1
|
Yi F, Li Y, Song A, Shi X, Hu S, Wu S, Shao L, Chu Z, Xu K, Li L, Tran LP, Li W, Cai Y. Positive roles of the Ca 2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance. MOLECULAR PLANT PATHOLOGY 2024; 25:e13483. [PMID: 38829344 PMCID: PMC11146148 DOI: 10.1111/mpp.13483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/18/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
As a universal second messenger, cytosolic calcium (Ca2+) functions in multifaceted intracellular processes, including growth, development and responses to biotic/abiotic stresses in plant. The plant-specific Ca2+ sensors, calmodulin and calmodulin-like (CML) proteins, function as members of the second-messenger system to transfer Ca2+ signal into downstream responses. However, the functions of CMLs in the responses of cotton (Gossypium spp.) after Verticillium dahliae infection, which causes the serious vascular disease Verticillium wilt, remain elusive. Here, we discovered that the expression level of GbCML45 was promoted after V. dahliae infection in roots of cotton, suggesting its potential role in Verticillium wilt resistance. We found that knockdown of GbCML45 in cotton plants decreased resistance while overexpression of GbCML45 in Arabidopsis thaliana plants enhanced resistance to V. dahliae infection. Furthermore, there was physiological interaction between GbCML45 and its close homologue GbCML50 by using yeast two-hybrid and bimolecular fluorescence assays, and both proteins enhanced cotton resistance to V. dahliae infection in a Ca2+-dependent way in a knockdown study. Detailed investigations indicated that several defence-related pathways, including salicylic acid, ethylene, reactive oxygen species and nitric oxide signalling pathways, as well as accumulations of lignin and callose, are responsible for GbCML45- and GbCML50-modulated V. dahliae resistance in cotton. These results collectively indicated that GbCML45 and GbCML50 act as positive regulators to improve cotton Verticillium wilt resistance, providing potential targets for exploitation of improved Verticillium wilt-tolerant cotton cultivars by genetic engineering and molecular breeding.
Collapse
Affiliation(s)
- Feifei Yi
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Yuzhe Li
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Aosong Song
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Xinying Shi
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Shanci Hu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Shuang Wu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Lili Shao
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Zongyan Chu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| | - Kun Xu
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Liangliang Li
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Lam‐Son Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress ResistanceTexas Tech UniversityLubbockTexasUSA
| | - Weiqiang Li
- Jilin Da'an Agro‐Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Yingfan Cai
- National Key Laboratory of Cotton Biological Breeding and Utilization, School of Life SciencesSanya Institute, Henan UniversityKaifengChina
| |
Collapse
|
2
|
Tian J, Zhang F, Zhang G, Li X, Wen C, Li H. A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase. PLANT PHYSIOLOGY 2024; 195:940-957. [PMID: 38417836 PMCID: PMC11142375 DOI: 10.1093/plphys/kiae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.
Collapse
Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaojie Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| |
Collapse
|
3
|
Wang J, Wang X, Wang L, Nazir MF, Fu G, Peng Z, Chen B, Xing A, Zhu M, Ma X, Wang X, Jia Y, Pan Z, Wang L, Xia Y, He S, Du X. Exploring the regulatory role of non-coding RNAs in fiber development and direct regulation of GhKCR2 in the fatty acid metabolic pathway in upland cotton. Int J Biol Macromol 2024; 266:131345. [PMID: 38574935 DOI: 10.1016/j.ijbiomac.2024.131345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Cotton fiber holds immense importance as the primary raw material for the textile industry. Consequently, comprehending the regulatory mechanisms governing fiber development is pivotal for enhancing fiber quality. Our study aimed to construct a regulatory network of competing endogenous RNAs (ceRNAs) and assess the impact of non-coding RNAs on gene expression throughout fiber development. Through whole transcriptome data analysis, we identified differentially expressed genes (DEGs) regulated by non-coding RNA (ncRNA) that were predominantly enriched in phenylpropanoid biosynthesis and the fatty acid elongation pathway. This analysis involved two contrasting phenotypic materials (J02-508 and ZRI015) at five stages of fiber development. Additionally, we conducted a detailed analysis of genes involved in fatty acid elongation, including KCS, KCR, HACD, ECR, and ACOT, to unveil the factors contributing to the variation in fatty acid elongation between J02-508 and ZRI015. Through the integration of histochemical GUS staining, dual luciferase assay experiments, and correlation analysis of expression levels during fiber development stages for lncRNA MSTRG.44818.23 (MST23) and GhKCR2, we elucidated that MST23 positively regulates GhKCR2 expression in the fatty acid elongation pathway. This identification provides valuable insights into the molecular mechanisms underlying fiber development, emphasizing the intricate interplay between non-coding RNAs and protein-coding genes.
Collapse
Affiliation(s)
- Jingjing Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liyuan Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Mian Faisal Nazir
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Guoyong Fu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhen Peng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Aishuang Xing
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Mengchen Zhu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xinli Ma
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Xiuxiu Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yinhua Jia
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liru Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yingying Xia
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou 455001, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 455001, China.
| |
Collapse
|
4
|
Xu J, Zhou T, Wang Y, Yang Y, Pu Y, Chen Q, Zheng K, Sun G. Functional Analysis of the GhIQD1 Gene in Cotton Resistance to Verticillium Wilt. PLANTS (BASEL, SWITZERLAND) 2024; 13:1005. [PMID: 38611533 PMCID: PMC11013105 DOI: 10.3390/plants13071005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Cotton is a critical crop with massive economic implications worldwide. Verticillium wilt is a soil-borne ailment caused by Verticillium dahliae, which harms the growth and development of cotton. Therefore, investigating the genes associated with resistance to verticillium wilt is of particular significance. In this study, we identified the GhIQD1 gene through transcriptome analysis and experimentally characterized the role of the GhIQD1 gene in cotton against V. dahliae. The findings indicated that GhIQD1 acts as a calmodulin-binding protein. The expression of GhIQD1 was the highest in stems, and the expression level increased significantly following infection with V. dahliae. The expression in resistant cotton varieties was higher than in susceptible cotton varieties. Through overexpression of the GhIQD1 gene in tobacco, these transgenic plants exhibited improved resistance to V. dahliae. In contrast, by silencing the GhIQD1 gene in cotton through VIGS, the resistance to V. dahliae was reduced. Following inoculation, the leaves yellowed, and the disease index was higher. Transcriptome analysis of transgenic tobacco 72 h after inoculation indicated that overexpression of GhIQD1 increased the enrichment of the calmodulin pathway and stimulated the production of plant hormones alongside secondary metabolites. Consequently, we investigated the relationship between the GhIQD1 gene and plant disease-resistant hormones SA, JA, and ABA. In summary, this study uncovered the mechanism by which GhIQD1 conferred resistance to V. dahliae in cotton through positive regulation of JA and ABA, providing crucial information for further research on the adaptation of plants to pathogen invasion.
Collapse
Affiliation(s)
- Jianglin Xu
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (J.X.); (Y.W.); (Q.C.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.Z.); (Y.Y.)
| | - Ting Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.Z.); (Y.Y.)
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China
| | - Yongqiang Wang
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (J.X.); (Y.W.); (Q.C.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.Z.); (Y.Y.)
| | - Yejun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.Z.); (Y.Y.)
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China
| | - Yuanchun Pu
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji 831100, China;
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (J.X.); (Y.W.); (Q.C.)
| | - Kai Zheng
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (J.X.); (Y.W.); (Q.C.)
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.Z.); (Y.Y.)
| |
Collapse
|
5
|
Mierziak J, Wojtasik W. Epigenetic weapons of plants against fungal pathogens. BMC PLANT BIOLOGY 2024; 24:175. [PMID: 38443788 PMCID: PMC10916060 DOI: 10.1186/s12870-024-04829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.
Collapse
Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland.
| |
Collapse
|
6
|
Liu S, Wei F, Liu R, Xue C, Chen Y, Zhao C, Chen P. A systematic analysis of ARM genes revealed that GhARM144 regulates the resistance against Verticillium dahliae via interaction with GhOSM34. PHYSIOLOGIA PLANTARUM 2024; 176:e14259. [PMID: 38511474 DOI: 10.1111/ppl.14259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Proteins of the armadillo repeat gene family play important roles in plant pathogen response. Here, 169 armadillo (ARM) genes were identified in upland cotton (Gossypium hirsutum). Phylogenetic analysis grouped these into 11 subfamilies, with conserved protein structures within each subfamily. The results signify that the expansion of the gene family occurred via whole genome duplication and dispersed duplication. Expression profiling and network analysis suggest that GhARM144 may regulate cotton resistance to Verticillium dahliae. GhARM144 was upregulated in roots by V. dahliae infection or salicylic acid treatment. This upregulation indicates a negative regulatory role of GhARM144' in the cotton immune responses, potentially by manipulating salicylic acid biosynthesis. Protein interaction studies found that GhARM144 associates with an osmotin-like protein, GhOSM34, at the plasma membrane. Silencing GhOSM34 reduced the resistance to V. dahliae, suggesting it may play a positive regulatory role. The results demonstrate that GhARM144 modulates cotton immunity through interaction with GhOSM34 and salicylic acid signalling. Further study of these proteins may yield insights into disease resistance mechanisms in cotton and other plants.
Collapse
Affiliation(s)
- Shichao Liu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan Province, Wanning, Hainan, China
| | - Fei Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, China
| | - Ruibing Liu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
| | - Chao Xue
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, China
| | - Yining Chen
- College of Cyber Science, Nankai University, Tianjin, China
| | - Chenchen Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Pengyun Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| |
Collapse
|
7
|
Chen D, Zhang Z, Chen Y, Li B, Chen T, Tian S. Transcriptional landscape of pathogen-responsive lncRNAs in tomato unveils the role of hydrolase encoding genes in response to Botrytis cinerea invasion. PLANT, CELL & ENVIRONMENT 2024; 47:651-663. [PMID: 37899711 DOI: 10.1111/pce.14757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/30/2023] [Accepted: 10/19/2023] [Indexed: 10/31/2023]
Abstract
LncRNAs have gained increasing attention owing to their important regulatory roles on growth and stress responses of plants. However, the mechanisms underlying the functions of lncRNAs in fruit-pathogen interaction are still largely unknown. In this study, a total of 273 lncRNAs responding to Botrytis cinerea infection were identified in tomato fruit, among which a higher percentage of antisense lncRNAs were targeted to the genes enriched in hydrolase activity. To ascertain the roles of these lncRNAs, seven hydrolase-related transcripts were transiently knocked-down by virus-induced gene silencing. Silencing of lncRNACXE20 reduced the expression level of a carboxylesterase gene, further enhancing the resistance of tomato to B. cinerea. In contrast, silencing of lncRNACHI, lncRNAMMP, lncRNASBT1.9 and lncRNAPME1.9 impaired the resistance to B. cinerea, respectively. Further RT-qPCR assay and enzymatic activity detection displayed that the attenuated resistance of lncRNAMMP and lncRNASBT1.9-silenced plants was associated with the inhibition on the expression of JA-related genes, while the decreased resistance of lncRNACHI-silenced plants resulted in reduced chitinase activity. Collectively, these results may provide references for deciphering the mechanisms underlying specific lncRNAs to interfere with B. cinerea infection by regulating the expression of defence-related genes or affecting hydrolase activity.
Collapse
Affiliation(s)
- Daoguo Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhanquan Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Boqiang Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Shiping Tian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Othman SMIS, Mustaffa AF, Mohd Zahid NII, Che-Othman MH, Samad AFA, Goh HH, Ismail I. Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108387. [PMID: 38266565 DOI: 10.1016/j.plaphy.2024.108387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.
Collapse
Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Nur Irdina Izzatie Mohd Zahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - M Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Abdul Fatah A Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia; Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia.
| |
Collapse
|
9
|
Li Y, Di Q, Luo L, Yu L. Phytosulfokine peptides, their receptors, and functions. FRONTIERS IN PLANT SCIENCE 2024; 14:1326964. [PMID: 38250441 PMCID: PMC10796568 DOI: 10.3389/fpls.2023.1326964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]
Abstract
Phytosulfokines (PSKs) are a class of disulfated pentapeptides and are regarded as plant peptide hormones. PSK-α, -γ, -δ, and -ϵ are four bioactive PSKs that are reported to have roles in plant growth, development, and immunity. In this review, we summarize recent advances in PSK biosynthesis, signaling, and function. PSKs are encoded by precursor genes that are widespread in higher plants. PSKs maturation from these precursors requires a sulfation step, which is catalyzed by a tyrosylprotein sulfotransferase, as well as proteolytic cleavage by subtilisin serine proteases. PSK signaling is mediated by plasma membrane-localized receptors PSKRs that belong to the leucine-rich repeat receptor-like kinase family. Moreover, multiple biological functions can be attributed to PSKs, including promoting cell division and cell growth, regulating plant reproduction, inducing somatic embryogenesis, enhancing legume nodulation, and regulating plant resistance to biotic and abiotic stress. Finally, we propose several research directions in this field. This review provides important insights into PSKs that will facilitate biotechnological development and PSK application in agriculture.
Collapse
Affiliation(s)
- Yi Li
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Qi Di
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Li Luo
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
| | - Liangliang Yu
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, Shanghai, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| |
Collapse
|
10
|
Li B, Feng C, Zhang W, Sun S, Yue D, Zhang X, Yang X. Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress. Int J Biol Macromol 2023; 253:126558. [PMID: 37659489 DOI: 10.1016/j.ijbiomac.2023.126558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/29/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
Collapse
Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Cheng Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| |
Collapse
|
11
|
Jobert F, Yadav S, Robert S. Auxin as an architect of the pectin matrix. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6933-6949. [PMID: 37166384 PMCID: PMC10690733 DOI: 10.1093/jxb/erad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.
Collapse
Affiliation(s)
- François Jobert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
- CRRBM, Université de Picardie Jules Verne, 80000, Amiens, France
| | - Sandeep Yadav
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
| |
Collapse
|
12
|
Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
Collapse
Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
13
|
Mu B, Teng Z, Tang R, Lu M, Chen J, Xu X, Wen YQ. An effector of Erysiphe necator translocates to chloroplasts and plasma membrane to suppress host immunity in grapevine. HORTICULTURE RESEARCH 2023; 10:uhad163. [PMID: 37746307 PMCID: PMC10516348 DOI: 10.1093/hr/uhad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/05/2023] [Indexed: 09/26/2023]
Abstract
The powdery mildew (Erysiphe necator) is a prevalent pathogen hampering grapevine growth in the vineyard. An arsenal of candidate secreted effector proteins (CSEPs) was encoded in the E. necator genome, but it is largely unclear what role CSEPs plays during the E. necator infection. In the present study, we identified a secreted effector CSEP080 of E. necator, which was located in plant chloroplasts and plasma membrane. Transient expressing CSEP080 promotes plant photosynthesis and inhibits INF1-induced cell death in tobacco leaves. We found that CSEP080 was a necessary effector for the E. necator pathogenicity, which interacted with grapevine chloroplast protein VviB6f (cytochrome b6-f complex iron-sulfur subunit), affecting plant photosynthesis. Transient silencing VviB6f increased the plant hydrogen peroxide production, and the plant resistance to powdery mildew. In addition, CSEP080 manipulated the VviPE (pectinesterase) to promote pectin degradation. Our results demonstrated the molecular mechanisms that an effector of E. necator translocates to host chloroplasts and plasma membrane, which suppresses with the grapevine immunity system by targeting the chloroplast protein VviB6f to suppress hydrogen peroxide accumulation and manipulating VviPE to promote pectin degradation.
Collapse
Affiliation(s)
- Bo Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Zhaolin Teng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Ruixin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Mengjiao Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Jinfu Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| | - Xiangnan Xu
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, Yangling 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture and Rural Affairs, Yangling 712100, Shaanxi, China
| |
Collapse
|
14
|
Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
Collapse
Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
| |
Collapse
|
15
|
Zhou R, Dong Y, Wang C, Liu J, Liang Q, Meng X, Lang X, Xu S, Liu W, Zhang S, Wang N, Yang KQ, Fang H. LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides. HORTICULTURE RESEARCH 2023; 10:uhad086. [PMID: 37786525 PMCID: PMC10541558 DOI: 10.1093/hr/uhad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/20/2023] [Indexed: 10/04/2023]
Abstract
Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.
Collapse
Affiliation(s)
- Rui Zhou
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Yuhui Dong
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Changxi Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Jianning Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Qiang Liang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Xiaoye Meng
- Department of Natural Resources Of Shandong Province, Forestry Protection and Development Service Center, Jinan, Shandong, China, 250000
| | - Xinya Lang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shengyi Xu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Wenjun Liu
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Shuhui Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Nan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Sciences and Engineering, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Ke Qiang Yang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| | - Hongcheng Fang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Taishan Forest Ecosystem Research Station, College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China, 271018
| |
Collapse
|
16
|
Yi F, Song A, Cheng K, Liu J, Wang C, Shao L, Wu S, Wang P, Zhu J, Liang Z, Chang Y, Chu Z, Cai C, Zhang X, Wang P, Chen A, Xu J, Burritt DJ, Herrera-Estrella L, Tran LSP, Li W, Cai Y. Strigolactones positively regulate Verticillium wilt resistance in cotton via crosstalk with other hormones. PLANT PHYSIOLOGY 2023; 192:945-966. [PMID: 36718522 PMCID: PMC10231467 DOI: 10.1093/plphys/kiad053] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 06/01/2023]
Abstract
Verticillium wilt caused by Verticillium dahliae is a serious vascular disease in cotton (Gossypium spp.). V. dahliae induces the expression of the CAROTENOID CLEAVAGE DIOXYGENASE 7 (GauCCD7) gene involved in strigolactone (SL) biosynthesis in Gossypium australe, suggesting a role for SLs in Verticillium wilt resistance. We found that the SL analog rac-GR24 enhanced while the SL biosynthesis inhibitor TIS108 decreased cotton resistance to Verticillium wilt. Knock-down of GbCCD7 and GbCCD8b genes in island cotton (Gossypium barbadense) decreased resistance, whereas overexpression of GbCCD8b in upland cotton (Gossypium hirsutum) increased resistance to Verticillium wilt. Additionally, Arabidopsis (Arabidopsis thaliana) SL mutants defective in CCD7 and CCD8 putative orthologs were susceptible, whereas both Arabidopsis GbCCD7- and GbCCD8b-overexpressing plants were more resistant to Verticillium wilt than wild-type (WT) plants. Transcriptome analyses showed that several genes related to the jasmonic acid (JA)- and abscisic acid (ABA)-signaling pathways, such as MYELOCYTOMATOSIS 2 (GbMYC2) and ABA-INSENSITIVE 5, respectively, were upregulated in the roots of WT cotton plants in responses to rac-GR24 and V. dahliae infection but downregulated in the roots of both GbCCD7- and GbCCD8b-silenced cotton plants. Furthermore, GbMYC2 suppressed the expression of GbCCD7 and GbCCD8b by binding to their promoters, which might regulate the homeostasis of SLs in cotton through a negative feedback loop. We also found that GbCCD7- and GbCCD8b-silenced cotton plants were impaired in V. dahliae-induced reactive oxygen species (ROS) accumulation. Taken together, our results suggest that SLs positively regulate cotton resistance to Verticillium wilt through crosstalk with the JA- and ABA-signaling pathways and by inducing ROS accumulation.
Collapse
Affiliation(s)
- Feifei Yi
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Aosong Song
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Kai Cheng
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jinlei Liu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Chenxiao Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Lili Shao
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Shuang Wu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Ping Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jiaxuan Zhu
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Zhilin Liang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Ying Chang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Zongyan Chu
- Cotton Institution, Kaifeng Academy of Agriculture and Forestry, Kaifeng 475000, China
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Pei Wang
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Aimin Chen
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu 030801, China
| | - David J Burritt
- Department of Botany, University of Otago, Dunedin 9054, New Zealand
| | - Luis Herrera-Estrella
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
- Unidad de Genomica Avanzada, Centro de Investigaciony de Estudios Avanzados del Intituto Politecnico Nacional, Irapuato 36821, Mexico
| | - Lam-Son Phan Tran
- Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
| | - Weiqiang Li
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Jilin Da’an Agro-ecosystem National Observation Research Station, Changchun 130102, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, School of Mathematics and Statistics, School of Computer and Information Engineering, Henan University, Kaifeng 475004, China
| |
Collapse
|
17
|
Wang Z, Cui Q, Su C, Zhao S, Wang R, Wang Z, Meng J, Luan Y. Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress. Int J Biol Macromol 2023:124952. [PMID: 37257526 DOI: 10.1016/j.ijbiomac.2023.124952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.
Collapse
Affiliation(s)
- Zhengjie Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qi Cui
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chenglin Su
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruiming Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
| |
Collapse
|
18
|
Lv G, Zhang Y, Ma L, Yan X, Yuan M, Chen J, Cheng Y, Yang X, Qiao Q, Zhang L, Niaz M, Sun X, Zhang Q, Zhong S, Chen F. A cell wall invertase modulates resistance to fusarium crown rot and sharp eyespot in common wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36912577 DOI: 10.1111/jipb.13478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/09/2023] [Indexed: 05/09/2023]
Abstract
Fusarium crown rot (FCR) and sharp eyespot (SE) are serious soil-borne diseases in wheat and its relatives that have been reported to cause wheat yield losses in many areas. In this study, the expression of a cell wall invertase gene, TaCWI-B1, was identified to be associated with FCR resistance through a combination of bulk segregant RNA sequencing and genome resequencing in a recombinant inbred line population. Two bi-parental populations were developed to further verify TaCWI-B1 association with FCR resistance. Overexpression lines and ethyl methanesulfonate (EMS) mutants revealed TaCWI-B1 positively regulating FCR resistance. Determination of cell wall thickness and components showed that the TaCWI-B1-overexpression lines exhibited considerably increased thickness and pectin and cellulose contents. Furthermore, we found that TaCWI-B1 directly interacted with an alpha-galactosidase (TaGAL). EMS mutants showed that TaGAL negatively modulated FCR resistance. The expression of TaGAL is negatively correlated with TaCWI-B1 levels, thus may reduce mannan degradation in the cell wall, consequently leading to thickening of the cell wall. Additionally, TaCWI-B1-overexpression lines and TaGAL mutants showed higher resistance to SE; however, TaCWI-B1 mutants were more susceptible to SE than controls. This study provides insights into a FCR and SE resistance gene to combat soil-borne diseases in common wheat.
Collapse
Affiliation(s)
- Guoguo Lv
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Yixiao Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Lin Ma
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Xiangning Yan
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Mingjie Yuan
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Jianhui Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Yongzhen Cheng
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Xi Yang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Qi Qiao
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Leilei Zhang
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Mohsin Niaz
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Xiaonan Sun
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| | - Qijun Zhang
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Feng Chen
- National Key Laboratory of Wheat and Maize Crop Science/CIMMYT-China Wheat and Maize Joint Research Center/Agronomy College, Henan Agricultural University, Zhengzhou, 450000, China
| |
Collapse
|
19
|
Zhao S, Meng J, Wekesa JS, Luan Y. Identification of small open reading frames in plant lncRNA using class-imbalance learning. Comput Biol Med 2023; 157:106773. [PMID: 36924731 DOI: 10.1016/j.compbiomed.2023.106773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Recently, small open reading frames (sORFs) in long noncoding RNA (lncRNA) have been demonstrated to encode small peptides that can help study the mechanisms of growth and development in organisms. Since machine learning-based computational methods are less costly compared with biological experiments, they can be used to identify sORFs and provide a basis for biological experiments. However, few computational methods and data resources have been exploited for identifying sORFs in plant lncRNA. Besides, machine learning models produce underperforming classifiers when faced with a class-imbalance problem. In this study, an alternative method called SMOTE based on weighted cosine distance (WCDSMOTE) which enables interaction with feature selection is put forward to synthesize minority class samples and weighted edited nearest neighbor (WENN) is applied to clean up majority class samples, thus, hybrid sampling WCDSMOTE-ENN is proposed to deal with imbalanced datasets with the multi-angle feature. A heterogeneous classifier ensemble is introduced to complete the classification task. Therefore, a novel computational method that is based on class-imbalance learning to identify the sORFs with coding potential in plant lncRNA (sORFplnc) is presented. Experimental results manifest that sORFplnc outperforms existing computational methods in identifying sORFs with coding potential. We anticipate that the proposed work can be a reference for relevant research and contribute to agriculture and biomedicine.
Collapse
Affiliation(s)
- Siyuan Zhao
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, 116024, China.
| | - Jael Sanyanda Wekesa
- Department of Information Technology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, China
| |
Collapse
|
20
|
Chen C, Lu LL, Ma SY, Zhao YP, Wu N, Li WJ, Ma L, Kong XH, Xie ZM, Hou YX. Analysis of PAT1 subfamily members in the GRAS family of upland cotton and functional characterization of GhSCL13-2A in Verticillium dahliae resistance. PLANT CELL REPORTS 2023; 42:487-504. [PMID: 36680639 DOI: 10.1007/s00299-022-02971-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
GhSCL13-2A, a member of the PAT1 subfamily in the GRAS family, positively regulates cotton resistance to Verticillium dahliae by mediating the jasmonic acid and salicylic acid signaling pathways and accumulation of reactive oxygen species. Verticillium wilt (VW) is a devastating disease of upland cotton (Gossypium hirsutum) that is primarily caused by the soil-borne fungus Verticillium dahliae. Scarecrow-like (SCL) proteins are known to be involved in plant abiotic and biotic stress responses, but their roles in cotton defense responses are still unclear. In this study, a total of 25 GhPAT1 subfamily members in the GRAS family were identified in upland cotton. Gene organization and protein domain analysis showed that GhPAT1 members were highly conserved. GhPAT1 genes were widely expressed in various tissues and at multiple developmental stages, and they were responsive to jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signals. Furthermore, GhSCL13-2A was induced by V. dahliae infection. V. dahliae resistance was enhanced in Arabidopsis thaliana by ectopic overexpression of GhSCL13-2A, whereas cotton GhSCL13-2A knockdowns showed increased susceptibility. Levels of reactive oxygen species (ROS) and JA were also increased and SA content was decreased in GhSCL13-2A knockdowns. At the gene expression level, PR genes and SA signaling marker genes were down-regulated and JA signaling marker genes were upregulated in GhSCL13-2A knockdowns. GhSCL13-2A was shown to be localized to the cell membrane and the nucleus. Yeast two-hybrid and luciferase complementation assays indicated that GhSCL13-2A interacted with GhERF5. In Arabidopsis, V. dahliae resistance was enhanced by GhERF5 overexpression; in cotton, resistance was reduced in GhERF5 knockdowns. This study revealed a positive role of GhSCL13-2A in V. dahliae resistance, establishing it as a strong candidate gene for future breeding of V. dahliae-resistant cotton cultivars.
Collapse
Affiliation(s)
- Chen Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li-Li Lu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National NanfanResearch Institute (Sanya), Chinese Academy ofAgricultural Sciences, Sanya, 572024, Hainan, China
| | - Shu-Ya Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan-Peng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Na Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wen-Jie Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li Ma
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
| | - Xian-Hui Kong
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zong-Ming Xie
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Yu-Xia Hou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- College of Science, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
21
|
Xue Y, Muhammad S, Yang J, Wang X, Zhao N, Qin B, Qiu Y, Du Z, Ulhassan Z, Zhou W, Liu F, Li R. Comparative transcriptome-wide identification and differential expression of genes and lncRNAs in rice near-isogenic line (KW- Bph36-NIL) in response to BPH feeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1095602. [PMID: 36874914 PMCID: PMC9981640 DOI: 10.3389/fpls.2022.1095602] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/30/2022] [Indexed: 06/18/2023]
Abstract
Brown planthopper (BPH) is the most devastating pest of rice in Asia, causing substantial yield losses and has become a challenging task to be controlled under field conditions. Although extensive measures have been taken over the past decades, which resulted in the evolution of new resistant BPH strains. Therefore, besides other possible approaches, equipping host plants with resistant genes is the most effective and environment-friendly technique for BPH control. Here, we systematically analyzed transcriptome changes in the susceptible rice variety Kangwenqingzhan (KW) and the resistant near-isogenic line (NIL) KW-Bph36-NIL, through RNA-seq, depicting the differential expression profiles of mRNAs and long non-coding RNAs (lncRNAs) in rice before and after BPH feeding. We observed a proportion of genes (1.48%) and (2.74%) were altered in KW and NIL, respectively, indicating different responses of rice strains against BPH feeding. Nevertheless, we characterized 384 differentially expressed long non-coding RNAs (DELs) that can be impacted by the two strains by alternatively changing the expression patterns of the respective coding genes, suggesting their certain involvement in response to BPH feeding. In BPH invasion, KW and NIL responded differently by modifying the synthesis, storage, and transformation of intracellular substances, adjusting the nutrient accumulation and utilization inside and outside the cells. In addition, NIL expressed stronger resistance by acutely up-regulating genes and other transcription factors related to stress resistance and plant immunity. Altogether, our study elaborates valuable insights into the genome-wide DEGs and DELs expression profiles of rice under BPH invasion by high throughput sequencing and further suggests that NILs can be utilized in BPH resistance breeding programs in developing high-resistance rice lines.
Collapse
Affiliation(s)
- Yanxia Xue
- School of Electrical and Control Engineering, North University of China, Taiyuan, China
| | - Sajid Muhammad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xuan Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yongfu Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimin Du
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zaid Ulhassan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Weijun Zhou
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| |
Collapse
|
22
|
Gu L, Hou B, Chen X, Wang Y, Chang P, He X, Gong D, Sun Q. The Bcl-2-associated athanogene gene family in tobacco ( Nicotiana tabacum) and the function of NtBAG5 in leaf senescence. FRONTIERS IN PLANT SCIENCE 2023; 14:1108588. [PMID: 36844065 PMCID: PMC9947661 DOI: 10.3389/fpls.2023.1108588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Leaf senescence in tobacco is closely related to leaf maturation and secondary metabolites. Bcl-2-associated athanogene (BAG) family members are highly conserved proteins and play key roles in senescence, growth and development, and resistance to biotic and abiotic stresses. Herein, the BAG family of tobacco was identified and characterized. In total, 19 tobacco BAG protein candidate genes were identified and divided into two classes, class I comprising NtBAG1a-e, NtBAG3a-b, and NtBAG4a-c and class II including NtBAG5a-e, NtBAG6a-b, and NtBAG7. Genes in the same subfamily or branch of the phylogenetic tree exhibited similarities in gene structure and the cis-element on promoters. RNA-seq and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that the expression of NtBAG5c-f and NtBAG6a-b was upregulated in senescent leaves, implying that they play a role in regulating leaf senescence. NtBAG5c was localized in the nucleus and cell wall as a homology of leaf senescence related gene AtBAG5. Further, the interaction of NtBAG5c with heat-shock protein 70 (HSP70) and sHSP20 was demonstrated using yeast two-hybrid experiment. Virus-induced gene silencing indicated that NtBAG5c reduced the lignin content and increased superoxide dismutase (SOD) activity and hydrogen peroxide (H2O2) accumulation. In NtBAG5c-silenced plants, the expression of multiple senescence-related genes cysteine proteinase (NtCP1), SENESCENCE 4 (SEN4) and SENESCENCE-ASSOCIATED GENE 12 (SAG12) was downregulated. In conclusion, tobacco BAG protein candidate genes were identified and characterized for the first time.
Collapse
Affiliation(s)
- Linxin Gu
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Bing Hou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Xiao Chen
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Yu Wang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Pingan Chang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Xiaohong He
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| | - Daping Gong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Quan Sun
- Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Nan'an, Chongqing, China
| |
Collapse
|
23
|
Zhu Y, Zhao M, Li T, Wang L, Liao C, Liu D, Zhang H, Zhao Y, Liu L, Ge X, Li B. Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt. FRONTIERS IN PLANT SCIENCE 2023; 14:1174281. [PMID: 37152175 PMCID: PMC10161258 DOI: 10.3389/fpls.2023.1174281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.
Collapse
Affiliation(s)
- Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| | - Mei Zhao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Taotao Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Lianzhe Wang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Chunli Liao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Dongxiao Liu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Huamin Zhang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Yanpeng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| |
Collapse
|
24
|
Wang F, Lu T, Zhu L, Cao A, Xie S, Chen X, Shen H, Xie Q, Li R, Zhu J, Jin X, Li H. Multicopper oxidases GbAO and GbSKS are involved in the Verticillium dahliae resistance in Gossypium barbadense. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153887. [PMID: 36543064 DOI: 10.1016/j.jplph.2022.153887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Ascorbate oxidase (AO) and skewed5 (SKU5)-similar (SKS) proteins belong to the multicopper oxidase (MCO) family and play important roles in plants in response to environmental stress via modulation of oxidoreduction homeostasis. Currently, reports on the response of Gossypium barbadense MCO to Verticillium wilt (VW) caused by Verticillium dahliae are still limited. Herein, RNA sequencing of two G. barbadense cultivars of VW-resistant XH21 and VW-susceptible XH7 under V. dahliae treatment, combined with physiological and genetic analysis, was performed to analyze the function and mechanism of multicopper oxidases GbAO and GbSKS involved in V. dahliae resistance. The identified differentially expressed genes are mainly involved in the regulation of oxidoreduction reaction, and extracellular components and signaling. Interestingly, ascorbate oxidase family members were discovered as the most significantly upregulated genes after V. dahliae treatment, including GbAO3A/D, GbSKS3A/D, and GbSKS16A/D. H2O2 and Asc contents, especially reductive Asc in both XH21 and XH7, were shown to be increased. Silenced expression of respective GbAO3A/D, GbSKS3A/D, and GbSKS16A/D in virus-induced gene silencing (VIGS) cotton plants significantly decreased the resistance to V. dahliae, coupled with the reduced contents of pectin and lignin. Our results indicate that AO might be involved in cotton VW resistance via the regulation of cell wall components.
Collapse
Affiliation(s)
- Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Tianxin Lu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Liping Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Aiping Cao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Shuangquan Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Xifeng Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Jianbo Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Xiang Jin
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China; College of Science, Qiongtai Normal University, Haikou, 571127, China; Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| |
Collapse
|
25
|
Fartash AH, Ben C, Mazurier M, Ebrahimi A, Ghalandar M, Gentzbittel L, Rickauer M. Medicago truncatula quantitative resistance to a new strain of Verticillium alfalfae from Iran revealed by a genome-wide association study. FRONTIERS IN PLANT SCIENCE 2023; 14:1125551. [PMID: 37123855 PMCID: PMC10140629 DOI: 10.3389/fpls.2023.1125551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Verticillium wilt is a major threat to many crops, among them alfalfa (Medicago sativa). The model plant Medicago truncatula, a close relative of alfalfa was used to study the genetic control of resistance towards a new Verticillium alfalfae isolate. The accidental introduction of pathogen strains through global trade is a threat to crop production and such new strains might also be better adapted to global warming. Isolates of V. alfalfae were obtained from alfalfa fields in Iran and characterized. The Iranian isolate AF1 was used in a genome-wide association study (GWAS) involving 242 accessions from the Mediterranean region. Root inoculations were performed with conidia at 25°C and symptoms were scored regularly. Maximum Symptom Score and Area under Disease Progess Curve were computed as phenotypic traits to be used in GWAS and for comparison to a previous study with French isolate V31.2 at 20°C. This comparison showed high correlation with a shift to higher susceptibility, and similar geographical distribution of resistant and susceptible accessions to AF1 at 25°C, with resistant accessions mainly in the western part. GWAS revealed 30 significant SNPs linked to resistance towards isolate AF1. None of them were common to the previous study with isolate V31.2 at 20°C. To confirm these loci, the expression of nine underlying genes was studied. All genes were induced in roots following inoculation, in susceptible and resistant plants. However, in resistant plants induction was higher and lasted longer. Taken together, the use of a new pathogen strain and a shift in temperature revealed a completely different genetic control compared to a previous study that demonstrated the existence of two major QTLs. These results can be useful for Medicago breeding programs to obtain varieties better adapted to future conditions.
Collapse
Affiliation(s)
- Amir Hossein Fartash
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
| | - Cécile Ben
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- Project Center for Agro Technologies, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mélanie Mazurier
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
| | - Asa Ebrahimi
- Department of Plant Breeding and Biotechnology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mojtaba Ghalandar
- Plant Protection Department, Markazi Agricultural and Natural Resources Research and Education Center, Arak, Iran
| | - Laurent Gentzbittel
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- Project Center for Agro Technologies, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Martina Rickauer
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Centre National de Recherche Scientifique, Toulouse Institut National Polytechnique, Université Toulouse 3 – Paul Sabatier (UPS), Toulouse, France
- *Correspondence: Martina Rickauer,
| |
Collapse
|
26
|
Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
Collapse
Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
27
|
Peng Y, Pan R, Liu Y, Medison MB, Shalmani A, Yang X, Zhang W. LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato. PHYSIOLOGIA PLANTARUM 2022; 174:e13826. [PMID: 36377281 DOI: 10.1111/ppl.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.
Collapse
Affiliation(s)
- Ying Peng
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Yi Liu
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Milca Banda Medison
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xinsun Yang
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| |
Collapse
|
28
|
Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
Collapse
|
29
|
Wang X, Wang Q, Yan L, Hao Y, Lian X, Zhang H, Zheng X, Cheng J, Wang W, Zhang L, Ye X, Li J, Tan B, Feng J. PpTCP18 is upregulated by lncRNA5 and controls branch number in peach ( Prunus persica) through positive feedback regulation of strigolactone biosynthesis. HORTICULTURE RESEARCH 2022; 10:uhac224. [PMID: 36643759 PMCID: PMC9832876 DOI: 10.1093/hr/uhac224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/27/2022] [Indexed: 06/17/2023]
Abstract
Branch number is an important agronomic trait in peach (Prunus persica) trees because plant architecture affects fruit yield and quality. Although breeders can select varieties with different tree architecture, the biological mechanisms underlying architecture remain largely unclear. In this study, a pillar peach ('Zhaoshouhong') and a standard peach ('Okubo') were compared. 'Zhaoshouhong' was found to have significantly fewer secondary branches than 'Okubo'. Treatment with the synthetic strigolactone (SL) GR24 decreased branch number. Transcriptome analysis indicated that PpTCP18 (a homologous gene of Arabidopsis thaliana BRC1) expression was negatively correlated with strigolactone synthesis gene expression, indicating that PpTCP18 may play an important role in peach branching. Yeast one-hybrid, electrophoretic mobility shift, dual-luciferase assays and PpTCP18-knockdown in peach leaf buds indicated that PpTCP18 could increase expression of PpLBO1, PpMAX1, and PpMAX4. Furthermore, transgenic Arabidopsis plants overexpressing PpTCP18 clearly exhibited reduced primary rosette-leaf branches. Moreover, lncRNA sequencing and transient expression analysis revealed that lncRNA5 targeted PpTCP18, significantly increasing PpTCP18 expression. These results provide insights into the mRNA and lncRNA network in the peach SL signaling pathway and indicate that PpTCP18, a transcription factor downstream of SL signaling, is involved in positive feedback regulation of SL biosynthesis. This role of PpTCP18 may represent a novel mechanism in peach branching regulation. Our study improves current understanding of the mechanisms underlying peach branching and provides theoretical support for genetic improvement of peach tree architecture.
Collapse
Affiliation(s)
| | | | - Lixia Yan
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Yuhang Hao
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Xiaodong Lian
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Haipeng Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Xianbo Zheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Jun Cheng
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Wei Wang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Langlang Zhang
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Xia Ye
- College of Horticulture, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | - Jidong Li
- College of Forestry, Henan Agricultural University, 95 Wenhua Road, 450002, Zhengzhou, China
| | | | | |
Collapse
|
30
|
Chen L, Shen E, Zhao Y, Wang H, Wilson I, Zhu QH. The Conservation of Long Intergenic Non-Coding RNAs and Their Response to Verticillium dahliae Infection in Cotton. Int J Mol Sci 2022; 23:ijms23158594. [PMID: 35955726 PMCID: PMC9368808 DOI: 10.3390/ijms23158594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been demonstrated to be vital regulators of diverse biological processes in both animals and plants. While many lincRNAs have been identified in cotton, we still know little about the repositories and conservativeness of lincRNAs in different cotton species or about their role in responding to biotic stresses. Here, by using publicly available RNA-seq datasets from diverse sources, including experiments of Verticillium dahliae (Vd) infection, we identified 24,425 and 17,713 lincRNAs, respectively, in Gossypium hirsutum (Ghr) and G. barbadense (Gba), the two cultivated allotetraploid cotton species, and 6933 and 5911 lincRNAs, respectively, in G. arboreum (Gar) and G. raimondii (Gra), the two extant diploid progenitors of the allotetraploid cotton. While closely related subgenomes, such as Ghr_At and Gba_At, tend to have more conserved lincRNAs, most lincRNAs are species-specific. The majority of the synthetic and transcribed lincRNAs (78.2%) have a one-to-one orthologous relationship between different (sub)genomes, although a few of them (0.7%) are retained in all (sub)genomes of the four species. The Vd responsiveness of lincRNAs seems to be positively associated with their conservation level. The major functionalities of the Vd-responsive lincRNAs seem to be largely conserved amongst Gra, Ghr, and Gba. Many Vd-responsive Ghr-lincRNAs overlap with Vd-responsive QTL, and several lincRNAs were predicted to be endogenous target mimicries of miR482/2118, with a pair being highly conserved between Ghr and Gba. On top of the confirmation of the feature characteristics of the lincRNAs previously reported in cotton and other species, our study provided new insights into the conservativeness and divergence of lincRNAs during cotton evolution and into the relationship between the conservativeness and Vd responsiveness of lincRNAs. The study also identified candidate lincRNAs with a potential role in disease response for functional characterization.
Collapse
Affiliation(s)
- Li Chen
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
| | - Enhui Shen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China;
| | - Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (Y.Z.); (H.W.)
| | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia;
- Correspondence:
| |
Collapse
|
31
|
He L, Han Z, Zang Y, Dai F, Chen J, Jin S, Huang C, Cheng Y, Zhang J, Xu B, Qi G, Cao Y, Yan S, Xuan L, Zhang T, Si Z, Hu Y. Advanced genes expression pattern greatly contributes to divergence in Verticillium wilt resistance between Gossypium barbadense and Gossupium hirsutum. FRONTIERS IN PLANT SCIENCE 2022; 13:979585. [PMID: 35979082 PMCID: PMC9376480 DOI: 10.3389/fpls.2022.979585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Verticillium, representing one of the world's major pathogens, causes Verticillium wilt in important woody species, ornamentals, agricultural, etc., consequently resulting in a serious decline in production and quality, especially in cotton. Gossupium hirutum and Gossypium barbadense are two kinds of widely cultivated cotton species that suffer from Verticillium wilt, while G. barbadense has much higher resistance toward it than G. hirsutum. However, the molecular mechanism regarding their divergence in Verticillium wilt resistance remains largely unknown. In the current study, G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 were compared at 0, 12, 24, 48, 72, 96, 120, and 144 h post-inoculation (hpi) utilizing high throughput RNA-Sequencing. As a result, a total of 3,549 and 4,725 differentially expressed genes (DEGs) were identified, respectively. In particular, the resistant type Hai7124 displayed an earlier and faster detection and signaling response to the Verticillium dahliae infection and demonstrated higher expression levels of defense-related genes over TM-1 with respect to transcription factors, plant hormone signal transduction, plant-pathogen interaction, and nucleotide-binding leucine-rich repeat (NLR) genes. This study provides new insights into the molecular mechanisms of divergence in Verticillium wilt resistance between G. barbadense and G. hirsutum and important candidate genes for breeding V. dahliae resistant cotton cultivars.
Collapse
Affiliation(s)
- Lu He
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zegang Han
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yihao Zang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shangkun Jin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Cheng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Juncheng Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Biyu Xu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoan Qi
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiwen Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianzhen Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- The Rural Development Academy, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| |
Collapse
|