and antibiotics, or by an indirect interaction involving competition for nutrients or space and the induction of host resistance (systemic acquired resistance (SAR) or induced systemic resistance (ISR) pathway). We mainly demonstrate the role of BCAs in the defense against fungal diseases of cereal leaves. To enhance a solution-based crop protection approach, it is also important to understand the mechanism of action of BCAs/molecules/plants. Research in the field of preventing cereal diseases is still ongoing.
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Affiliation(s)
- Ilham Dehbi
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
- Laboratory of Plant Biotechnology and Molecular Biology, Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco;
| | - Oussama Achemrk
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Rachid Ezzouggari
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
- Laboratory of Biotechnology, Conservation, and Valorization of Natural Resources (LBCVNR), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Moussa El Jarroudi
- Department of Environmental Sciences and Management, SPHERES Research Unit, University of Liège, 6700 Arlon, Belgium;
| | - Fouad Mokrini
- Biotechnology Unit, Regional Center of Agricultural Research, INRA–Morocco, Rabat 10080, Morocco;
| | - Ikram Legrifi
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Zineb Belabess
- Plant Protection Laboratory, Regional Center of Agricultural Research of Meknes, National Institute of Agricultural Research, Km 13, Route Haj Kaddour, BP 578, Meknes 50001, Morocco;
| | - Salah-Eddine Laasli
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Hamid Mazouz
- Laboratory of Plant Biotechnology and Molecular Biology, Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco;
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
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Liu J, Wang L, Jiang S, Wang Z, Li H, Wang H. Mining of Minor Disease Resistance Genes in V. vinifera Grapes Based on Transcriptome. Int J Mol Sci 2023; 24:15311. [PMID: 37894991 PMCID: PMC10607095 DOI: 10.3390/ijms242015311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Intraspecific recurrent selection in V. vinifera is an effective method for grape breeding with high quality and disease resistance. The core theory of this method is the substitution accumulation of multi-genes with low disease resistance. The discovery of multi-genes for disease resistance in V. vinifera may provide a molecular basis for breeding for disease resistance in V. vinifera. In this study, resistance to downy mildew was identified, and genetic analysis was carried out in the intraspecific crossing population of V. vinifera (Ecolly × Dunkelfelder) to screen immune, highly resistant and disease-resistant plant samples; transcriptome sequencing and differential expression analysis were performed using high-throughput sequencing. The results showed that there were 546 differential genes (194 up-regulated and 352 down-regulated) in the immune group compared to the highly resistant group, and 199 differential genes (50 up-regulated and 149 down-regulated) in the highly resistant group compared to the resistant group, there were 103 differential genes (54 up-regulated and 49 down-regulated) in the immune group compared to the resistant group. KEGG analysis of differentially expressed genes in the immune versus high-resistance group. The pathway is mainly concentrated in phenylpropanoid biosynthesis, starch and sucrose metabolism, MAPK signaling pathway-plant, carotenoid biosyn-thesis and isoquinoline alkaloid biosynthesis. The differential gene functions of immune and resistant, high-resistant and resistant combinations were mainly enriched in plant-pathogen interaction pathway. Through the analysis of disease resistance-related genes in each pathway, the potential minor resistance genes in V. vinifera were mined, and the accumulation of minor resistance genes was analyzed from the molecular level.
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Affiliation(s)
- Junli Liu
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Liang Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Shan Jiang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Zhilei Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Hua Li
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
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Quiroz-Figueroa FR, Cruz-Mendívil A, Ibarra-Laclette E, García-Pérez LM, Gómez-Peraza RL, Hanako-Rosas G, Ruíz-May E, Santamaría-Miranda A, Singh RK, Campos-Rivero G, García-Ramírez E, Narváez-Zapata JA. Cell wall-related genes and lignin accumulation contribute to the root resistance in different maize ( Zea mays L.) genotypes to Fusarium verticillioides (Sacc.) Nirenberg infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1195794. [PMID: 37441182 PMCID: PMC10335812 DOI: 10.3389/fpls.2023.1195794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023]
Abstract
Introduction The fungal pathogen Fusarium verticillioides (Sacc.) Nirenberg (Fv) causes considerable agricultural and economic losses and is harmful to animal and human health. Fv can infect maize throughout its long agricultural cycle, and root infection drastically affects maize growth and yield. Methods The root cell wall is the first physical and defensive barrier against soilborne pathogens such as Fv. This study compares two contrasting genotypes of maize (Zea mays L.) roots that are resistant (RES) or susceptible (SUS) to Fv infection by using transcriptomics, fluorescence, scanning electron microscopy analyses, and ddPCR. Results Seeds were infected with a highly virulent local Fv isolate. Although Fv infected both the RES and SUS genotypes, infection occurred faster in SUS, notably showing a difference of three to four days. In addition, root infections in RES were less severe in comparison to SUS infections. Comparative transcriptomics (rate +Fv/control) were performed seven days after inoculation (DAI). The analysis of differentially expressed genes (DEGs) in each rate revealed 733 and 559 unique transcripts that were significantly (P ≤0.05) up and downregulated in RES (+Fv/C) and SUS (+Fv/C), respectively. KEGG pathway enrichment analysis identified coumarin and furanocoumarin biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways as being highly enriched with specific genes involved in cell wall modifications in the RES genotype, whereas the SUS genotype mainly displayed a repressed plant-pathogen interaction pathway and did not show any enriched cell wall genes. In particular, cell wall-related gene expression showed a higher level in RES than in SUS under Fv infection. Analysis of DEG abundance made it possible to identify transcripts involved in response to abiotic and biotic stresses, biosynthetic and catabolic processes, pectin biosynthesis, phenylpropanoid metabolism, and cell wall biosynthesis and organization. Root histological analysis in RES showed an increase in lignified cells in the sclerenchymatous hypodermis zone during Fv infection. Discussion These differences in the cell wall and lignification could be related to an enhanced degradation of the root hairs and the epidermis cell wall in SUS, as was visualized by SEM. These findings reveal that components of the root cell wall are important against Fv infection and possibly other soilborne phytopathogens.
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Affiliation(s)
- Francisco Roberto Quiroz-Figueroa
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Abraham Cruz-Mendívil
- Consejo Nacional de Ciencia y Tecnología (CONACYT)-Instituto Politécnico Nacional, (CIIDIR) Unidad Sinaloa, Guasave, Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Luz María García-Pérez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Rosa Luz Gómez-Peraza
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Greta Hanako-Rosas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Cluster BioMimic®, Xalapa, Mexico
| | - Apolinar Santamaría-Miranda
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Rupesh Kumar Singh
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Gerardo Campos-Rivero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR)—Unidad Sinaloa, Guasave, Mexico
| | - Elpidio García-Ramírez
- Facultad de Química, Departamento de Bioquímica, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Chirivì D, Betti C. Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:331. [PMID: 36679044 PMCID: PMC9866591 DOI: 10.3390/plants12020331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.
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Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan ( Carya illinoinensis) Resistance to Pestalotiopsis microspora. Int J Mol Sci 2022; 23:ijms231911621. [PMID: 36232919 PMCID: PMC9570006 DOI: 10.3390/ijms231911621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant−pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan−Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.
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Jiao C, Sun X, Yan X, Xu X, Yan Q, Gao M, Fei Z, Wang X. Grape Transcriptome Response to Powdery Mildew Infection: Comparative Transcriptome Profiling of Chinese Wild Grapes Provides Insights Into Powdery Mildew Resistance. PHYTOPATHOLOGY 2021; 111:2041-2051. [PMID: 33870727 DOI: 10.1094/phyto-01-21-0006-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Erysiphe necator, the fungal pathogen of grape powdery mildew disease, poses a great threat to the grape market and the wine industry. To better understand the molecular basis of grape responses to E. necator, we performed comparative transcriptome profiling on two Chinese wild grape accessions with varying degrees of resistance to E. necator. At 6-, 24-, and 96-h postinoculation of E. necator, 2,856, 2,678, and 1,542 differentially expressed genes (DEGs) were identified in the susceptible accession Vitis pseudoreticulata 'Hunan-1', and at those same time points, 1,921, 2,498, and 3,249 DEGs, respectively, were identified in the resistant accession V. quinquangularis 'Shang-24'. 'Hunan-1' had a substantially larger fraction of down-regulated genes than 'Shang-24' at every infection stage. Analysis of DEGs revealed that up-regulated genes were mostly associated with defense response and disease resistance-related metabolite biosynthesis, and such signaling genes were significantly suppressed in 'Hunan-1'. Interestingly, fatty acid biosynthesis- and elongation-related genes were suppressed by the fungus in the 'Shang-24' accession but somehow induced in the 'Hunan-1' accession, consistent with the concept that E. necator is likely to be a fatty acid auxotroph that requires lipids from the host. Moreover, genes involved in biosynthesis and signaling of phytohormones, such as jasmonic acid and cytokinin, as well as genes encoding protein kinases and nucleotide-binding domain leucine-rich repeat proteins, differentially responded to E. necator in the two wild grapes. The variation of gene regulation associated with nutrient uptake by the fungus and with signaling transduction and pathogen recognition suggests a multilayered regulatory network that works in concert to assist in the establishment of fungal pathogen infections.
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Affiliation(s)
- Chen Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca 14853, U.S.A
| | - Xuepeng Sun
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca 14853, U.S.A
- College of Agriculture and Food Science, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaoxiao Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaozhao Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qin Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca 14853, U.S.A
- Agricultural Research Service, U.S. Department of Agriculture, Robert W. Holley Center for Agriculture and Health, Ithaca 14853, U.S.A
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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He W, Zhu Y, Leng Y, Yang L, Zhang B, Yang J, Zhang X, Lan H, Tang H, Chen J, Gao S, Tan J, Kang J, Deng L, Li Y, He Y, Rong T, Cao M. Transcriptomic Analysis Reveals Candidate Genes Responding Maize Gray Leaf Spot Caused by Cercospora zeina. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112257. [PMID: 34834621 PMCID: PMC8625984 DOI: 10.3390/plants10112257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 05/27/2023]
Abstract
Gray leaf spot (GLS), caused by the fungal pathogen Cercospora zeina (C. zeina), is one of the most destructive soil-borne diseases in maize (Zea mays L.), and severely reduces maize production in Southwest China. However, the mechanism of resistance to GLS is not clear and few resistant alleles have been identified. Two maize inbred lines, which were shown to be resistant (R6) and susceptible (S8) to GLS, were injected by C. zeina spore suspensions. Transcriptome analysis was carried out with leaf tissue at 0, 6, 24, 144, and 240 h after inoculation. Compared with 0 h of inoculation, a total of 667 and 419 stable common differentially expressed genes (DEGs) were found in the resistant and susceptible lines across the four timepoints, respectively. The DEGs were usually enriched in 'response to stimulus' and 'response to stress' in GO term analysis, and 'plant-pathogen interaction', 'MAPK signaling pathways', and 'plant hormone signal transduction' pathways, which were related to maize's response to GLS, were enriched in KEGG analysis. Weighted-Genes Co-expression Network Analysis (WGCNA) identified two modules, while twenty hub genes identified from these indicated that plant hormone signaling, calcium signaling pathways, and transcription factors played a central role in GLS sensing and response. Combing DEGs and QTL mapping, five genes were identified as the consensus genes for the resistance of GLS. Two genes, were both putative Leucine-rich repeat protein kinase family proteins, specifically expressed in R6. In summary, our results can provide resources for gene mining and exploring the mechanism of resistance to GLS in maize.
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Affiliation(s)
- Wenzhu He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yifeng Leng
- College of Agricultural Sciences, Xichang University, Xichang 615000, China;
| | - Lin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Biao Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Junpin Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Haitao Tang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jie Chen
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Jun Tan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Jiwei Kang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Luchang Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yan Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Yuanyuan He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.Z.); (L.Y.); (B.Z.); (J.Y.); (H.T.); (J.C.); (J.T.); (J.K.); (L.D.); (Y.L.); (Y.H.)
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.Z.); (H.L.); (S.G.); (T.R.)
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Su H, Liang J, Abou-Elwafa SF, Cheng H, Dou D, Ren Z, Xie J, Chen Z, Gao F, Ku L, Chen Y. ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize. BMC PLANT BIOLOGY 2021; 21:453. [PMID: 34615461 PMCID: PMC8493678 DOI: 10.1186/s12870-021-03231-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/23/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Appropriate flowering time is very important to the success of modern agriculture. Maize (Zea mays L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that ZmCCT is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear. RESULTS Here, we showed that ZmCCT overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that ZmCCT has a transcriptional inhibitory activity, while the yeast system showed that ZmCCT has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that ZmCCT mainly binds to promoters containing the novel motifs CAAAAATC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that ZmCCT could directly repress the expression of ZmPRR5 and ZmCOL9, and promote the expression of ZmRVE6 to delay flowering under long-day conditions. Moreover, we also demonstrated that ZmCCT directly binds to the promoters of ZmHY5, ZmMPK3, ZmVOZ1 and ZmARR16 and promotes the expression of ZmHY5 and ZmMPK3, but represses ZmVOZ1 and ZmARR16 to enhance stress resistance. Additionally, ZmCCT regulates a set of genes associated with plant development. CONCLUSIONS ZmCCT has dual functions in regulating maize flowering time and stress response under LD conditions. ZmCCT negatively regulates flowering time and enhances maize drought tolerance under LD conditions. ZmCCT represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of ZmCCT in controlling maize flowering time and stress response.
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Affiliation(s)
- Huihui Su
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiachen Liang
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | | | - Haiyang Cheng
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Dandan Dou
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhenzhen Ren
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiarong Xie
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhihui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Fengran Gao
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Lixia Ku
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
| | - Yanhui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
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Xu F, Meng Q, Suo X, Xie Y, Cheng Y, Luo M. Transcriptome analysis reveals the molecular mechanisms of response to an emergent yellow-flower disease in green Chinese prickly ash (Zanthoxylum schinifolium). Sci Rep 2021; 11:18886. [PMID: 34556742 PMCID: PMC8460732 DOI: 10.1038/s41598-021-98427-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Chinese prickly ash (Zanthoxylum) is extensively used as spice and traditional medicine in eastern Asian countries. Recently, an emergent yellow-flower disease (YFD) break out in green Chinese prickly ash (Zanthoxylum schinifolium, Qinghuajiao in Chinese) at Chongqing municipality, and then leads to a sharp reduction in the yield of Qinghuajiao, and thus results in great economic losses for farmers. To address the molecular response for the emergent YFD of Qinghuajiao, we analyzed the transcriptome of 12 samples including the leaves and inflorescences of asymptomatic and symptomatic plants from three different towns at Chongqing by high-throughput RNA-Seq technique. A total of 126,550 genes and 229,643 transcripts were obtained, and 21,054 unigenes were expressed in all 12 samples. There were 56 and 164 different expressed genes (DEGs) for the AL_vs_SL (asymptomatic leaf vs symptomatic leaf) and AF_vs_SF (asymptomatic flower vs symptomatic flower) groups, respectively. The results of KEGG analysis showed that the “phenylpropanoid biosynthesis” pathway that related to plant–pathogen interaction were found in AL_vs_SL and AF_vs_SF groups, and the “Plant–pathogen interaction” found in AF_vs_SF group, implying that this Qinghuajiao YFD might cause by plant pathogen. Interestingly, we detected 33 common unigenes for the 2 groups, and almost these unigenes were up-regulated in the symptomatic plants. Moreover, most of which were homologs to virus RNA, the components of viruses, implying that this YFD was related to virus. Our results provided a primary molecular basis for the prevention and treatment of YFD of Qinghuajiao trees.
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Affiliation(s)
- Fan Xu
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China
| | - Qian Meng
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China
| | - Xiaodong Suo
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yonghong Xie
- Fruit Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, China
| | - Yueqing Cheng
- Fruit Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, China.
| | - Ming Luo
- Key Laboratory of Biotechnology and Crop Quality Improvement of Ministry of Agriculture, Biotechnology Research Center, Southwest University, Chongqing, China.
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Kaur B, Sandhu KS, Kamal R, Kaur K, Singh J, Röder MS, Muqaddasi QH. Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects. PLANTS 2021; 10:plants10101989. [PMID: 34685799 PMCID: PMC8541486 DOI: 10.3390/plants10101989] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/22/2022]
Abstract
Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.
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Affiliation(s)
- Balwinder Kaur
- Everglades Research and Education Center, University of Florida, 3200 E. Palm Beach Rd., Belle Glade, FL 33430, USA;
| | - Karansher S. Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA;
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Kawalpreet Kaur
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
| | - Quddoos H. Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Stadt Seeland, Germany; (R.K.); or (M.S.R.)
- Correspondence: or
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14
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Mu X, Li J, Dai Z, Xu L, Fan T, Jing T, Chen M, Gou M. Commonly and Specifically Activated Defense Responses in Maize Disease Lesion Mimic Mutants Revealed by Integrated Transcriptomics and Metabolomics Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:638792. [PMID: 34079566 PMCID: PMC8165315 DOI: 10.3389/fpls.2021.638792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Disease lesion mimic (Les/les) mutants display disease-like spontaneous lesions in the absence of pathogen infection, implying the constitutive activation of defense responses. However, the genetic and biochemical bases underlying the activated defense responses in those mutants remain largely unknown. Here, we performed integrated transcriptomics and metabolomics analysis on three typical maize Les mutants Les4, Les10, and Les17 with large, medium, and small lesion size, respectively, thereby dissecting the activated defense responses at the transcriptional and metabolomic level. A total of 1,714, 4,887, and 1,625 differentially expressed genes (DEGs) were identified in Les4, Les10, and Les17, respectively. Among them, 570, 3,299, and 447 specific differentially expressed genes (SGs) were identified, implying a specific function of each LES gene. In addition, 480 common differentially expressed genes (CGs) and 42 common differentially accumulated metabolites (CMs) were identified in all Les mutants, suggesting the robust activation of shared signaling pathways. Intriguingly, substantial analysis of the CGs indicated that genes involved in the programmed cell death, defense responses, and phenylpropanoid and terpenoid biosynthesis were most commonly activated. Genes involved in photosynthetic biosynthesis, however, were generally repressed. Consistently, the dominant CMs identified were phenylpropanoids and flavonoids. In particular, lignin, the phenylpropanoid-based polymer, was significantly increased in all three mutants. These data collectively imply that transcriptional activation of defense-related gene expression; increase of phenylpropanoid, lignin, flavonoid, and terpenoid biosynthesis; and inhibition of photosynthesis are generalnatures associated with the lesion formation and constitutively activated defense responses in those mutants. Further studies on the identified SGs and CGs will shed new light on the function of each LES gene as well as the regulatory network of defense responses in maize.
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Affiliation(s)
| | | | | | | | | | | | | | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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Chen L, Liu L, Li Z, Zhang Y, Kang MS, Wang Y, Fan X. High-density mapping for gray leaf spot resistance using two related tropical maize recombinant inbred line populations. Mol Biol Rep 2021; 48:3379-3392. [PMID: 33890197 DOI: 10.1007/s11033-021-06350-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/08/2021] [Indexed: 01/18/2023]
Abstract
Gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora zeina is one of the devastating maize foliar diseases worldwide. Identification of GLS-resistant quantitative trait loci (QTL)/genes plays an urgent role in improving GLS resistance in maize breeding practice. Two groups of recombinant inbred line (RIL) populations derived from CML373 × Ye107 and Chang7-2 × Ye107 were generated and subjected to genotyping-by-sequencing (GBS). A total of 1,929,222,287 reads in CML373 × Ye107 (RIL-YCML) and 2,585,728,312 reads in Chang7-2 × Ye107 (RIL-YChang), with an average of 10,961,490 (RIL-YCML) and 13,609,096 (RIL-YChang) reads per individual, were got, which was roughly equal to 0.70-fold and 0.87-fold coverage of the maize B73 RefGen_V4 genome for each F7 individual, respectively. 6418 and 5139 SNP markers were extracted to construct two high-density genetic maps. Comparative analysis using these physically mapped marker loci demonstrated a satisfactory colinear relationship with the reference genome. 11 GLS-resistant QTL have been detected. The individual QTL accounted for 1.53-24.00% of the phenotypic variance explained (PVE). The new consensus QTL (qYCM-DS3-3/qYCM-LT3-1/qYCM-LT3-2) with the largest effect was located in chromosome bin 3.05, with an interval of 2.7 Mb, representing 13.08 to 24.00% of the PVE. Further gene annotation indicated that there were four candidate genes (GRMZM2G032384, GRMZM2G041415, GRMZM2G041544, and GRMZM2G035992) for qYCM-LT3-1, which may be related to GLS resistance. Combining RIL populations and GBS-based high-density genetic maps, a new larger effect QTL was delimited to a narrow genomic interval, which will provide a new resistance source for maize breeding programs.
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Affiliation(s)
- Long Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Li Liu
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Ziwei Li
- Yunnan Dehong Dai and Jingpo Nationality Institute of Agricultural Sciences, Mangshi, Yunnan, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Manjit S Kang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Yunyue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, Yunnan Agricultural University, Kunming, 650201, China.
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
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16
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Kim S, Van den Broeck L, Karre S, Choi H, Christensen SA, Wang G, Jo Y, Cho WK, Balint‐Kurti P. Analysis of the transcriptomic, metabolomic, and gene regulatory responses to Puccinia sorghi in maize. MOLECULAR PLANT PATHOLOGY 2021; 22:465-479. [PMID: 33641256 PMCID: PMC7938627 DOI: 10.1111/mpp.13040] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 05/22/2023]
Abstract
Common rust, caused by Puccinia sorghi, is a widespread and destructive disease of maize. The Rp1-D gene confers resistance to the P. sorghi IN2 isolate, mediating a hypersensitive cell death response (HR). To identify differentially expressed genes (DEGs) and metabolites associated with the compatible (susceptible) interaction and with Rp1-D-mediated resistance in maize, we performed transcriptomics and targeted metabolome analyses of P. sorghi IN2-infected leaves from the near-isogenic lines H95 and H95:Rp1-D, which differed for the presence of Rp1-D. We observed up-regulation of genes involved in the defence response and secondary metabolism, including the phenylpropanoid, flavonoid, and terpenoid pathways. Metabolome analyses confirmed that intermediates from several transcriptionally up-regulated pathways accumulated during the defence response. We identified a common response in H95:Rp1-D and H95 with an additional H95:Rp1-D-specific resistance response observed at early time points at both transcriptional and metabolic levels. To better understand the mechanisms underlying Rp1-D-mediated resistance, we inferred gene regulatory networks occurring in response to P. sorghi infection. A number of transcription factors including WRKY53, BHLH124, NKD1, BZIP84, and MYB100 were identified as potentially important signalling hubs in the resistance-specific response. Overall, this study provides a novel and multifaceted understanding of the maize susceptible and resistance-specific responses to P. sorghi.
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Affiliation(s)
- Saet‐Byul Kim
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Lisa Van den Broeck
- Department of Plant and Microbial BiologyNC State UniversityRaleighNorth CarolinaUSA
| | - Shailesh Karre
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Hoseong Choi
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Shawn A. Christensen
- Chemistry Research UnitDepartment of Agriculture–Agricultural Research Service (USDA‐ARS)Center for Medical, Agricultural, and Veterinary EntomologyGainesvilleFloridaUSA
| | - Guan‐Feng Wang
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- The Key Laboratory of Plant Development and Environmental Adaptation BiologyMinistry of EducationSchool of Life SciencesShandong UniversityQingdaoChina
| | - Yeonhwa Jo
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Peter Balint‐Kurti
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Plant Science Research Unit USDA‐ARSRaleighNorth CarolinaUSA
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17
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Liu Y, Gong X, Zhou Q, Liu Y, Liu Z, Han J, Dong J, Gu S. Comparative proteomic analysis reveals insights into the dynamic responses of maize (Zea mays L.) to Setosphaeria turcica infection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110811. [PMID: 33568308 DOI: 10.1016/j.plantsci.2020.110811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) production is severely affected by northern corn leaf blight (NCLB), which is a destructive foliar disease caused by Setosphaeria turcica. In recent years, studies on the interaction between maize and S. turcica have been focused at the transcription level, with no research yet at the protein level. Here, we applied tandem mass tag labelling and liquid chromatography-tandem mass spectrometry to investigate the proteomes of maize leaves at 24 h and 72 h post-inoculation (hpi) with S. turcica. In total, 4740 proteins encoded by 4711 genes were quantified in this study. Clustering analyses provided an understanding of the dynamic reprogramming of leaves proteomes by revealing the functions of different proteins during S. turcica infection. Screening and classification of differentially expressed proteins (DEPs) revealed that numerous defense-related proteins, including defense marker proteins and proteins related to the phenylpropanoid lignin biosynthesis, benzoxazine biosynthesis and the jasmonic acid signalling pathway, participated in the defense responses of maize to S. turcica infection. Furthermore, the earlier induction of GST family proteins contributed to the resistance to S. turcica. In addition, the protein-protein interaction network of DEPs suggests that some defense-related proteins, for example, ZmGEB1, a hub node, play key roles in defense responses against S. turcica infection. Our study findings provide insight into the complex responses triggered by S. turcica at the protein level and lay the foundation for studying the interaction process between maize and S. turcica infection.
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Affiliation(s)
- Yuwei Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China
| | - Xiaodong Gong
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China
| | - Qihui Zhou
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China
| | - Yajie Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China
| | - Zhenpan Liu
- Economic Forsetry Research Institute of Liaoning Province, China
| | - Jianmin Han
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, 071001, China
| | - Shouqin Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, 071001, China; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei, 071001, China.
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18
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Delplace F, Huard-Chauveau C, Dubiella U, Khafif M, Alvarez E, Langin G, Roux F, Peyraud R, Roby D. Robustness of plant quantitative disease resistance is provided by a decentralized immune network. Proc Natl Acad Sci U S A 2020; 117:18099-18109. [PMID: 32669441 PMCID: PMC7395444 DOI: 10.1073/pnas.2000078117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Quantitative disease resistance (QDR) represents the predominant form of resistance in natural populations and crops. Surprisingly, very limited information exists on the biomolecular network of the signaling machineries underlying this form of plant immunity. This lack of information may result from its complex and quantitative nature. Here, we used an integrative approach including genomics, network reconstruction, and mutational analysis to identify and validate molecular networks that control QDR in Arabidopsis thaliana in response to the bacterial pathogen Xanthomonas campestris To tackle this challenge, we first performed a transcriptomic analysis focused on the early stages of infection and using transgenic lines deregulated for the expression of RKS1, a gene underlying a QTL conferring quantitative and broad-spectrum resistance to XcampestrisRKS1-dependent gene expression was shown to involve multiple cellular activities (signaling, transport, and metabolism processes), mainly distinct from effector-triggered immunity (ETI) and pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) responses already characterized in Athaliana Protein-protein interaction network reconstitution then revealed a highly interconnected and distributed RKS1-dependent network, organized in five gene modules. Finally, knockout mutants for 41 genes belonging to the different functional modules of the network revealed that 76% of the genes and all gene modules participate partially in RKS1-mediated resistance. However, these functional modules exhibit differential robustness to genetic mutations, indicating that, within the decentralized structure of the QDR network, some modules are more resilient than others. In conclusion, our work sheds light on the complexity of QDR and provides comprehensive understanding of a QDR immune network.
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Affiliation(s)
- Florent Delplace
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Carine Huard-Chauveau
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Ullrich Dubiella
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
- KWS SAAT SE & Co, 37574 Einbeck, Germany
| | - Mehdi Khafif
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Eva Alvarez
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Gautier Langin
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Rémi Peyraud
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France
- iMean, 31520 Toulouse, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microorganismes, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France;
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19
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Zhang Y, Rahmani RS, Yang X, Chen J, Shi T. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC Genomics 2020; 21:429. [PMID: 32586276 PMCID: PMC7315500 DOI: 10.1186/s12864-020-06853-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 01/29/2023] Open
Abstract
Background Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Results Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
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Affiliation(s)
- Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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20
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Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss's Wilt of Maize. G3-GENES GENOMES GENETICS 2019; 9:3139-3152. [PMID: 31362973 PMCID: PMC6778796 DOI: 10.1534/g3.119.400347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Goss’s bacterial wilt and leaf blight is a disease of maize caused by the gram positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn). First discovered in Nebraska, Goss’s wilt has now spread to major maize growing states in the United States and three provinces in Canada. Previous studies conducted using elite maize inbred lines and their hybrids have shown that resistance to Goss’s wilt is a quantitative trait. The objective of this study was to further our understanding of the genetic basis of resistance to Goss’s wilt by using a combined approach of genome-wide association mapping and gene co-expression network analysis. Genome-wide association analysis was accomplished using a diversity panel consisting of 555 maize inbred lines and a set of 450 recombinant inbred lines (RILs) from three bi-parental mapping populations, providing the most comprehensive screening of Goss’s wilt resistance to date. Three SNPs in the diversity panel and 10 SNPs in the combined dataset, including the diversity panel and RILs, were found to be significantly associated with Goss’s wilt resistance. Each significant SNP explained 1–5% of the phenotypic variation for Goss’s wilt (total of 8–11%). To augment the results of genome-wide association mapping and help identify candidate genes, a time course RNA sequencing experiment was conducted using resistant (N551) and susceptible (B14A) maize inbred lines. Gene co-expression network analysis of this time course experiment identified one module of 141 correlated genes that showed differential regulation in response to Cmn inoculations in both resistant and susceptible lines. SNPs inside and flanking these genes explained 13.3% of the phenotypic variation. Among 1,000 random samples of genes, only 8% of samples explained more phenotypic variance for Goss’s wilt resistance than those implicated by the co-expression network analysis. While a statistically significant enrichment was not observed (P < 0.05), these results suggest a possible role for these genes in quantitative resistance at the field level and warrant more research on combining gene co-expression network analysis with quantitative genetic analyses to dissect complex disease resistance traits. The results of the GWAS and co-expression analysis both support the complex nature of resistance to this important disease of maize.
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21
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Zhao XY, Qi CH, Jiang H, Zhong MS, Zhao Q, You CX, Li YY, Hao YJ. MdWRKY46-Enhanced Apple Resistance to Botryosphaeria dothidea by Activating the Expression of MdPBS3.1 in the Salicylic Acid Signaling Pathway. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1391-1401. [PMID: 31408392 DOI: 10.1094/mpmi-03-19-0089-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Salicylic acid (SA) is closely related to disease resistance of plants. WRKY transcription factors have been linked to the growth and development of plants, especially under stress conditions. However, the regulatory mechanism of WRKY proteins involved in SA production and disease resistance in apple is not clear. In this study, MdPBS3.1 responded to Botryosphaeria dothidea and enhanced resistance to B. dothidea. Electrophoretic mobility shift assays, yeast one-hybrid assays, and chromatin immunoprecipitation and quantitative PCR demonstrated that MdWRKY46 can directly bind to a W-box motif in the promoter of MdPBS3.1. Glucuronidase transactivation and luciferase analysis further showed that MdWRKY46 can activate the expression of MdPBS3.1. Finally, B. dothidea inoculation in transgenic apple calli and fruits revealed that MdWRKY46 improved resistance to B. dothidea by the transcriptional activation of MdPBS3.1. Viral vector-based transformation assays indicated that MdWRKY46 elevates SA content and transcription of SA-related genes, including MdPR1, MdPR5, and MdNPR1 in an MdPBS3.1-dependent way. These findings provide new insights into how MdWRKY46 regulates plant resistance to B. dothidea through the SA signaling pathway.
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Affiliation(s)
- Xian-Yan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chen-Hui Qi
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Han Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ming-Shuang Zhong
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Qiang Zhao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, Shandong, China
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22
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Pan Y, Zhao SW, Tang XL, Wang S, Wang X, Zhang XX, Zhou JJ, Xi JH. Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore Holotrichia parallela larvae feeding. Genome 2019; 63:1-12. [PMID: 31533014 DOI: 10.1139/gen-2019-0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The larvae of Holotrichia parallela, a destructive belowground herbivore, causes tremendous damages to maize plants. However, little is known if there are any defense mechanisms in maize roots to defend themselves against this herbivore. In the current research, we carried out RNA-sequencing to investigate the changes in gene transcription level in maize roots after H. parallela larvae infestation. A total of 644 up-regulated genes and 474 down-regulated genes was found. In addition, Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Weighted gene co-expression network analysis (WGCNA) indicated that peroxidase genes may be the hub genes that regulate maize defenses to H. parallela larvae attack. We also found 105 transcription factors, 44 hormone-related genes, and 62 secondary metabolism-related genes within differentially expressed genes (DEGs). Furthermore, the expression profiles of 12 DEGs from the transcriptome analysis were confirmed by quantitative real-time PCR experiments. This transcriptome analysis provides insights into the molecular mechanisms of the underground defense in maize roots to H. parallela larvae attack and will help to select target genes of maize for defense against belowground herbivory.
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Affiliation(s)
- Yu Pan
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Shi-Wen Zhao
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xin-Long Tang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Shang Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xiao Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xin-Xin Zhang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Jing-Jiang Zhou
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Jing-Hui Xi
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
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23
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Cowger C, Brown JKM. Durability of Quantitative Resistance in Crops: Greater Than We Know? ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:253-277. [PMID: 31206351 DOI: 10.1146/annurev-phyto-082718-100016] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Quantitative resistance (QR) to crop diseases has usually been much more durable than major-gene, effector-triggered resistance. It has been observed that the effectiveness of some QR has eroded as pathogens adapt to it, especially when deployment is extensive and epidemics occur regularly, but it generally declines more slowly than effector-triggered resistance. Changes in aggressiveness and specificity of diverse pathogens on cultivars with QR have been recorded, along with experimental data on fitness costs of pathogen adaptation to QR, but there is little information about molecular mechanisms of adaptation. Some QR has correlated or antagonistic effects on multiple diseases. Longitudinal data on cultivars' disease ratings in trials over several years can be used to assess the significance of QR for durable resistance in crops. It is argued that published data likely underreport the durability of QR, owing to publication bias. The implications of research on QR for plant breeding are discussed.
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Affiliation(s)
- Christina Cowger
- USDA-ARS and North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - James K M Brown
- Department of Crop Genetics, John Innes Centre, Colney, Norwich NR4 7UK, United Kingdom;
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