1
|
Hua X, Li Z, Dou M, Zhang Y, Zhao D, Shi H, Li Y, Li S, Huang Y, Qi Y, Wang B, Wang Q, Wang Q, Gao R, Ming R, Tang H, Yao W, Zhang M, Zhang J. Transcriptome and small RNA analysis unveils novel insights into the C 4 gene regulation in sugarcane. PLANTA 2024; 259:120. [PMID: 38607398 DOI: 10.1007/s00425-024-04390-6] [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: 12/12/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
MAIN CONCLUSION This study reveals miRNA indirect regulation of C4 genes in sugarcane through transcription factors, highlighting potential key regulators like SsHAM3a. C4 photosynthesis is crucial for the high productivity and biomass of sugarcane, however, the miRNA regulation of C4 genes in sugarcane remains elusive. We have identified 384 miRNAs along the leaf gradients, including 293 known miRNAs and 91 novel miRNAs. Among these, 86 unique miRNAs exhibited differential expression patterns, and we identified 3511 potential expressed targets of these differentially expressed miRNAs (DEmiRNAs). Analyses using Pearson correlation coefficient (PCC) and Gene Ontology (GO) enrichment revealed that targets of miRNAs with positive correlations are integral to chlorophyll-related photosynthetic processes. In contrast, negatively correlated pairs are primarily associated with metabolic functions. It is worth noting that no C4 genes were predicted as targets of DEmiRNAs. Our application of weighted gene co-expression network analysis (WGCNA) led to a gene regulatory network (GRN) suggesting miRNAs might indirectly regulate C4 genes via transcription factors (TFs). The GRAS TF SsHAM3a emerged as a potential regulator of C4 genes, targeted by miR171y and miR171am, and exhibiting a negative correlation with miRNA expression along the leaf gradient. This study sheds light on the complex involvement of miRNAs in regulating C4 genes, offering a foundation for future research into enhancing sugarcane's photosynthetic efficiency.
Collapse
Affiliation(s)
- Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Zhen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Meijie Dou
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Dongxu Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihong Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yihan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Shuangyu Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yumin Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiying Qi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Qiyun Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiaoyu Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruiting Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Biology, The University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, 530004, China.
| |
Collapse
|
2
|
Li C, Iqbal MA. Leveraging the sugarcane CRISPR/Cas9 technique for genetic improvement of non-cultivated grasses. FRONTIERS IN PLANT SCIENCE 2024; 15:1369416. [PMID: 38601306 PMCID: PMC11004347 DOI: 10.3389/fpls.2024.1369416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Under changing climatic scenarios, grassland conservation and development have become imperative to impart functional sustainability to their ecosystem services. These goals could be effectively and efficiently achieved with targeted genetic improvement of native grass species. To the best of our literature search, very scant research findings are available pertaining to gene editing of non-cultivated grass species (switch grass, wild sugarcane, Prairie cordgrass, Bermuda grass, Chinese silver grass, etc.) prevalent in natural and semi-natural grasslands. Thus, to explore this novel research aspect, this study purposes that gene editing techniques employed for improvement of cultivated grasses especially sugarcane might be used for non-cultivated grasses as well. Our hypothesis behind suggesting sugarcane as a model crop for genetic improvement of non-cultivated grasses is the intricacy of gene editing owing to polyploidy and aneuploidy compared to other cultivated grasses (rice, wheat, barley, maize, etc.). Another reason is that genome editing protocols in sugarcane (x = 10-13) have been developed and optimized, taking into consideration the high level of genetic redundancy. Thus, as per our knowledge, this review is the first study that objectively evaluates the concept and functioning of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 technique in sugarcane regarding high versatility, target specificity, efficiency, design simplicity, and multiplexing capacity in order to explore novel research perspectives for gene editing of non-cultivated grasses against biotic and abiotic stresses. Additionally, pronounced challenges confronting sugarcane gene editing have resulted in the development of different variants (Cas9, Cas12a, Cas12b, and SpRY) of the CRISPR tool, whose technicalities have also been critically assessed. Moreover, different limitations of this technique that could emerge during gene editing of non-cultivated grass species have also been highlighted.
Collapse
Affiliation(s)
- Chunjia Li
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, Yunnan, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, China
| | - Muhammad Aamir Iqbal
- National Key Laboratory for Biological Breeding of Tropical Crops, Kunming, Yunnan, China
- Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences/Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan, Yunnan, China
| |
Collapse
|
3
|
Liu J, Ren Y, Sun Y, Yin Y, Han B, Zhang L, Song Y, Zhang Z, Xu Y, Fan D, Li J, Liu H, Ma C. Identification and Analysis of the MIR399 Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress. Int J Mol Sci 2024; 25:2979. [PMID: 38474225 PMCID: PMC10931670 DOI: 10.3390/ijms25052979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem-loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding.
Collapse
Affiliation(s)
- Jingjing Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yi Ren
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Yan Sun
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Yonggang Yin
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Bin Han
- Changli Research Institute of Fruit Trees, Hebei Academy of Agricultural and Forestry Sciences, Changli 066600, China
| | - Lipeng Zhang
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junpeng Li
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaifeng Liu
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Department of Horticulture, Agricultural College of Shihezi University, Shihezi 832003, China; (J.L.)
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
4
|
Vignesh P, Mahadevaiah C, Selvamuthu K, Mahadeva Swamy HK, Sreenivasa V, Appunu C. Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus. 3 Biotech 2024; 14:24. [PMID: 38162015 PMCID: PMC10756875 DOI: 10.1007/s13205-023-03867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03867-7.
Collapse
Affiliation(s)
- Palanisamy Vignesh
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Channappa Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
- ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bangalore, 560089 India
| | - Kannan Selvamuthu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | | | - Venkatarayappa Sreenivasa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| |
Collapse
|
5
|
Yu Y, Wang P, Wan H, Wang Y, Hu H, Ni Z. The Gma-miR394a/GmFBX176 module is involved in regulating the soybean (Glycine max L.) response to drought stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111879. [PMID: 37778470 DOI: 10.1016/j.plantsci.2023.111879] [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: 08/22/2023] [Revised: 09/10/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Drought seriously affects the yield and quality of soybean. Previous studies have shown that the gma-miR394a/GmFBX176 module regulates the response of Arabidopsis to drought stress. However, whether the gma-miR394a/GmFBX176 module is involved in the regulation of the soybean drought stress response remains unclear. Here, the function of the gma-miR394a/GmFBX176 module in the soybean drought stress response was evaluated. In soybean hairy roots, drought stress induced the transcription of gma-miR394a and inhibited the transcription of GmFBX176. GUS histochemical staining showed that transgenic GmFBX176p:GUS soybean hairy root staining was weak and that GUS transcript levels decreased under drought stress. A transient expression experiment in tobacco showed that gma-miR394a inhibited GmFBX176 transcription. Under drought stress, composite soybean plants overexpressing gma-miR394a showed increased drought resistance compared with control K599 composite soybean plants (K599); their survival rate and peroxidase activity were higher than those of K599, and their malondialdehyde content was lower. In contrast, composite soybean plants overexpressing GmFBX176m3 (gma-miR394a complement site mutation) presented lower drought resistance than K599 plants. Transcriptomic sequencing showed that the gma-miR394a/GmFBX176 module affected the transcript levels of stress response genes and transcription factors. These results indicate that the gma-miR394a/GmFBX176 module can be used to improve the drought resistance of soybean.
Collapse
Affiliation(s)
- Yuehua Yu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Ping Wang
- College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Huina Wan
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Yi Wang
- College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Hao Hu
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Zhiyong Ni
- College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, PR China.
| |
Collapse
|
6
|
Rodriguez Gallo MC, Li Q, Talasila M, Uhrig RG. Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA. Mol Cell Proteomics 2023; 22:100638. [PMID: 37704098 PMCID: PMC10663867 DOI: 10.1016/j.mcpro.2023.100638] [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: 02/16/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.
Collapse
Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - M Talasila
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| |
Collapse
|
7
|
Inal B, Mirzapour M, Tufekci ED, Rustemoglu M, Kaba A, Albalawi MA, Alalawy AI, Sakran M, Alqurashi M, Ditta A. Drought-Induced miRNA Expression Correlated with Heavy Metal, Phenolic Acid, and Protein and Nitrogen Levels in Five Chickpea Genotypes. ACS OMEGA 2023; 8:35746-35754. [PMID: 37810661 PMCID: PMC10552140 DOI: 10.1021/acsomega.3c03003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Drought is a prime stress, drastically affecting plant growth, development, and yield. Plants have evolved various physiological, molecular, and biochemical mechanisms to cope with drought. Investigating specific biochemical pathways related to drought tolerance mechanisms of plants through biotechnology approaches is one of the quickest and most effective strategies for enhancing crop production. Among them, microRNAs (miRNAs) are the principal post-transcriptional regulators of gene expression in plants during plant growth under biotic and abiotic stresses. In this study, five different chickpea genotypes (İnci, Hasan bey, Arda, Seçkin, and Diyar 95) were grown under normal and drought stress. We recorded the expression levels of microRNAs in these genotypes and found differential expression (miRNA396, miR408, miRNA414, miRNA528, and miRNA1533) under contrasting conditions. Results revealed that miRNA414 and miRNA528 considerably increased in all genotypes under drought stress, and expression levels of miRNA418, miRNA1533, and miRNA396 (except for the Seçkin genotype) were found to be higher under the watered conditions. These genotypes were also investigated for heavy metal, phenolic acid, protein, and nitrogen concentrations under normal and drought stress conditions. The Arda genotype showed a significant increase in nitrogen (5.46%) and protein contents (28.3%), while protein contents were decreased in the Hasan bey and Seçkin genotypes subjected to drought stress. In the case of metals, iron was the most abundant element in all genotypes (İnci = 15.4 ppm, Hasan bey = 29.6 ppm, Seçkin = 37.8 ppm, Arda = 26.3 ppm, and Diyar 95 = 40.8 ppm) under normal conditions. Interestingly, these results were related to miRNA expression in the chickpea genotypes and hint at the regulation of multiple pathways under drought conditions. Overall, the present study will help us to understand the miRNA-mediated regulation of various pathways in chickpea genotypes.
Collapse
Affiliation(s)
- Behcet Inal
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Mohsen Mirzapour
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Ebru Derelli Tufekci
- Food
and Agriculture Vocational High School, Department of Field Crops, Cankiri Karatekin University, Cankiri 18100, Turkey
| | - Mustafa Rustemoglu
- Faculty
of Agriculture, Department of Plant Protection, Sirnak University, Sirnak 73000, Turkey
| | - Adem Kaba
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Marzough Aziz Albalawi
- Department
of Chemistry, University College at Alwajh, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Adel I. Alalawy
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
| | - Mohamed Sakran
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
- Biochemistry
Section, Chemistry Department, Faculty of Science, Tanta University, Tanta31527,Egypt
| | - Mohammed Alqurashi
- Department
of Biotechnology, Faculty of Science, Taif
University, Taif 21974, Saudi Arabia
| | - Allah Ditta
- Department
of Environmental Sciences, Shaheed Benazir
Bhutto University Sheringal, Dir (U), Khyber Pakhtunkhwa 18000, Pakistan
- School
of Biological Sciences, The University of
Western Australia, 35
Stirling Highway, Perth, WA 6009, Australia
| |
Collapse
|
8
|
Rehman OU, Uzair M, Farooq MS, Saleem B, Attacha S, Attia KA, Farooq U, Fiaz S, El-Kallawy WH, Kimiko I, Khan MR. Comprehensive insights into the regulatory mechanisms of lncRNA in alkaline-salt stress tolerance in rice. Mol Biol Rep 2023; 50:7381-7392. [PMID: 37450076 DOI: 10.1007/s11033-023-08648-2] [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: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses. METHOD lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions. RESULTS Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response. CONCLUSION The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
Collapse
Affiliation(s)
- Obaid Ur Rehman
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| | - Muhammad Shahbaz Farooq
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Safira Attacha
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, Science College, King Saud University, POX, Riyadh, 2455-11451, Saudi Arabia.
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Wael H El-Kallawy
- Agriculture Research Center, (ARC), Rice Research and Training Center, (RRTC) Sakha, Field Crop Research Institute, Sakha, Egypt
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| |
Collapse
|
9
|
Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
Collapse
Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
| |
Collapse
|
10
|
Li AM, Liao F, Wang M, Chen ZL, Qin CX, Huang RQ, Verma KK, Li YR, Que YX, Pan YQ, Huang DL. Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors. Int J Mol Sci 2023; 24:ijms24108913. [PMID: 37240257 DOI: 10.3390/ijms24108913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.
Collapse
Affiliation(s)
- Ao-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Cui-Xian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Ruo-Qi Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - You-Xiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - You-Qiang Pan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Dong-Liang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| |
Collapse
|
11
|
Dinesh Babu KS, Janakiraman V, Palaniswamy H, Kasirajan L, Gomathi R, Ramkumar TR. A short review on sugarcane: its domestication, molecular manipulations and future perspectives. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2623-2643. [PMID: 36159774 PMCID: PMC9483297 DOI: 10.1007/s10722-022-01430-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/11/2022] [Indexed: 06/16/2023]
Abstract
Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.
Collapse
Affiliation(s)
| | - Vardhana Janakiraman
- Department of Biotechnology, Vels Institute of Science, Technology & Advanced studies (VISTAS), Chennai, TN 600117 India
| | - Harunipriya Palaniswamy
- Tissue Culture Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Lakshmi Kasirajan
- Genomics Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Raju Gomathi
- Plant Physiology Laboratory, Division of Crop Production, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Thakku R. Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL 32611 USA
- Department of Biological Sciences, Delaware State University, Dover, DE 19001 USA
| |
Collapse
|
12
|
Duarte KE, Basso MF, de Oliveira NG, da Silva JCF, de Oliveira Garcia B, Cunha BADB, Cardoso TB, Nepomuceno AL, Kobayashi AK, Santiago TR, de Souza WR, Molinari HBC. MicroRNAs expression profiles in early responses to different levels of water deficit in Setaria viridis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1607-1624. [PMID: 36389096 PMCID: PMC9530107 DOI: 10.1007/s12298-022-01226-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Water deficit is a major constraint for crops of economic importance in almost all agricultural regions. However, plants have an active defense system to adapt to these adverse conditions, acting in the reprogramming of gene expression responsible for encoding microRNAs (miRNAs). These miRNAs promote the regulation to the target gene expression by the post-transcriptional (PTGS) and transcriptional gene silencing (TGS), modulating several pathways including defense response to water deficit. The broader knowledge of the miRNA expression profile and its regulatory networks in response to water deficit can provide evidence for the development of new biotechnological tools for genetic improvement of several important crops. In this study, we used Setaria viridis accession A10.1 as a C4 model plant to widely investigate the miRNA expression profile in early responses to different levels of water deficit. Ecophysiological studies in Setaria viridis under water deficit and after rewatering demonstrated a drought tolerant accession, capable of a rapid recovery from the stress. Deep small RNA sequencing and degradome studies were performed in plants submitted to drought to identify differentially expressed miRNA genes and their predicted targets, using in silico analysis. Our findings showed that several miRNAs were differentially modulated in response to distinctive levels of water deficit and after rewatering. The predicted mRNA targets mainly corresponded to genes related to cell wall remodeling, antioxidant system and drought-related transcription factors, indicating that these genes are rapidly regulated in early responses to drought stress. The implications of these modulations are extensively discussed, and higher-effect miRNAs are suggested as major players for potential use in genetic engineering to improve drought tolerance in economically important crops, such as sugarcane, maize, and sorghum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01226-z.
Collapse
Affiliation(s)
- Karoline Estefani Duarte
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
| | - Marcos Fernando Basso
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT 78740-970 Brazil
| | | | | | - Bruno de Oliveira Garcia
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of Lavras, Lavras, MG 37200-900 Brazil
| | | | | | | | | | - Thaís Ribeiro Santiago
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- University of Brasília, Brasília, DF 70910-900 Brazil
| | - Wagner Rodrigo de Souza
- Embrapa Agroenergy, Brasília, DF 70297-400 Brazil
- Federal University of ABC, Santo André, SP 09210-580 Brazil
| | | |
Collapse
|
13
|
Zhang N, Feng X, Zeng Q, Lin H, Wu Z, Gao X, Huang Y, Wu J, Qi Y. Integrated Analysis of miRNAs Associated With Sugarcane Responses to Low-Potassium Stress. FRONTIERS IN PLANT SCIENCE 2022; 12:750805. [PMID: 35058942 PMCID: PMC8763679 DOI: 10.3389/fpls.2021.750805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Sugarcane is among the most important global crops and a key bioenergy source. Sugarcane production is restricted by limited levels of available soil potassium (K+). The ability of plants to respond to stressors can be regulated by a range of microRNAs (miRNAs). However, there have been few studies regarding the roles of miRNAs in the regulation of sugarcane responses to K+-deficiency. To understand how these non-coding RNAs may influence sugarcane responses to low-K+ stress, we conducted expression profiling of miRNAs in sugarcane roots under low-K+ conditions via high-throughput sequencing. This approach led to the identification of 324 and 42 known and novel miRNAs, respectively, of which 36 were found to be differentially expressed miRNAs (DEMs) under low-K+ conditions. These results also suggested that miR156-x/z and miR171-x are involved in these responses as potential regulators of lateral root formation and the ethylene signaling pathway, respectively. A total of 705 putative targets of these DEMs were further identified through bioinformatics predictions and degradome analyses, and GO and KEGG enrichment analyses revealed these target mRNAs to be enriched for catalytic activity, binding functions, metabolic processes, plant hormone signal transduction, and mitogen-activated protein kinase (MAPK) signaling. In summary, these data provide an overview of the roles of miRNAs in the regulation of sugarcane response to low-K+ conditions.
Collapse
Affiliation(s)
- Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaomin Feng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Huanzhang Lin
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Yonghong Huang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Yongwen Qi
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
14
|
Chen J, Zhong Y, Qi X. LncRNA TCONS_00021861 is functionally associated with drought tolerance in rice (Oryza sativa L.) via competing endogenous RNA regulation. BMC PLANT BIOLOGY 2021; 21:410. [PMID: 34493227 PMCID: PMC8424815 DOI: 10.1186/s12870-021-03195-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/30/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Water deficit is an abiotic stress that retards plant growth and destabilizes crop production. Long non coding RNAs (lncRNAs) are a class of non-coding endogenous RNAs that participate in diverse cellular processes and stress responses in plants. lncRNAs could function as competing endogenous RNAs (ceRNA) and represent a novel layer of gene regulation. However, the regulatory mechanism of lncRNAs as ceRNA in drought stress response is yet unclear. RESULTS In this study, we performed transcriptome-wide identification of drought-responsive lncRNAs in rice. Thereafter, we constructed a lncRNA-mediated ceRNA network by analyzing competing relationships between mRNAs and lncRNAs based on ceRNA hypothesis. A drought responsive ceRNA network with 40 lncRNAs, 23 miRNAs and 103 mRNAs was obtained. Network analysis revealed TCONS_00021861/miR528-3p/YUCCA7 regulatory axis as a hub involved in drought response. The miRNA-target expression and interaction were validated by RT-qPCR and RLM-5'RACE. TCONS_00021861 showed significant positive correlation (r = 0.7102) with YUCCA7 and negative correlation with miR528-3p (r = -0.7483). Overexpression of TCONS_00021861 attenuated the repression of miR528-3p on YUCCA7, leading to increased IAA (Indole-3-acetic acid) content and auxin overproduction phenotypes. CONCLUSIONS TCONS_00021861 could regulate YUCCA7 by sponging miR528-3p, which in turn activates IAA biosynthetic pathway and confer resistance to drought stress. Our findings provide a new perspective of the regulatory roles of lncRNAs as ceRNAs in drought resistance of rice.
Collapse
Affiliation(s)
- Jiajia Chen
- School of Chemistry and Life Science, Suzhou University of Science and Technology, No.1 Kerui Road, 215011, Suzhou, China.
| | - Yuqing Zhong
- School of Chemistry and Life Science, Suzhou University of Science and Technology, No.1 Kerui Road, 215011, Suzhou, China
| | - Xin Qi
- School of Chemistry and Life Science, Suzhou University of Science and Technology, No.1 Kerui Road, 215011, Suzhou, China
| |
Collapse
|
15
|
Wang M, Guo W, Li J, Pan X, Pan L, Zhao J, Zhang Y, Cai S, Huang X, Wang A, Liu Q. The miR528- AO Module Confers Enhanced Salt Tolerance in Rice by Modulating the Ascorbic Acid and Abscisic Acid Metabolism and ROS Scavenging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8634-8648. [PMID: 34339211 DOI: 10.1021/acs.jafc.1c01096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The monocot lineage-specific miR528 was previously established as a multistress regulator. However, it remains largely unclear how miR528 participates in response to salinity stress in rice. Here, we show that miR528 positively regulates rice salt tolerance by down-regulating a gene encoding l-ascorbate oxidase (AO), thereby bolstering up the AO-mediated abscisic acid (ABA) synthesis and ROS scavenging. Overexpression of miR528 caused a substantial increase in ascorbic acid (AsA) and ABA contents but a significant reduction in ROS accumulation, resulting in the enhanced salt tolerance of rice plants. Conversely, knockdown of miR528 or overexpression of AO stimulated the expression of the AO gene, hence lowering the level of AsA, a critical antioxidant that promotes the ABA content but reduces the ROS level, and then compromising rice tolerance to salinity. Together, the findings reveal a novel mechanism of the miR528-AO module-mediated salt tolerance by modulating the processes of AsA and ABA metabolism as well as ROS detoxification, which adds a new regulatory role to the miR528-AO stress defense pathway in rice.
Collapse
Affiliation(s)
- Mei Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Wenping Guo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Jun Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Xiangjian Pan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Lihao Pan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Juan Zhao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Yiwei Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Shitian Cai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Xia Huang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - An Wang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, P. R. China
| |
Collapse
|
16
|
|
17
|
Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. PHYSIOLOGIA PLANTARUM 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
Collapse
Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
18
|
Selvi A, Devi K, Manimekalai R, Prathima PT, Valiyaparambth R, Lakshmi K. High-throughput miRNA deep sequencing in response to drought stress in sugarcane. 3 Biotech 2021; 11:312. [PMID: 34109097 DOI: 10.1007/s13205-021-02857-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-02857-x.
Collapse
Affiliation(s)
- Athiappan Selvi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kaliannan Devi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Ramaswamy Manimekalai
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | | | - Rabisha Valiyaparambth
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kasirajan Lakshmi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| |
Collapse
|
19
|
Nandakumar M, Malathi P, Sundar AR, Rajadurai CP, Philip M, Viswanathan R. Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen. PLANT CELL REPORTS 2021; 40:851-870. [PMID: 33818644 DOI: 10.1007/s00299-021-02682-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
KEY MESSAGE Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.
Collapse
Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - A R Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - C P Rajadurai
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - Manuel Philip
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
| |
Collapse
|
20
|
Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
Collapse
Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
| |
Collapse
|
21
|
Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
Collapse
Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| |
Collapse
|
22
|
Global transcriptome changes of elongating internode of sugarcane in response to mepiquat chloride. BMC Genomics 2021; 22:79. [PMID: 33494722 PMCID: PMC7831198 DOI: 10.1186/s12864-020-07352-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/27/2020] [Indexed: 11/10/2022] Open
Abstract
Background Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results In the present study, we first obtained high-quality long transcripts from the internodes of sugarcane using the PacBio Sequel System. A total of 72,671 isoforms, with N50 at 3073, were generated. These long isoforms were used as a reference for the subsequent RNA-seq. Afterwards, short reads generated from the Illumina HiSeq 4000 platform were used to compare the differentially expressed genes in both the DPC and the control groups. Transcriptome profiling showed that most significant gene changes occurred after six days post DPC treatment. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating that DPC affected multiple pathways, in addition to suppressing gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the 36 constructed modules, the top positive correlated module, at the stage of six days post spraying DPC, was sienna3. Notably, Stf0 sulfotransferase, cyclin-like F-box, and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. Furthermore, the qPCR validated the high accuracy of the RNA-seq results. Conclusion Taken together, we have demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07352-w.
Collapse
|
23
|
Tang X, Jiang J, Huang Z, Wu H, Wang J, He L, Xiong F, Zhong R, Liu J, Han Z, Tang R, He L. Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes. J Basic Microbiol 2021; 61:165-176. [PMID: 33448033 DOI: 10.1002/jobm.202000750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 01/02/2021] [Indexed: 11/11/2022]
Abstract
Sugarcane/peanut intercropping is a highly efficient planting pattern in South China. However, the effects of sugarcane/peanut intercropping on soil quality need to be clarified. This study characterized the soil microbial community and the soil quality in sugarcane/peanut intercropping systems by the Illumina MiSeq platform. The results showed that the intercropping sugarcane (IS) system significantly increased the total N (TN), available N (AN), available P (AP), pH value, and acid phosphatase activity (ACP), but it had little effect on the total P (TP), total K (TK), available K (AK), organic matter (OM), urease activity, protease activity, catalase activity, and sucrase activity, compared with those in monocropping sugarcane (MS) and monocropping peanut (MP) systems. Both intercropping peanut (IP) and IS soils contained more bacteria and fungi than soils in the MP and MS fields, and the microbes identified were mainly Chloroflexi and Acidobacteria, respectively. Intercropping significantly increased the number of unique microbes in IS soils (68 genera), compared with the numbers in the IP (14), MS (17), and MP (16) systems. The redundancy analysis revealed that the abundances of culturable Acidobacteriaceae subgroup 1, nonculturable DA111, and culturable Acidobacteria were positively correlated with the measured soil quality in the intercropping system. Furthermore, the sugarcane/peanut intercropping significantly increased the economic benefit by 87.84% and 36.38%, as compared with that of the MP and MS, respectively. These results suggest that peanut and sugarcane intercropping increases the available N and P content by increasing the abundance of rhizospheric microbes, especially Acidobacteriaceae subgroup 1, DA111, and Acidobacteria.
Collapse
Affiliation(s)
- Xiumei Tang
- Agricultural College of Guangxi University, Nanning, Guangxi, China.,Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Jing Jiang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Zhipeng Huang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Haining Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Jin Wang
- Agricultural Resource and Environment Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Liangqiong He
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ruichun Zhong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Jing Liu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Zhuqiang Han
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Ronghua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Longfei He
- Agricultural College of Guangxi University, Nanning, Guangxi, China
| |
Collapse
|
24
|
Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions. 3 Biotech 2020; 10:440. [PMID: 33014683 PMCID: PMC7501393 DOI: 10.1007/s13205-020-02416-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.
Collapse
|
25
|
Queiroz de Pinho Tavares E, Camara Mattos Martins M, Grandis A, Romim GH, Rusiska Piovezani A, Weissmann Gaiarsa J, Silveira Buckeridge M. Newly identified miRNAs may contribute to aerenchyma formation in sugarcane roots. PLANT DIRECT 2020; 4:e00204. [PMID: 32226917 PMCID: PMC7098396 DOI: 10.1002/pld3.204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/11/2020] [Accepted: 01/24/2020] [Indexed: 05/14/2023]
Abstract
Small RNAs comprise three families of noncoding regulatory RNAs that control gene expression by blocking mRNA translation or leading to mRNA cleavage. Such post-transcriptional negative regulation is relevant for both plant development and environmental adaptations. An important biotechnological application of miRNA identification is the discovery of regulators and effectors of cell wall degradation, which can improve/facilitate hydrolysis of cell wall polymers for second-generation bioethanol production. The recent characterization of plant innate cell wall modifications occurring during root aerenchyma development triggered by ethylene led to the possibility of prospection for mechanisms of cell wall disassembly in sugarcane. By using next-generation sequencing, 39 miRNAs were identified in root segments along the process of aerenchyma development. Among them, 31 miRNAs were unknown to the sugarcane miRBase repository but previously identified as produced by its relative Sorghum bicolor. Key putative targets related to signal transduction, carbohydrate metabolic process, and cell wall organization or biogenesis were among the most representative gene categories targeted by miRNA. They belong to the subclasses of genes associated with the four modules of cell wall modification in sugarcane roots: cell expansion, cell separation, hemicellulose, and cellulose hydrolysis. Thirteen miRNAs possibly related to ethylene perception and signaling were also identified. Our findings suggest that miRNAs may be involved in the regulation of cell wall degradation during aerenchyma formation. This work also points out to potential molecular tools for sugarcane improvement in the context of second-generation biofuels.
Collapse
Affiliation(s)
| | | | - Adriana Grandis
- Departamento de Botânica Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | - Grayce H Romim
- Departamento de Botânica Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Jonas Weissmann Gaiarsa
- Centro de Facilidades Para a Pesquisa Instituto de Ciências Biomédicas Universidade de São Paulo São Paulo Brazil
| | | |
Collapse
|
26
|
Zhao Y, Ma W, Wei X, Long Y, Zhao Y, Su M, Luo Q. Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa ( Medicago sativa L.) under Drought Stress by High-Throughput Sequencing. Genes (Basel) 2019; 11:genes11010030. [PMID: 31888061 PMCID: PMC7016817 DOI: 10.3390/genes11010030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/17/2019] [Accepted: 12/24/2019] [Indexed: 01/01/2023] Open
Abstract
Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.
Collapse
Affiliation(s)
- Yaodong Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
| | - Wenjing Ma
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-138-9331-7951
| | - Yu Long
- College of Business Administration, Kent State University, Kent, OH 44240, USA;
| | - Ying Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
| | - Meifei Su
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
| | - Qiaojuan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.Z.); (W.M.); (Y.Z.); (M.S.); (Q.L.)
- Gansu Key Laboratory of Crop Genetic Improvement and Germplasm Innovation, Lanzhou 730070, China
- Gansu Key Laboratory of Arid Habitat Crop Science, Lanzhou 730070, China
| |
Collapse
|
27
|
da Silva RG, Rosa-Santos TM, França SDC, Kottapalli P, Kottapalli KR, Zingaretti SM. Microtranscriptome analysis of sugarcane cultivars in response to aluminum stress. PLoS One 2019; 14:e0217806. [PMID: 31697688 PMCID: PMC6837492 DOI: 10.1371/journal.pone.0217806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Although several metallic elements are required for plant growth, excessive amounts of aluminum ions (Al3+) can result in the inhibition of root growth, thus triggering water and nutrient deficiencies. Plants under stress undergo gene expression changes in specific genes or post-transcriptional gene regulators, such as miRNAs, that can lead to stress tolerance. In this study, we investigated the miRNAs involved in the response of sugarcane to aluminum stress. Four miRNA libraries were generated using sugarcane roots of one tolerant and one sensitive sugarcane cultivar grown under aluminum stress and used to identify the miRNAs involved in the sugarcane aluminum toxicity response. The contrast in field phenotypes of sugarcane cultivars in the field during aluminum stress was reflected in the micro-transcriptome expression profiles. We identified 394 differentially expressed miRNAs in both cultivars, 104 of which were tolerant cultivar-specific, 116 were sensitive cultivar-specific, and 87 of which were common among cultivars. In addition, 52% of differentially expressed miRNAs were upregulated in the tolerant cultivar while the majority of differentially expressed miRNAs in the sensitive cultivar were downregulated. Real-time quantitative polymerase chain reaction was used to validate the expression levels of differentially expressed miRNAs. We also attempted to identify target genes of miRNAs of interest. Our results show that selected differentially expressed miRNAs of aluminum-stressed sugarcane cultivars play roles in signaling, root development, and lateral root formation. These genes thus may be important for aluminum tolerance in sugarcane and could be used in breeding programs to develop tolerant cultivars.
Collapse
Affiliation(s)
- Renan Gonçalves da Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Thiago Mateus Rosa-Santos
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Pratibha Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Kameswara Rao Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Sonia Marli Zingaretti
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- * E-mail:
| |
Collapse
|
28
|
Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. BMC Genomics 2019; 20:610. [PMID: 31345162 PMCID: PMC6657096 DOI: 10.1186/s12864-019-5947-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
Background Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. Results RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). Conclusions These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5947-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matt Hunt
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA.,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sagnik Banerjee
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Priyanka Surana
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Meiling Liu
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Greg Fuerst
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA
| | - Sandra Mathioni
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA
| | - Dan Nettleton
- Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.,Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA. .,Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA. .,Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA. .,Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA.
| |
Collapse
|
29
|
Zeng W, Sun Z, Lai Z, Yang S, Chen H, Yang X, Tao J, Tang X. Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing. Int J Mol Sci 2019; 20:E2966. [PMID: 31216642 PMCID: PMC6628378 DOI: 10.3390/ijms20122966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/05/2023] Open
Abstract
Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean's defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on-as well as their negatively regulated differentially expressed target genes-may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.
Collapse
Affiliation(s)
- Weiying Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zudong Sun
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zhenguang Lai
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Shouzhen Yang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Huaizhu Chen
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Jiangrong Tao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Xiangmin Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| |
Collapse
|
30
|
Li P, Tian Z, Zhang Q, Zhang Y, Wang M, Fang X, Shi W, Cai X. MicroRNAome Profile of Euphorbia kansui in Response to Methyl Jasmonate. Int J Mol Sci 2019; 20:ijms20061267. [PMID: 30871196 PMCID: PMC6471261 DOI: 10.3390/ijms20061267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/30/2022] Open
Abstract
miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the relevant regulatory mechanisms of Euphorbia kansui in response to methyl jasmonate (MeJA) through Illumina RNA-Seq. As a result, we identified 875 miRNAs corresponding to 11,277 target mRNAs, among them, 168 known miRNA families representing 6019 target mRNAs sequences were obtained. 452 miRNA-mRNA pairs presented an anti-correlationship (Cor < −0.50 and p-value of correlation ≤ 0.05). The miRNA with a fold change ≥ 2 and a p (p-Value) < 0.05 in pairwise comparison were identified as significant differentially expressed miRNAs (DEMs). The DEMs in MeJA treatment of 0, 24, 36 and 48 h were compared by using Short Time Expression Miner (STEM) cluster and 4 significant gene profiles (p-value ≤ 0.02) were identified. Through the kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) enrichment analysis on all miRNA targets, we identified 33 mRNAs in terpenoid biosynthesis, which were regulated by miRNAs under MeJA treatment, so the miRNA maybe involved in the response of E. kansui plant to exogenous MeJA and the results would provide very useful information on illustrating the regulatory mechanism of E. kansui and also provide an overall view of the miRNAs response to MeJA stress of a non-model plant.
Collapse
Affiliation(s)
- Peng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Zheni Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Qing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Yue Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Meng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Xiaoai Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| | - Wenjing Shi
- Shaanxi Pharmaceutical Holding Group Co., Ltd., Xi'an 710069, China.
| | - Xia Cai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, China.
| |
Collapse
|
31
|
Sun X, Lin L, Sui N. Regulation mechanism of microRNA in plant response to abiotic stress and breeding. Mol Biol Rep 2018; 46:1447-1457. [PMID: 30465132 DOI: 10.1007/s11033-018-4511-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
microRNAs (miRNAs) in plants are a class of small RNAs consisting of approximately 21-24 nucleotides. The mature miRNA binds to the target mRNA through the formation of a miRNA-induced silencing complex (MIRISC), and cleaves or inhibits translation, thereby achieving negative regulation of the target gene. Based on miRNA plays an important role in regulating plant gene expression, studies on the prediction, identification, function and evolution of plant miRNAs have been carried out. In addition, many researches prove that miRNAs are also involved in many kinds of abiotic and biotic stress, under abiotic stress, plants can express some miRNA, and act on stress-related target genes, which can make plants adapt to stress in physiological response. In this review, the synthetic pathway and mechanism of plant miRNA are briefly described, and we discuss the biological functions and regulatory mechanisms of miRNAs responding to abiotic stresses including low temperature, salt, drought stress and breeding to lay the foundation for further exploring the mechanism of action of miRNAs in stress resistance of plant. And analyze its utilization prospects in plant stress resistance research.
Collapse
Affiliation(s)
- Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China
| | - Lin Lin
- Water Research Institute of Shandong Province, Jinan, People's Republic of China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China.
| |
Collapse
|
32
|
Identification of miRNAs Associated with Graft Union Development in Pecan [Carya illinoinensis (Wangenh.) K. Koch]. FORESTS 2018. [DOI: 10.3390/f9080472] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a high-value fruit tree with a long juvenile period. The fruiting process of pecan seedlings can be largely accelerated through grafting. As non-coding small RNAs, plant miRNAs participate in various biological processes through negative regulation of gene expression. To reveal the roles of miRNAs in the graft union development of pecan, four small RNA libraries were constructed from the graft union at days 0, 8, 15, and 30 after grafting. A total of 47 conserved miRNAs belonging to 31 families and 39 novel miRNAs were identified. For identified miRNAs, 584 target genes were bioinformatically predicted, and 266 of them were annotated; 29 miRNAs (including 16 conserved and 13 novel miRNAs) were differentially expressed during the graft process. The expression profiles of 12 miRNA were further validated by quantitative reverse transcription PCR (qRT-PCR). In addition, qRT-PCR revealed that the expression levels of 3 target genes were negatively correlated with their corresponding miRNAs. We found that miRS26 might be involved in callus formation; miR156, miR160, miR164, miR166, and miRS10 might be associated with vascular bundle formation. These results indicate that the miRNA-mediated gene regulations play important roles in the graft union development of pecan.
Collapse
|
33
|
Tian X, Song L, Wang Y, Jin W, Tong F, Wu F. miR394 Acts as a Negative Regulator of Arabidopsis Resistance to B. cinerea Infection by Targeting LCR. FRONTIERS IN PLANT SCIENCE 2018; 9:903. [PMID: 30018624 PMCID: PMC6037856 DOI: 10.3389/fpls.2018.00903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/07/2018] [Indexed: 05/11/2023]
Abstract
Gray mold of tomato is caused by the pathogen Botrytis cinerea. MicroRNAs play a crucial role in the biotic and abiotic stress responses of plants and regulate their targets by gene silencing. miR394 is an ancient and conserved miRNA in plants, and it participates in the regulation of plant development and stress responses. In our previous study, miR394 was found to respond to B. cinerea infection in tomato, but the roles and regulatory mechanisms of miR394 in B. cinerea-infected tomato remain unclear. miR394 was down-regulated in tomato in response to B. cinerea infection, showing an expression pattern opposite to the previous finding that miR394 was up-regulated in tomato cv. Jinpeng 1 infected by B. cinerea. We obtained transgenic Arabidopsis overexpressing miR394, which resulted in low expression levels of its target LEAF CURLING RESPONSIVENESS (LCR). Leaf lesion size and trypan blue staining showed that miR394 overexpression led to increased sensitivity of transgenic Arabidopsis to B. cinerea compared to wild type. We also detected changes in the expression levels of stress-related miRNAs, including miR159, miR156, miR168, and miR172. In the transgenic plants, it indicated potential cross talk between these miRNAs and miR394, except for miR159. miR394 also enhanced the expression of ARGONAUTE 1 (AGO1), DSRNA-BINDING PROTEIN 4 (DRB4) and the RNA-binding protein gene DAWDLE (DDL), which are involved in the pathways of miRNA biosynthesis and regulation, suggesting that miR394 overexpression has a feedback effect on these genes. Our data indicate that overexpression of miR394 in Arabidopsis increased the susceptibility of plants to B. cinerea by affecting the expression of its target gene LCR along with a number of key genes involved in plant miRNA metabolism (AGO1). Thus, miR394 is a negative regulator of Arabidopsis resistance to B. cinerea infection by targeting LCR.
Collapse
Affiliation(s)
| | | | | | - Weibo Jin
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fudan Tong
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| | - Fangli Wu
- *Correspondence: Weibo Jin, Fudan Tong, Fangli Wu,
| |
Collapse
|
34
|
|
35
|
Li M, Liang Z, He S, Zeng Y, Jing Y, Fang W, Wu K, Wang G, Ning X, Wang L, Li S, Tan H, Tan F. Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.). BMC Genomics 2017; 18:754. [PMID: 28946845 PMCID: PMC5613641 DOI: 10.1186/s12864-017-4053-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Results To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. Conclusions We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Weikuan Fang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Xia Ning
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Hongwei Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| |
Collapse
|
36
|
da Silva MD, de Oliveira Silva RL, Ferreira Neto JRC, Benko-Iseppon AM, Kido EA. Genotype-dependent regulation of drought-responsive genes in tolerant and sensitive sugarcane cultivars. Gene 2017; 633:17-27. [PMID: 28855118 DOI: 10.1016/j.gene.2017.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/28/2017] [Accepted: 08/23/2017] [Indexed: 12/20/2022]
Abstract
Drought is the most damaging among the major abiotic stresses. Transcriptomic studies allow a global overview of expressed genes, providing the basis for molecular markers development. Here, the HT-SuperSAGE technique allowed the evaluation of four drought-tolerant cultivars and four-sensitive cultivars, after 24h of irrigation suppression. We identified 9831 induced unitags from roots of the tolerant cultivars with different regulations by the -sensitive cultivars after the applied stress. These unitags allowed a proposal of 15 genes, whose expressed profiles were validated by RT-qPCR, evaluating each cultivar independently. These genes covered broad metabolic processes: ethylene stress attenuation (ACCD); root growth (β-EXP8); protein degradation [ubiquitination pathway (E2, 20SPβ4); plant proteases (AP, C13)]; oxidative detoxification (TRX); fatty acid synthesis (ACC); amino acid transport (AAT), and carbohydrate metabolism [glycolysis (PFK, TPI, FBA); TCA cycle (LDP, MDH); pentose phosphate pathway (TKT)]. The expressed profiles showed a genotype-dependent regulation of the target genes. Two drought-tolerant cultivars (SP83-2847; CTC6) presented each one, nine of the induced genes. Among the -sensitive cultivars, CTC13 induced only one, while SP90-1636 induced two genes. These genes should help breeders to identify accessions managing drought stress tolerance responses, showing better ethylene stress attenuation, energy allocation, amino acid transport, and protein homeostasis.
Collapse
Affiliation(s)
- Manassés Daniel da Silva
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil
| | | | | | - Ana Maria Benko-Iseppon
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil
| | - Ederson Akio Kido
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil.
| |
Collapse
|
37
|
Wu J, Wang L, Wang S. MicroRNAs associated with drought response in the pulse crop common bean (Phaseolus vulgaris L.). Gene 2017; 628:78-86. [PMID: 28711666 DOI: 10.1016/j.gene.2017.07.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/20/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively. Among these miRNAs, four miRNAs shared the same pattern of expression between Long 22-0579 and Naihua. Target genes of these miRNAs included transcription factors, protein kinases, and nuclear transcription factors. Finally, we verified all of the differentially expressed miRNAs by RT-qPCR, and we identified 16 miRNAs that are potentially associated with the drought stress response. These miRNAs and target genes will be useful in future basic studies and in applied studies investigating how miRNA regulation can be used to enhance drought resistance in plant species.
Collapse
Affiliation(s)
- Jing Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China
| | - Shumin Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, MOA, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, CAAS, Beijing 100081, China.
| |
Collapse
|
38
|
Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/06/2017] [Indexed: 05/20/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
Collapse
Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| |
Collapse
|
39
|
Swapna M, Kumar S. MicroRNAs and Their Regulatory Role in Sugarcane. FRONTIERS IN PLANT SCIENCE 2017; 8:997. [PMID: 28659947 PMCID: PMC5468422 DOI: 10.3389/fpls.2017.00997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/26/2017] [Indexed: 05/31/2023]
Abstract
Sugarcane, one of the most photosynthetically efficient crops, is an important source of sugar and feedstock for green energy and co-generation. The high level of polyploidy and genomic peculiarities in this crop point towards a complex mechanism of regulation for the economically important traits like sugar content, cane yield related traits, resistance to biotic and abiotic stresses etc. The regulatory pathways for these traits comprise of a number of genes, transcription factors and different categories of RNAs like small interference RNAs (siRNAs), and Micro RNAs (miRNAs). MicroRNAs (miRNAs) are found to play an important regulatory role in many crops. As in other crops, several miRNAs have been identified in sugarcane too and these are speculated to have a role in regulating the various metabolic processes. Role of miRNAs in relation to drought tolerance has been studied to a great extent in this crop. miRNAs have been predicted to be linked to expression of other traits like disease resistance, salinity tolerance, waterlogging and axillary bud growth in sugarcane. miRNAs can have a significant role in biomass production in sugarcane, as reported in several biofuel crops. Till now, miRNAs linked to sugar accumulation have not been identified in sugarcane, but studies suggest an important role for miRNAs in sugar metabolic pathway in crops like Sorghum and switch grass. It is presumed that in sugarcane too, sugar accumulation as well as the other important metabolic pathways might be regulated to some extent by the miRNAs. The review examines the progress made in understanding the miRNA regulation in sugarcane and the extent to which miRNA mediated regulation can be utilized in sugarcane improvement.
Collapse
|
40
|
Li Y, Wan L, Bi S, Wan X, Li Z, Cao J, Tong Z, Xu H, He F, Li X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8040119. [PMID: 28406444 PMCID: PMC5406866 DOI: 10.3390/genes8040119] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.
Collapse
Affiliation(s)
- Yue Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liqiang Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shuyi Bi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiufu Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zhenyi Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jing Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hongyu Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
41
|
Pagliarani C, Vitali M, Ferrero M, Vitulo N, Incarbone M, Lovisolo C, Valle G, Schubert A. The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine. PLANT PHYSIOLOGY 2017; 173:2180-2195. [PMID: 28235889 PMCID: PMC5373040 DOI: 10.1104/pp.16.01119] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 02/21/2017] [Indexed: 05/19/2023]
Abstract
Grapevine (Vitis vinifera) is routinely grafted, and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on microRNA (miRNA) abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera × Vitis berlandieri), compared with a commercial cultivar, Cabernet Sauvignon, using their autografts and reciprocal grafts. RNA extracted from roots and leaves of droughted and irrigated plants of different graft combinations was used to prepare cDNA libraries for small RNA sequencing and to analyze miRNAs by quantitative real-time polymerase chain reaction (RT-qPCR). Measurements of leaf water potential, leaf gas exchange, and root hydraulic conductance attested that, under irrigation, M4 reduced water loss in comparison with cultivar Cabernet Sauvignon mostly through nonhydraulic, root-specific mechanisms. Under drought, stomatal conductance decreased at similar levels in the two genotypes. Small RNA sequencing allowed the identification of 70 conserved miRNAs and the prediction of 28 novel miRNAs. Different accumulation trends of miRNAs, observed upon drought and in different genotypes and organs, were confirmed by RT-qPCR Corresponding target transcripts, predicted in silico and validated by RT-qPCR, often showed opposite expression profiles than the related miRNAs. Drought effects on miRNA abundance differed between the two genotypes. Furthermore, the concentration of drought-responsive miRNAs in each genotype was affected by reciprocal grafting, suggesting either the movement of signals inducing miRNA expression in the graft partner or, possibly, miRNA transport between scion and rootstock. These results open new perspectives in the selection of rootstocks for improving grapevine adaptation to drought.
Collapse
Affiliation(s)
- Chiara Pagliarani
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Marco Vitali
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Manuela Ferrero
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Nicola Vitulo
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Marco Incarbone
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Claudio Lovisolo
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Giorgio Valle
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| | - Andrea Schubert
- Department of Agricultural, Forest, and Food Sciences, University of Turin, I-10095 Grugliasco, Italy (C.P., M.V., M.F., M.I., C.L., A.S.); and
- Department of Biology, University of Padua, I-35121 Padua, Italy (N.V., G.V.)
| |
Collapse
|
42
|
Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
Collapse
Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
| |
Collapse
|
43
|
Ordóñez-Baquera PL, González-Rodríguez E, Aguado-Santacruz GA, Rascón-Cruz Q, Conesa A, Moreno-Brito V, Echavarria R, Dominguez-Viveros J. Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis. Comput Biol Chem 2017; 66:26-35. [DOI: 10.1016/j.compbiolchem.2016.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/04/2016] [Accepted: 11/04/2016] [Indexed: 11/26/2022]
|
44
|
Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077/full 10.3389/fpls.2017.01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
Collapse
Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
- *Correspondence: Marcelo Menossi
| |
Collapse
|
45
|
Liu SC, Xu YX, Ma JQ, Wang WW, Chen W, Huang DJ, Fang J, Li XJ, Chen L. Small RNA and degradome profiling reveals important roles for microRNAs and their targets in tea plant response to drought stress. PHYSIOLOGIA PLANTARUM 2016; 158:435-451. [PMID: 27282332 DOI: 10.1111/ppl.12477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/25/2016] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
Tea (Camellia sinensis) is a popular beverage worldwide. Drought stress (DS) is a major constraint on the growth, yield and quality of tea plants. MicroRNAs (miRNAs) play important roles in plant responses to DS. We constructed eight small RNA libraries from the drought-tolerant 'Ningzhou 2' (NZ2) and drought-susceptible 'Zhuyeqi' (ZYQ) cultivars during four stages [control (CK), the fourth day of DS, the eighth day of DS and after recovery (RC)]. A total of 268 conserved and 62 novel miRNAs were identified using small RNA sequencing. In total, 139 (52.9%) and 96 (36.0%) conserved miRNAs were differentially expressed during the four stages (P ≤ 0.05) in NZ2 and ZYQ, respectively. A total of 814 predicted target genes were identified as differentially regulated by 199 miRNAs through degradome sequencing. Among them, 201 and 218 genes were specific to the NZ2 and ZYQ cultivars, respectively, and 395 were common to both cultivars. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological roles of these targets and showed that some of the targets responded to DS in a stress- and cultivar-dependent manner. Correlated expression patterns between miRNA and their targets showed that specific miRNAs target the miRNA effector Argonaute 1 (AGO1), drought signaling-related receptors and enzymes, transcription factors, and other structural and functional proteins. The predicted regulatory networks provide insights into a potential miRNA-mediated regulatory mechanism. These results will contribute to the breeding of drought-tolerant tea plants and to elucidating miRNA regulation in response to drought.
Collapse
Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
- Tea Research Institute, Guizhou Academy of Agricultrural Sciences, Guiyang, 550006, China
| | - Yan-Xia Xu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei-Wei Wang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Dan-Juan Huang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jie Fang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xiao-Jie Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| |
Collapse
|
46
|
Zhao Z, Xue Y, Yang H, Li H, Sun G, Zhao X, Ding D, Tang J. Genome-Wide Identification of miRNAs and Their Targets Involved in the Developing Internodes under Maize Ears by Responding to Hormone Signaling. PLoS One 2016; 11:e0164026. [PMID: 27695059 PMCID: PMC5047619 DOI: 10.1371/journal.pone.0164026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 09/19/2016] [Indexed: 12/04/2022] Open
Abstract
Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, 'Xun928' and 'Xun9058', which had significantly different internode lengths. A total of 45 and 54 miRNAs showed significant changes for each pairwise comparison among the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928', respectively. The expression of 31 miRNAs showed significant changes were common to the corresponding comparison groups of the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928'. For the corresponding internodes of 'Xun9058' and 'Xun928', compared with the expression of miRNAs in the 7th, 8th and 9th internodes of 'Xun928', the numbers of up-regulated and down-regulated miRNAs were 11 and 36 in the 7th internode, 9 and 45 in the 8th internode, and 9 and 25 in the 9th internode of 'Xun9058', respectively. Moreover, 10 miRNA families containing 45 members showed significant changes at least in two internodes of 'Xun928' by comparing with the corresponding internodes of 'Xun9058'. Based on the sequencing data, 20 miRNAs related to hormone signaling among the candidates, belonging to five conserved miRNA families, were selected for expression profiling using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The five miRNA families, zma-miR160, zma-miR167, zma-miR164, zma-miR169 and zma-miR393, targeted the genes encoding auxin response factor, N-acetylcysteine domain containing protein, nuclear transcription factor Y and auxin signaling F-BOX 2 through degradome sequencing. The miRNAs might regulate their targets to respond to hormone signaling, thereby regulating the internode elongation and development under maize ear. These results provide valuable reference for understanding the possible regulation mechanism of the ILs under the ear.
Collapse
Affiliation(s)
- Zhan Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yadong Xue
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Huili Yang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Huimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Gaoyang Sun
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiaofeng Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, Hubei, China
| |
Collapse
|
47
|
Kaur A, Gupta OP, Meena NL, Grewal A, Sharma P. Comparative Temporal Expression Analysis of MicroRNAs and Their Target Genes in Contrasting Wheat Genotypes During Osmotic Stress. Appl Biochem Biotechnol 2016; 181:613-626. [DOI: 10.1007/s12010-016-2236-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/02/2016] [Indexed: 01/29/2023]
|
48
|
To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages. Sci Rep 2016; 6:23212. [PMID: 26983497 PMCID: PMC4794708 DOI: 10.1038/srep23212] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 03/02/2016] [Indexed: 12/14/2022] Open
Abstract
The architecture of the cotton plant, including fruit branch formation and flowering pattern, is the most important characteristic that directly influences light exploitation, yield and cost of planting. Nulliplex branch is a useful phenotype to study cotton architecture. We used RNA sequencing to obtain mRNA and miRNA profiles from nulliplex- and normal-branch cotton at three developmental stages. The differentially expressed genes (DEGs) and miRNAs were identified that preferentially/specifically expressed in the pre-squaring stage, which is a key stage controlling the transition from vegetative to reproductive growth. The DEGs identified were primarily enriched in RNA, protein, and signalling categories in Gossypium barbadense and Gossypium hirsutum. Interestingly, during the pre-squaring stage, the DEGs were predominantly enriched in transcription factors in both G. barbadense and G. hirsutum, and these transcription factors were mainly involved in branching and flowering. Related miRNAs were also identified. The results showed that fruit branching in cotton is controlled by molecular pathways similar to those in Arabidopsis and that multiple regulated pathways may affect the development of floral buds. Our study showed that the development of fruit branches is closely related to flowering induction and provides insight into the molecular mechanisms of branch and flower development in cotton.
Collapse
|
49
|
Hamza NB, Sharma N, Tripathi A, Sanan-Mishra N. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expr Patterns 2016; 20:88-98. [PMID: 26772909 DOI: 10.1016/j.gep.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
Abstract
The regulatory role of small non-coding RNAs that are 20-24 nucleotides in length has become the foremost area of research for biologists. A major class of small RNAs represented by the microRNAs (miRNAs), has been implicated in various aspects of plant development including leaf pattering, meristem function, root patterning etc. Recent findings support that miRNAs are regulated by drought and other abiotic stresses in various plant species. In this study, were report the expression profiling of 8 known abiotic stress deregulated miRNAs in 11 elite sorghum genotypes, under watered and drought conditions. Significant deregulation was observed with miR396, miR393, miR397-5p, miR166, miR167 and miR168. Among these, the expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes. The expression of sbi-miR396 was maximum in the grain sorghum HSD3226 under well-watered conditions and the profile shifted towards HSD3221 under drought stress. Forage accessions, N98 and Atlas, showed an opposite behavior in expression patterns of miR397-5p in drought physiologies. Such dynamic expression patterns could be indicative of prevailing drought tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRNAs which may have potential use in improving drought tolerance in sorghum and other cereal crops.
Collapse
Affiliation(s)
- Nada Babiker Hamza
- Department of Molecular Biology, Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box: 2404, Khartoum, Sudan.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India.
| |
Collapse
|
50
|
Yang Y, Zhang X, Chen Y, Guo J, Ling H, Gao S, Su Y, Que Y, Xu L. Selection of Reference Genes for Normalization of MicroRNA Expression by RT-qPCR in Sugarcane Buds under Cold Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:86. [PMID: 26904058 PMCID: PMC4742636 DOI: 10.3389/fpls.2016.00086] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/17/2016] [Indexed: 05/15/2023]
Abstract
Sugarcane, accounting for 80% of world's sugar, originates in the tropics but is cultivated mainly in the subtropics. Therefore, chilling injury frequently occurs and results in serious losses. Recent studies in various plant species have established microRNAs as key elements in the post-transcriptional regulation of response to biotic and abiotic stresses including cold stress. Though, its accuracy is largely influenced by the use of reference gene for normalization, quantitative PCR is undoubtedly a popular method used for identification of microRNAs. For identifying the most suitable reference genes for normalizing miRNAs expression in sugarcane under cold stress, 13 candidates among 17 were investigated using four algorithms: geNorm, NormFinder, deltaCt, and Bestkeeper, and four candidates were excluded because of unsatisfactory efficiency and specificity. Verification was carried out using cold-related genes miR319 and miR393 in cold-tolerant and sensitive cultivars. The results suggested that miR171/18S rRNA and miR171/miR5059 were the best reference gene sets for normalization for miRNA RT-qPCR, followed by the single miR171 and 18S rRNA. These results can aid research on miRNA responses during sugarcane stress, and the development of sugarcane tolerant to cold stress. This study is the first report concerning the reference gene selection of miRNA RT-qPCR in sugarcane.
Collapse
|