1
|
Li H, Gui Y, Zhu K, Wei J, Zhang R, Yang R, Tang L, Zhou H, Liu X. Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1243664. [PMID: 37885666 PMCID: PMC10598656 DOI: 10.3389/fpls.2023.1243664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
Collapse
Affiliation(s)
- Haibi Li
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Yiyun Gui
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai Zhu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jinju Wei
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ronghua Zhang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongzhong Yang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liqiu Tang
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Hui Zhou
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xihui Liu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| |
Collapse
|
2
|
Kumar R, Sagar V, Verma VC, Kumari M, Gujjar RS, Goswami SK, Kumar Jha S, Pandey H, Dubey AK, Srivastava S, Singh SP, Mall AK, Pathak AD, Singh H, Jha PK, Prasad PVV. Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1225234. [PMID: 37645467 PMCID: PMC10461627 DOI: 10.3389/fpls.2023.1225234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.
Collapse
Affiliation(s)
- Rajeev Kumar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Vidya Sagar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, India
| | | | - Mala Kumari
- Integral Institute of Agriculture Science and Technology, Integral University, Lucknow, India
| | - Ranjit Singh Gujjar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sanjay K. Goswami
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sudhir Kumar Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research, Kanpur, India
| | - Himanshu Pandey
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Abhishek Kumar Dubey
- Indian Council of Agricultural Research (ICAR)-Research Complex for Eastern Region, Patna, India
| | - Sangeeta Srivastava
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - S. P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashutosh K. Mall
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashwini Dutt Pathak
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Hemlata Singh
- Department of Botany, Plant Physiology & Biochemistry, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, India
| | - Prakash Kumar Jha
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| |
Collapse
|
3
|
Manimekalai R, Selvi A, Narayanan J, Vannish R, Shalini R, Gayathri S, Rabisha VP. Comparative physiological and transcriptome analysis in cultivated and wild sugarcane species in response to hydrogen peroxide-induced oxidative stress. BMC Genomics 2023; 24:155. [PMID: 36973642 PMCID: PMC10045617 DOI: 10.1186/s12864-023-09218-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Sugarcane is an important energy crop grown worldwide,supplementing various renewable energy sources. Cultivated and wild sugarcane species respond differently to biotic and abiotic stresses. Generally, wild species are tolerant to various abiotic stresses. In the present study, the physiological and molecular responses of cultivated and wild sugarcane species to oxidative stress at the transcriptional levels were compared. Transcriptional responses were determined using RNAseq. The representative RNA-seq transcript values were validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and confirmed through physiological responses. RESULTS Oxidative stress causes leaf-rolling and -tip drying in cultivated sugarcane, but the wild species are tolerant. Higher chlorophyll fluorescence was observed in the wild species than that in the cultivated varieties under stress. Wild species can maintain a higher chlorophyll stability index than the cultivated species, which was confirmed by the lower transcripts of the chlorophyllase gene in the wild species than that in the cultivated variety. Transcription factor genes (NAC, MYB, and WRKY) were markedly expressed in response to oxidative stress, revealing their involvement in stress tolerance. The analysis revealed synchronized expression of acetyl-transferase, histone2A, cellulose synthase, and secondary cell wall biosynthetic genes in the wild species. The validation of selected genes and 15 NAC transcription factors using RT-qPCR revealed that their expression profiles were strongly correlated with RNA-seq. To the best of our knowledge, this is the first report on the oxidative stress response in cultivated and wild sugarcane species. CONCLUSION Physiological and biochemical changes in response to oxidative stress markedly differ between cultivated and wild sugarcane species. The differentially expressed stress-responsive genes are grouped intothe response to oxidative stress, heme-binding, peroxidase activity, and metal ion binding categories. Chlorophyll maintenance is a stress tolerance response enhanced by the differential regulation of the chlorophyllase gene.There is a considerable difference in the chlorophyll stability index between wild and cultivated varieties. We observed a substantial regulation of secondary wall biosynthesis genes in the wild species compared with that in the cultivated variety, suggesting differences in stress tolerance mechanisms.
Collapse
Affiliation(s)
- R Manimekalai
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India.
| | - A Selvi
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - Jini Narayanan
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - Ram Vannish
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - R Shalini
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - S Gayathri
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| | - V P Rabisha
- Crop Improvement Division, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, 641 007, India
| |
Collapse
|
4
|
Wu KC, Huang CM, Verma KK, Deng ZN, Huang HR, Pang T, Cao HQ, Luo HB, Jiang SL, Xu L. Transcriptomic responses of Saccharum spontaneum roots in response to polyethylene glycol - 6000 stimulated drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:992755. [PMID: 36352884 PMCID: PMC9638123 DOI: 10.3389/fpls.2022.992755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Drought is the abiotic factor that adversely affects plant growth, development survival, and crop productivity, posing a substantial threat to sustainable agriculture worldwide, especially in warm and dry areas. However, the extent of damage depends upon the crop growth stage, severity and frequency of the stress. In general, the reproductive growth phase is more sensitive to stresses causing a substantial loss in crop productivity. Saccharum spontaneum (L.) is the most variable wild relative of sugarcane with potential for use in sugarcane crop improvement programs. In the present study addresses the transcriptomic analysis of drought stress imposed by polyethylene glycol-6000 (PED-6000; w/v- 25%) on the root tip tissues of S. spontaneum GX83-10. The analysis of microarrays of drought-stressed roots was performed at 0 (CK), 2 (T2), 4 (T4), 8 (T8) and 24 h (T24). The analyzed data were compared with the gene function annotations of four major databases, such as Nr, KOG/COG, Swiss-Prot, and KEGG, and a total of 62,988 single-gene information was obtained. The differently expressed genes of 56237 (T4), 59319 (T8), and 58583 (T24), among which CK obtained the most significant number of expressed genes (35920) as compared to T24, with a total of 53683 trend genes. Gene ontology (GO) and KEGG analysis were performed on the 6 important trends, and a total of 598 significant GO IDs and 42 significantly enriched metabolic pathways. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with enhanced stress resistance efficiency for sustainable agriculture.
Collapse
Affiliation(s)
- Kai-Chao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Cheng-Mei Huang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Krishan K. Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Zhi-Nian Deng
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Hai-Rong Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Tian Pang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Hui-Qing Cao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Hai-Bin Luo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| | - Sheng-Li Jiang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | - Lin Xu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Area, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, China
| |
Collapse
|
5
|
Cardoso-Silva CB, Aono AH, Mancini MC, Sforça DA, da Silva CC, Pinto LR, Adams KL, de Souza AP. Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:923069. [PMID: 35845637 PMCID: PMC9280035 DOI: 10.3389/fpls.2022.923069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.
Collapse
Affiliation(s)
- Cláudio Benício Cardoso-Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre Hild Aono
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Melina Cristina Mancini
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Agronomy Department, Federal University of Viçosa (UFV), Viçosa, Brazil
| | - Luciana Rossini Pinto
- Sugarcane Research Advanced Centre, Agronomic Institute of Campinas (IAC/APTA), Ribeirão Preto, Brazil
| | - Keith L. Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Anete Pereira de Souza
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
6
|
Vignesh P, Mahadevaiah C, Parimalan R, Valarmathi R, Dharshini S, Nisha S, Suresha GS, Swathi S, Mahadeva Swamy HK, Sreenivasa V, Mohanraj K, Hemaprabha G, Bakshi R, Appunu C. Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet. Sci Rep 2021; 11:24514. [PMID: 34972826 PMCID: PMC8720094 DOI: 10.1038/s41598-021-03735-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/08/2021] [Indexed: 11/09/2022] Open
Abstract
Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.
Collapse
Affiliation(s)
- P Vignesh
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Mahadevaiah
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
| | - R Parimalan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Dharshini
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Singh Nisha
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - G S Suresha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - S Swathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | - V Sreenivasa
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - K Mohanraj
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - G Hemaprabha
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Ram Bakshi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India.
| |
Collapse
|
7
|
Rehman SU, Muhammad K, Novaes E, Que Y, Din A, Islam M, Porto ACM, Inamullah M, Sajid M, Ullah N, Iqsa S. Expression analysis of transcription factors in sugarcane during cold stress. BRAZ J BIOL 2021; 83:e242603. [PMID: 34932612 DOI: 10.1590/1519-6984.242603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.
Collapse
Affiliation(s)
- S U Rehman
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - K Muhammad
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - E Novaes
- Universidade Federal de Lavras, Natural Scincey Institute, Department of Biology, Lavras, MG, Brasil
| | - Y Que
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - A Din
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - M Islam
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - A C M Porto
- Universidade Federal de Lavras, Natural Scincey Institute, Department of Biology, Lavras, MG, Brasil
| | - M Inamullah
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - M Sajid
- Department of Agriculture, Hazara University, Mansehra, 21300- Khyber Pakhtunkhwa-Pakistan
| | - N Ullah
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - S Iqsa
- Hazara University, Department of Biotechnology and Genetic Engineering, Mansehra, Khyber Pakhtunkhwa, Pakistan
| |
Collapse
|
8
|
Shabbir R, Javed T, Afzal I, Sabagh AE, Ali A, Vicente O, Chen P. Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses. AGRONOMY 2021; 11:1042. [DOI: 10.3390/agronomy11061042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.
Collapse
|
9
|
Li C, Wang Z, Nong Q, Lin L, Xie J, Mo Z, Huang X, Song X, Malviya MK, Solanki MK, Li Y. Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions. Sci Rep 2021; 11:5525. [PMID: 33750876 PMCID: PMC7943799 DOI: 10.1038/s41598-021-85072-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
As the polyploidy progenitor of modern sugarcane, Saccharum spontaneum is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported on the mechanism of drought tolerance in S. spontaneum. Herein, the physiological changes of S. spontaneum GXS87-16 at three water-deficit levels (mild, moderate, and severe) and after re-watering during the elongation stage were investigated. RNA sequencing was utilized for global transcriptome profiling of GXS87-16 under severe drought and re-watered conditions. There were significant alterations in the physiological parameters of GXS87-16 in response to drought stress and then recovered differently after re-watering. A total of 1569 differentially expressed genes (DEGs) associated with water stress and re-watering were identified. Notably, the majority of the DEGs were induced by stress. GO functional annotations and KEGG pathway analysis assigned the DEGs to 47 GO categories and 93 pathway categories. The pathway categories were involved in various processes, such as RNA transport, mRNA surveillance, plant hormone signal transduction, and plant-pathogen interaction. The reliability of the RNA-seq results was confirmed by qRT-PCR. This study shed light on the regulatory processes of drought tolerance in S. spontaneum and identifies useful genes for genetic improvement of drought tolerance in sugarcane.
Collapse
Affiliation(s)
- Changning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhen Wang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, 537000, China
| | - Qian Nong
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Li Lin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Jinlan Xie
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Zhanghong Mo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xing Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Xiupeng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China
| | - Manoj Kumar Solanki
- Department of Food Quality and Safety, The Volcani Center, Institute for Post-Harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, 530007, China.
| |
Collapse
|
10
|
Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
11
|
Carrillo-Bermejo EA, Gamboa-Tuz SD, Pereira-Santana A, Keb-Llanes MA, Castaño E, Figueroa-Yañez LJ, Rodriguez-Zapata LC. The SoNAP gene from sugarcane (Saccharum officinarum) encodes a senescence-associated NAC transcription factor involved in response to osmotic and salt stress. JOURNAL OF PLANT RESEARCH 2020; 133:897-909. [DOI: https:/doi.org/10.1007/s10265-020-01230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/08/2020] [Indexed: 03/08/2024]
|
12
|
Carrillo-Bermejo EA, Gamboa-Tuz SD, Pereira-Santana A, Keb-Llanes MA, Castaño E, Figueroa-Yañez LJ, Rodriguez-Zapata LC. The SoNAP gene from sugarcane (Saccharum officinarum) encodes a senescence-associated NAC transcription factor involved in response to osmotic and salt stress. JOURNAL OF PLANT RESEARCH 2020; 133:897-909. [PMID: 33094397 DOI: 10.1007/s10265-020-01230-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Climate change has caused serious problems related to the productivity of agricultural crops directly affecting human well-being. Plants have evolved to produce molecular mechanisms in response to environmental stresses, such as transcription factors (TFs), to cope with abiotic stress. The NAC proteins constitute a plant-specific family of TFs involved in plant development processes and tolerance to biotic and abiotic stress. Sugarcane is a perennial grass that accumulates a large amount of sucrose and is a crucial agro-industry crop in tropical regions. Our previous transcriptome analyses on sugarcane that were exposed to drought conditions revealed significant increases in the expression of several NAC TFs through all of the time-point stress conditions. In this work, we characterize all previously detected sugarcane NAC genes, utilizing phylogenetics and expression analyses. Furthermore, we characterized a sugarcane NAC gene orthologous to the senescence-associated genes AtNAP and OsNAP via transient expression in tobacco calluses, from Arabidopsis and rice respectively, thus we named it the SoNAP gene. Transient localization assays on onion epidermal cells confirmed the nuclear localization of the SoNAP. Expression analysis showed that the SoNAP gene was induced by high salinity, drought, and abscisic acid treatments. The overexpression of the SoNAP gene in tobacco calluses caused a senescence associated phenotype. Overall, our results indicated that the SoNAP gene from sugarcane is transcriptionally induced under abiotic stress conditions and conserved the predicted senescence-associated functions when it was overexpressed in a heterologous plant model. This work provides key insights about the senescence mechanisms related to abiotic stress and it provides a benchmark for future work on the improvement of this economically important crop.
Collapse
Affiliation(s)
| | - Samuel David Gamboa-Tuz
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico
| | - Alejandro Pereira-Santana
- Industrial Biotechnology Unit, Centro de Investigacion y Asistencia en Tecnologia y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
- Direccion de Catedras, Consejo Nacional de Ciencia y Tecnologia, Ciudad de Mexico, Mexico
| | - Miguel A Keb-Llanes
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico
| | - Enrique Castaño
- Plant Biochemistry and Molecular Biology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatán, Mexico
| | - Luis Joel Figueroa-Yañez
- Industrial Biotechnology Unit, Centro de Investigacion y Asistencia en Tecnologia y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico.
| | - Luis C Rodriguez-Zapata
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico.
| |
Collapse
|
13
|
Selvi A, Devi K, Manimekalai R, Prathima PT. Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought. 3 Biotech 2020; 10:236. [PMID: 32399386 PMCID: PMC7203378 DOI: 10.1007/s13205-020-02226-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.
Collapse
Affiliation(s)
- A. Selvi
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - K. Devi
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - R. Manimekalai
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - P. T. Prathima
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| |
Collapse
|
14
|
Reyes-Hernández SJ, Zamora-Briseño JA, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Alterations in the sap-associated microbiota of Carica papaya in response to drought stress. Symbiosis 2020. [DOI: 10.1007/s13199-020-00682-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Malviya MK, Li CN, Solanki MK, Singh RK, Htun R, Singh P, Verma KK, Yang LT, Li YR. Comparative analysis of sugarcane root transcriptome in response to the plant growth-promoting Burkholderia anthina MYSP113. PLoS One 2020; 15:e0231206. [PMID: 32267863 PMCID: PMC7141665 DOI: 10.1371/journal.pone.0231206] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/18/2020] [Indexed: 12/23/2022] Open
Abstract
The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. The present study based on a detailed analysis of sugarcane root transcriptome by using the HiSeq-Illumina platform in response to the strain MYSP113. The bacterium was initially isolated from the rhizosphere of sugarcane. To better understand biological, cellular, and molecular mechanisms, a de novo transcriptomic assembly of sugarcane root was performed. HiSeq-Illumina platformwas employed for the sequencing of an overall of 16 libraries at a 2×100 bp configuration. Differentially expressed genes (DEGs) analysis identified altered gene expression in 370 genes (total of 199 up-regulated genes and 171 down-regulated genes). Deciphering the huge datasets, concerning the functioning and production of biological systems, a high throughput genome sequencing analysis was attempted with Gene ontology functional analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The report revealed a total of 148930 unigenes. 70414 (47.28%) of them were annotated successfully to Gene Ontology (GO) terms. 774 at 45 days, 4985 of 30 days and 15 days of 6846 terms were significantly regulated. GO analysis revealed that many genes involved in the metabolic, oxidation-reduction process and biological regulatory processes in response to strain MYSP113 and significantly enriched as compare to the control. Moreover, KEGG enriched results show that differentially expressed genes were classified into different pathway categories involved in various processes, such as nitrogen metabolism, plant hormone signal transduction, etc. The sample correlation analyses could help examine the similarity at the gene expression level. The reliability of the observed differential gene expression patterns was validated with quantitative real-time PCR (qRT-PCR). Additionally, plant enzymes activities such as peroxidase and superoxide dismutase were significantly increased in plant roots after the inoculation of strain MYSP113. The results of the research may help in understanding the plant growth-promoting rhizobacteria and plant interaction.
Collapse
Affiliation(s)
- Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Chang-Ning Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Manoj Kumar Solanki
- Department of Food Quality & Safety, Institute for Post-Harvest and Food Sciences, The Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Reemon Htun
- Department of Biotechnology, Mandalay Technological University, Mandalay, Myanmar
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, Guangxi, China
| | - Li-Tao Yang
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- College of Agriculture, Guangxi University, Nanning, Guangxi, China
- * E-mail:
| |
Collapse
|
16
|
Ali A, Khan M, Sharif R, Mujtaba M, Gao SJ. Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E344. [PMID: 31547331 PMCID: PMC6784093 DOI: 10.3390/plants8090344] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022]
Abstract
Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world's sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.
Collapse
Affiliation(s)
- Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Muhammad Mujtaba
- Institute of Biotechnology, Ankara University, Ankara 06110, Turkey
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| |
Collapse
|
17
|
Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
Collapse
Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
| |
Collapse
|