1
|
Li T, Luo W, Du C, Lin X, Lin G, Chen R, He H, Wang R, Lu L, Xie X. Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L. BMC Genomics 2024; 25:671. [PMID: 38970011 PMCID: PMC11229024 DOI: 10.1186/s12864-024-10577-8] [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: 04/11/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.
Collapse
Affiliation(s)
- Tong Li
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Wenbin Luo
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Chaofan Du
- Longyan Tobacco Company, Longyan, 364000, China
| | - Xiaolu Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Guojian Lin
- Longyan Tobacco Company, Longyan, 364000, China
| | - Rui Chen
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Ruiqi Wang
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China
| | - Libing Lu
- Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture & Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
2
|
Walker PL, Belmonte MF, McCallum BD, McCartney CA, Randhawa HS, Henriquez MA. Dual RNA-sequencing of Fusarium head blight resistance in winter wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1299461. [PMID: 38239218 PMCID: PMC10794533 DOI: 10.3389/fpls.2023.1299461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/29/2023] [Indexed: 01/22/2024]
Abstract
Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.
Collapse
Affiliation(s)
- Philip L. Walker
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curt A. McCartney
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Harpinder S. Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Maria A. Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
3
|
Ramadan E, Freeg HA, Shalaby N, Rizk MS, Ma J, Du W, Ibrahim OM, Alwutayd KM, AbdElgawad H, Jo IH, El-Tahan AM. Response of nine triticale genotypes to different salt concentrations at the germination and early seedling stages. PeerJ 2023; 11:e16256. [PMID: 38152345 PMCID: PMC10752223 DOI: 10.7717/peerj.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/18/2023] [Indexed: 12/29/2023] Open
Abstract
Salinity stress poses a major challenge to agricultural productivity worldwide, and understanding their responses at the early growth stage is vital for devising strategies to cope with this stress. Therefore, to improve triticale productivity, this study investigated the salinity stress tolerance of different salt-tolerant triticale genotypes aiming to cultivate them on saline soils. To this end, salinity stress impacts on nine triticale genotypes, i.e., Zhongsi 1084, Gannong No. 2, Gannong No. 4, Shida No. 1, C6, C16, C23, C25 and C36 at germination and early seedling stages was evaluated. Each genotype was subjected to six treatments inducing control, 40, 80, 120, 160, and 200 mM NaCl treatments to study their effect on seedling and termination traits of the nine genotypes. Compared to the overall mean seedling vigor index, the seedling vigor index was higher in the genotypes Zhongsi 1084 and C6 (39% and 18.1%, respectively) and lower in Gannong No.2 (41%). Increasing NaCl concentrations negatively affected germination and seedling traits. Compared to other genotypes, Zhongsi 1084 had the highest mean germination rate, germination vigor index, germination percentage, mean daily germination and germination energy. It also showed the lowest relative salt injury. The relative salt injury was higher in the genotype Shida No. 1 than those in Gannong No. 2, Gannong No. 4, Shida No. 1, C16, and C36 genotypes. All genotypes exhibited desirable mean germination time except for line C6. High significant positive correlations were observed among germination rate, germination vigor index, germination percentage, mean daily germination, seedling vigor index, and root length. Principal component analysis (PCA) grouped the most desirable genotypes into two clusters. Our study determined salt stress tolerance of nine triticale genotypes at germination and early seedling stages. to select salt-tolerant genotypes that can be cultivated on saline soil or after salt irrigation.
Collapse
Affiliation(s)
- Ebrahim Ramadan
- Field Crops Research Institute, Agricultural Research Center, Egypt, Kafr Elshiekh, Egypt
| | - Haytham A. Freeg
- Field Crops Research Institute, Agricultural Research Center, Egypt, Kafr Elshiekh, Egypt
| | - Nagwa Shalaby
- Field Crops Research Institute, Agricultural Research Center, Egypt, Kafr Elshiekh, Egypt
| | - Mosa S. Rizk
- Field Crops Research Institute, Agricultural Research Center, Egypt, Kafr Elshiekh, Egypt
| | - Jun Ma
- College of Grassland Science, Gansu Agricultural University, Gansu, China
| | - Wenhua Du
- College of Grassland Science, Gansu Agricultural University, Gansu, China
| | - Omar M. Ibrahim
- Plant Production Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Borg El Arab, Alexandria, Egypt
| | - Khairiah M. Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hamada AbdElgawad
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Ick-Hyun Jo
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Amira M. El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications, Borg El Arab, Alexandria, Egypt
| |
Collapse
|
4
|
Zhao X, Sun X, Chen Y, Wu H, Liu Y, Jiang Y, Xie F, Chen Y. Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1158035. [PMID: 37229126 PMCID: PMC10204806 DOI: 10.3389/fpls.2023.1158035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 05/27/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant-pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.
Collapse
Affiliation(s)
- Xueying Zhao
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xiaoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yang Chen
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Hanfu Wu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yujiao Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Fuchun Xie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- College of Horticulture, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| |
Collapse
|
5
|
Liu W, Wang X, Song L, Yao W, Guo M, Cheng G, Guo J, Bai S, Gao Y, Li J, Kang Z. Comparative Transcriptome and Widely Targeted Metabolome Analysis Reveals the Molecular Mechanism of Powdery Mildew Resistance in Tomato. Int J Mol Sci 2023; 24:ijms24098236. [PMID: 37175940 PMCID: PMC10178879 DOI: 10.3390/ijms24098236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Powdery mildew is a serious problem in tomato production; therefore, the PM-resistant tomato inbred line, '63187', and the susceptible tomato variety, 'Moneymaker (MM)', were used as experimental materials for the combined analysis of transcriptome and widely targeted metabolome on tomato leaves at 0 h post inoculation (hpi), 12 hpi, and 48 hpi. The results indicated that 276 genes were expressed in all treatments, and the K-means cluster analysis showed that these genes were divided into eight classes in '63187' and ten classes in 'MM'. KEGG enrichment showed that amino acid metabolism, signal transduction, energy metabolism, and other secondary metabolites biosynthesis pathways were significantly enriched. Interestingly, the analysis of WRKY family transcription factors (TFs) showed that the expression of four TFs in '63187' increased with no obvious change in 'MM'; and the expression of one TF in 'MM' increased with no obvious change in '63187'. The combined analysis revealed that both phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were enriched in '63187' and 'MM'. In '63187', six metabolites involved in this pathway were downregulated, and four genes were highly expressed, while in 'MM', three metabolites were upregulated, four metabolites were downregulated, and ten genes were highly expressed. These metabolites and genes might be candidates for PM resistance or susceptibility in subsequent studies. These results provide favorable molecular information for the study of the different resistances of tomatoes to PM, and they provide a basis for the breeding of tomato varieties resistant to PM.
Collapse
Affiliation(s)
- Wenjuan Liu
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
| | - Xiaomin Wang
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Lina Song
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
| | - Wenkong Yao
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Meng Guo
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Guoxin Cheng
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Shengyi Bai
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
| | - Yanming Gao
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Jianshe Li
- College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan 750021, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan 750021, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
6
|
Li G, Li J, Zhang Y, Ma Q, Yang E, Zhang P, Dundas I, Yang Z. Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:1035784. [PMID: 36299784 PMCID: PMC9589168 DOI: 10.3389/fpls.2022.1035784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Rye 6R-derived stripe rust resistance gene Yr83 in wheat background was physically mapped to fraction length (FL) 0.87-1.00 on the long arm by non-denaturing-fluorescence in situ hybridization (ND-FISH), Oligo-FISH painting and 6R-specific PCR markers.Stripe rust resistance gene Yr83 derived from chromosome 6R of rye (Secale cereale) "Merced" has displayed high resistance to both Australian and Chinese wheat stripe rust isolates. With the aim to physically map Yr83 to a more precise region, new wheat- 6R deletion and translocation lines were produced from derived progenies of the 6R(6D) substitution line. The non-denaturing fluorescence in situ hybridization (ND-FISH) patterns of 6R were established to precisely characterize the variations of 6R in different wheat backgrounds. Comparative ND-FISH analysis localized the breakpoints of 6RL chromosomes relative to Oligo-pSc200 and Oligo-pSc119.2 rich sites in deletion lines. Molecular marker and resistance analyses confirmed that Yr83 is physically located at the fraction length (FL) 0.87-1.00 of 6RL and covers the corresponding region of 806-881 Mb in the reference genome of Lo7. Oligo-FISH painting demonstrated that the region carrying Yr83 is syntenic to the distal end of long arm of homoeologous group 7 of the Triticeae genome. The developed wheat-6R lines carrying the Yr83 gene will be useful for breeding for rust resistance.
Collapse
Affiliation(s)
- Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jianbo Li
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Yao Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiang Ma
- Characteristic Crops Research Institute, Chongqing Academy of Agricultural Sciences, Yongchuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Ian Dundas
- School of Agriculture, Food and Wine, The University of Adelaide, Waite, Glen Osmond, SA, Australia
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|