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Zhou SL, Zhang JX, Jiang S, Lu Y, Huang YS, Dong XM, Hu Q, Yao W, Zhang MQ, Xiao SH. Genome-wide identification of JAZ gene family in sugarcane and function analysis of ScJAZ1/2 in drought stress response and flowering regulation. Plant Physiol Biochem 2024; 210:108577. [PMID: 38579542 DOI: 10.1016/j.plaphy.2024.108577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
The JASMONATE ZIM DOMAIN (JAZ) proteins are a key inhibitors of the jasmonic acid (JA) signaling pathway that play an important role in the regulation of plant growth and development and environmental stress responses. However, there is no systematic identification and functional analysis of JAZ gene family members in sugarcane. In this study, a total of 49 SsJAZ genes were identified from the wild sugarcane species Saccharum spontaneum genome that were unevenly distributed on 13 chromosomes. Phylogenetic analysis showed that all SsJAZ members can be divided into six groups, and most of the SsJAZ genes contained photoreactive and ABA-responsive elements. RNA-seq analysis revealed that SsJAZ1-1/2/3/4 and SsJAZ7-1 were significantly upregulated under drought stress. The transcript level of ScJAZ1 which is the homologous gene of SsJAZ1 in modern sugarcane cultivars was upregulated by JA, PEG, and abscisic acid (ABA). Moreover, ScJAZ1 can interact with three other JAZ proteins to form heterodimers. The spatial and temporal expression analysis showed that SsJAZ2-1/2/3/4 were highly expressed in different tissues and growth stages and during the day-night rhythm between 10:00 and 18:00. Overexpression of ScJAZ2 in Arabidopsis accelerated flowering through activating the expression of AtSOC1, AtFT, and AtLFY. Moreover, the transcription level of ScJAZ2 was about 30-fold in the early-flowering sugarcane variety than that of the non-flowering variety, indicating ScJAZ2 positively regulated flowering. This first systematic analysis of the JAZ gene family and function analysis of ScJAZ1/2 in sugarcane provide key candidate genes and lay the foundation for sugarcane breeding.
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Affiliation(s)
- Shao-Li Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jin-Xu Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Shuo Jiang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yan Lu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yong-Shuang Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Xian-Man Dong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Mu-Qing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Sheng-Hua Xiao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China; Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530005, China.
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Ding H, Feng X, Yuan Y, Wang B, Wang Y, Zhang J. Genomic investigation of duplication, functional conservation, and divergence in the LRR-RLK Family of Saccharum. BMC Genomics 2024; 25:165. [PMID: 38336615 PMCID: PMC10854099 DOI: 10.1186/s12864-024-10073-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) holds exceptional global significance as a vital crop, serving as a primary source of sucrose, bioenergy, and various by-products. The optimization of sugarcane breeding by fine-tuning essential traits has become crucial for enhancing crop productivity and stress resilience. Leucine-rich repeat receptor-like kinases (LRR-RLK) genes present promising targets for this purpose, as they are involved in various aspects of plant development and defense processes. RESULTS Here, we present a detailed overview of phylogeny and expression of 288 (495 alleles) and 312 (1365 alleles) LRR-RLK genes from two founding Saccharum species, respectively. Phylogenetic analysis categorized these genes into 15 subfamilies, revealing considerable expansion or reduction in certain LRR-type subfamilies. Compared to other plant species, both Saccharum species had more significant LRR-RLK genes. Examination of cis-acting elements demonstrated that SsLRR-RLK and SoLRR-RLK genes exhibited no significant difference in the types of elements included, primarily involved in four physiological processes. This suggests a broad conservation of LRR-RLK gene function during Saccharum evolution. Synteny analysis indicated that all LRR-RLK genes in both Saccharum species underwent gene duplication, primarily through whole-genome duplication (WGD) or segmental duplication. We identified 28 LRR-RLK genes exhibiting novel expression patterns in response to different tissues, gradient development leaves, and circadian rhythm in the two Saccharum species. Additionally, SoLRR-RLK104, SoLRR-RLK7, SoLRR-RLK113, and SsLRR-RLK134 were identified as candidate genes for sugarcane disease defense response regulators through transcriptome data analysis of two disease stresses. This suggests LRR-RLK genes of sugarcane involvement in regulating various biological processes, including leaf development, plant morphology, photosynthesis, maintenance of circadian rhythm stability, and defense against sugarcane diseases. CONCLUSIONS This investigation into gene duplication, functional conservation, and divergence of LRR-RLK genes in two founding Saccharum species lays the groundwork for a comprehensive genomic analysis of the entire LRR-RLK gene family in Saccharum. The results reveal LRR-RLK gene played a critical role in Saccharum adaptation to diverse conditions, offering valuable insights for targeted breeding and precise phenotypic adjustments.
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Affiliation(s)
- Hongyan Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Xiaoxi Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuan Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Baiyu Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Yuhao Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Sugarcane Biology and Genetic Breeding, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
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Bharadwaj B, Dutta S, Qaiyum MA, Samal PP, Dey B, Dey S. Pristine wild sugarcane ( Saccharum spontaneum) as a biosorbent for removal of methylene blue from wastewater: isotherm, kinetics and regeneration studies. Int J Phytoremediation 2023; 26:684-698. [PMID: 37789562 DOI: 10.1080/15226514.2023.2260002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Saccharum spontaneum, popularly known as Kashful (KF) is a seasonal perennial grass with thin culms, mostly an abundantly growing shrub during the autumn season in southern Asia. It is used as no-cost scavenger to convincingly arrest methylene blue, a recalcitrant dye from colored effluent. FTIR, FESEM-EDX, and BET surface area characterize the material well whereas the surface activity was evaluated from zero-point charge (pHZPC = 6.720). FTIR highlights the presence of polyphenolic and carboxylate moieties. The surface texture is rod-like with intermittent non-homogeneous pores with occasional fractures. The equilibrium reaches within 60 min with the maximum adsorption capacity of 20.917 mg/g. The fibrous powder of kashful stalk (KFS) follows pseudo-second-order (R2 = 0.999 for linear and R2 = 0.985 for non-linear) kinetics and both Langmuir and Freundlich isotherm model (for linear, Langmuir R2=0.995; for non-linear, R2 = 0.994 for both Langmuir and Freundlich model). The uptake process was spontaneous (ΔG= -3.077 kJ/mol) and endothermic (ΔH = 17.815 kJ/mol). 1:1 methanol could regenerate the dye-loaded material in up to 55% and onward efficiency was conducive for three consecutive cycles. Industrial effluent analysis suggests a real-time removal of ∼55% in the first cycle. Saccharum spontaneum could be exercised to solve environmental problems related to colored water.
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Affiliation(s)
- Bidisha Bharadwaj
- Environment Protection Laboratory, Department of Chemistry, Central University of Jharkhand, Brambe, India
| | - Subhashri Dutta
- Environment Protection Laboratory, Department of Chemistry, Central University of Jharkhand, Brambe, India
| | - Md Atif Qaiyum
- Environment Protection Laboratory, Department of Chemistry, Central University of Jharkhand, Brambe, India
| | | | - Banashree Dey
- Department of Chemistry, The Graduate School College for Women Jamshedpur, Jamshedpur, India
| | - Soumen Dey
- Environment Protection Laboratory, Department of Chemistry, Central University of Jharkhand, Brambe, India
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Thirugnanasambandam PP, Singode A, Thalambedu LP, Athiappan S, Krishnasamy M, Purakkal SV, Govind H, Furtado A, Henry R. Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum. Front Plant Sci 2023; 14:1199748. [PMID: 37662143 PMCID: PMC10469502 DOI: 10.3389/fpls.2023.1199748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023]
Abstract
Commercial sugarcane hybrids are derivatives from Saccharum officinarum and Saccharum spontaneum hybrids containing the full complement of S. officinarum and a few S. spontaneum chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species S. officinarum (Black Cheribon), and S. spontaneum (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from S. officinarum while several stress and senescence related transcripts were from S. spontaneum in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both S. officinarum and the hybrid had an abundance of novel genes like sugar phosphate translocator, while S. spontaneum had just one. In general, the hybrid shared a larger number of transcripts with S. officinarum than with S. spontaneum, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.
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Affiliation(s)
| | - Avinash Singode
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Millets Research, Hyderabad, Telangana, India
| | | | - Selvi Athiappan
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Mohanraj Krishnasamy
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | | | - Hemaprabha Govind
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, QLD, Australia
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Zhang N, Lin H, Zeng Q, Fu D, Gao X, Wu J, Feng X, Wang Q, Ling Q, Wu Z. Genome-wide identification and expression analysis of the cyclic nucleotide-gated ion channel (CNGC) gene family in Saccharum spontaneum. BMC Genomics 2023; 24:281. [PMID: 37231370 DOI: 10.1186/s12864-023-09307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Cyclic nucleotide-gated ion channels (CNGCs) are nonselective cation channels that are ubiquitous in eukaryotic organisms. As Ca2+ channels, some CNGCs have also proven to be K+-permeable and involved in plant development and responses to environmental stimuli. Sugarcane is an important sugar and energy crop worldwide. However, reports on CNGC genes in sugarcane are limited. RESULTS In this study, 16 CNGC genes and their alleles were identified from Saccharum spontaneum and classified into 5 groups based on phylogenetic analysis. Investigation of gene duplication and syntenic relationships between S. spontaneum and both rice and Arabidopsis demonstrated that the CNGC gene family in S. spontaneum expanded primarily by segmental duplication events. Many SsCNGCs showed variable expression during growth and development as well as in tissues, suggesting functional divergence. Light-responsive cis-acting elements were discovered in the promoters of all the identified SsCNGCs, and the expression of most of the SsCNGCs showed a diurnal rhythm. In sugarcane, the expression of some SsCNGCs was regulated by low-K+ treatment. Notably, SsCNGC13 may be involved in both sugarcane development and its response to environmental stimuli, including response to low-K+ stress. CONCLUSION This study identified the CNGC genes in S. spontaneum and provided insights into the transcriptional regulation of these SsCNGCs during development, circadian rhythm and under low-K+ stress. These findings lay a theoretical foundation for future investigations of the CNGC gene family in sugarcane.
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Affiliation(s)
- Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Huanzhang Lin
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
- Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Danwen Fu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Xiaomin Feng
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Qinnan Wang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Qiuping Ling
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
| | - Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
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Liu Y, Jiang Y, Liu X, Cheng H, Han Y, Zhang D, Wu J, Liu L, Yan M, Que Y, Zhou D. Identification and Expression Analysis of Hexokinases Family in Saccharum spontaneum L. under Drought and Cold Stresses. Plants (Basel) 2023; 12:1215. [PMID: 36986904 PMCID: PMC10056587 DOI: 10.3390/plants12061215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/28/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
In plants, the multi-gene family of dual-function hexokinases (HXKs) plays an important role in sugar metabolism and sensing, that affects growth and stress adaptation. Sugarcane is an important sucrose crop and biofuel crop. However, little is known about the HXK gene family in sugarcane. A comprehensive survey of sugarcane HXKs, including physicochemical properties, chromosomal distribution, conserved motifs, and gene structure was conducted, identifying 20 members of the SsHXK gene family that were located on seven of the 32 Saccharum spontaneum L. chromosomes. Phylogenetic analysis showed that the SsHXK family could be divided into three subfamilies (group I, II and III). Motifs and gene structure were related to the classification of SsHXKs. Most SsHXKs contained 8-11 introns which was consistent with other monocots. Duplication event analysis indicated that HXKs in S. spontaneum L. primarily originated from segmental duplication. We also identified putative cis-elements in the SsHXK promoter regions which were involved in phytohormone, light and abiotic stress responses (drought, cold et al.). During normal growth and development, 17 SsHXKs were constitutively expressed in all ten tissues. Among them, SsHXK2, SsHXK12 and SsHXK14 had similar expression patterns and were more highly expressed than other genes at all times. The RNA-seq analysis showed that 14/20 SsHXKs had the highest expression level after cold stress for 6 h, especially SsHXK15, SsHXK16 and SsHXK18. As for drought treatment, 7/20 SsHXKs had the highest expression level after drought stress for 10 days, 3/20 (SsHKX1, SsHKX10 and SsHKX11) had the highest expression level after 10 days of recovery. Overall, our results revealed the potential biological function of SsHXKs, which may provide information for in-depth functional verification.
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Affiliation(s)
- Ying Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yaolan Jiang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiaolan Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Hefen Cheng
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Yuekun Han
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Dawei Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Jinfeng Wu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Lili Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410000, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, China
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Luo T, Li CN, Yan R, Huang K, Li YR, Liu XY, Lakshmanan P. Physiological and molecular insights into the resilience of biological nitrogen fixation to applied nitrogen in Saccharum spontaneum, wild progenitor of sugarcane. Front Plant Sci 2023; 13:1099701. [PMID: 36714748 PMCID: PMC9881415 DOI: 10.3389/fpls.2022.1099701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Excessive use of nitrogen (N) fertilizer for sugarcane cultivation is a significant cause of greenhouse gas emission. N use-efficiency (NUE) of sugarcane is relatively low, and considerable effort is now directed to exploit biological nitrogen fixation (BNF) in sugarcane. We hypothesize that genetic base-broadening of sugarcane using high-BNF Saccharum spontaneum, a wild progenitor of sugarcane, will help develop N-efficient varieties. We found remarkable genetic variation for BNF and growth in S. spontaneum accessions, and BNF in some accessions remained highly resilient to inorganic N application. Physiological and molecular analyses of two S. spontaneum accessions with high-BNF capacity and growth, namely G152 and G3, grown under N replete and low N conditions showed considerable similarity for total N, NH4-N, soluble sugar, indoleacetic acid, gibberellic acid, zeatin and abscisic acid content; yet, they were strikingly different at molecular level. Global gene expression analysis of G152 and G3 grown under contrasting N supply showed genotype effect explaining much of the gene expression variation observed. Differential gene expression analysis found an over-representation of carbohydrate and amino acid metabolism and transmembrane transport genes in G152 and an enrichment of lipid metabolism and single-organism processes genes in G3, suggesting that distinctly divergent metabolic strategies are driving N-related processes in these accessions. This was attested by the remarkable variation in carbon, N, amino acid and hormone metabolism-related gene expression in G152 and G3 under high- and low-N supply. We conclude that both accessions may be achieving similar BNF and growth phenotypes through overlapping but distinctly different biochemical and molecular mechanisms.
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Affiliation(s)
- Ting Luo
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Chang-Ning Li
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rui Yan
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kejun Huang
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yang-Rui Li
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiao-Yan Liu
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Prakash Lakshmanan
- Sugarcane Research Institute; Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Academy of Agricultural Sciences, Nanning, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
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Meng Z, Wang F, Xie Q, Li R, Shen H, Li H. Reconstruction of karyotypic evolution in Saccharum spontaneum species by comparative oligo-FISH mapping. BMC Plant Biol 2022; 22:599. [PMID: 36539690 PMCID: PMC9764494 DOI: 10.1186/s12870-022-04008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. RESULTS In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012-46 (x = 9, hexaploid) and AP85-441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. CONCLUSIONS Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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Zhang BQ, Huang YX, Zhou ZF, Zhou S, Duan WX, Yang CF, Gao YJ, Zhang GM, Song XP, Zhang XQ, Li AM, Huang DL, Li YR. Cold-Induced Physiological and Biochemical Alternations and Proteomic Insight into the Response of Saccharum spontaneum to Low Temperature. Int J Mol Sci 2022; 23. [PMID: 36430736 DOI: 10.3390/ijms232214244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane.
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Li Y, Wang Y, Feng X, Hua X, Dou M, Yao W, Zhang M, Zhang J. Expression Profiling and MicroRNA Regulatory Networks of Homeobox Family Genes in Sugarcane Saccharum spontaneum L. Int J Mol Sci 2022; 23:8724. [PMID: 35955858 DOI: 10.3390/ijms23158724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 01/13/2023] Open
Abstract
Homeobox (HB) genes play important roles in plant growth and development processes, particularly in the formation of lateral organs. Thus, they could influence leaf morphogenesis and biomass formation in plants. However, little is known about HBs in sugarcane, a crucial sugar crop, due to its complex genetic background. Here, 302 allelic sequences for 104 HBs were identified and divided into 13 subfamilies in sugarcane Saccharum spontaneum. Comparative genomics revealed that whole-genome duplication (WGD)/segmental duplication significantly promoted the expansion of the HB family in S. spontaneum, with SsHB26, SsHB63, SsHB64, SsHB65, SsHB67, SsHB95, and SsHB96 being retained from the evolutionary event before the divergence of dicots and monocots. Based on the analysis of transcriptome and degradome data, we speculated that SsHB15 and SsHB97 might play important roles in regulating sugarcane leaf morphogenesis, with miR166 and SsAGO10 being involved in the regulation of SsHB15 expression. Moreover, subcellular localization and transcriptional activity detection assays demonstrated that these two genes, SsHB15 and SsHB97, were functional transcription factors. This study demonstrated the evolutionary relationship and potential functions of SsHB genes and will enable the further investigation of the functional characterization and the regulatory mechanisms of SsHBs.
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Hua X, Shen Q, Li Y, Zhou D, Zhang Z, Akbar S, Wang Z, Zhang J. Functional characterization and analysis of transcriptional regulation of sugar transporter SWEET13c in sugarcane Saccharum spontaneum. BMC Plant Biol 2022; 22:363. [PMID: 35869432 PMCID: PMC9308298 DOI: 10.1186/s12870-022-03749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sugarcane is an important crop for sugar production worldwide. The Sugars Will Eventually be Exported Transporters (SWEETs) are a group of sugar transporters recently identified in sugarcane. In Saccharum spontaneum, SsSWEET13c played a role in the sucrose transportation from the source to the sink tissues, which was found to be mainly active in the mature leaf. However, the function and regulation of SWEETs in sugarcane remain elusive despite extensive studies performed on sugar metabolism. RESULTS In this study, we showed that SsSWEET13c is a member of SWEET gene family in S. spontaneum, constituting highest circadian rhythm-dependent expression. It is a functional gene that facilitates plant root elongation and increase fresh weight of Arabidopsis thaliana, when overexpressed. Furthermore, yeast one-hybrid assays indicate that 20 potential transcription factors (TFs) could bind to the SsSWEET13c promoter in S. spontaneum. We combined transcriptome data from developmental gradient leaf with distinct times during circadian cycles and stems/leaves at different growth stages. We have uncovered that 14 out of 20 TFs exhibited positive/negative gene expression patterns relative to SsSWEET13c. In the source tissues, SsSWEET13c was mainly positively regulated by SsbHLH34, SsTFIIIA-a, SsMYR2, SsRAP2.4 and SsbHLH035, while negatively regulated by SsABS5, SsTFIIIA-b and SsERF4. During the circadian rhythm, it was noticed that SsSWEET13c was more active in the morning than in the afternoon. It was likely due to the high level of sugar accumulation at night, which was negatively regulated by SsbZIP44, and positively regulated by SsbHLH34. Furthermore, in the sink tissues, SsSWEET13c was also active for sugar accumulation, which was positively regulated by SsbZIP44, SsTFIIIA-b, SsbHLH34 and SsTFIIIA-a, and negatively regulated by SsERF4, SsHB36, SsDEL1 and SsABS5. Our results were further supported by one-to-one yeast hybridization assay which verified that 12 potential TFs could bind to the promoter of SsSWEET13c. CONCLUSIONS A module of the regulatory network was proposed for the SsSWEET13c in the developmental gradient of leaf and circadian rhythm in S. spontaneum. These results provide a novel understanding of the function and regulation of SWEET13c during the sugar transport and biomass production in S. spontaneum.
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Affiliation(s)
- Xiuting Hua
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China
| | - Qiaochu Shen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yihan Li
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dong Zhou
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sehrish Akbar
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Jisen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, China.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Aslam M, She Z, Jakada BH, Fakher B, Greaves JG, Yan M, Chen Y, Zheng P, Cheng Y, Qin Y. Interspecific complementation-restoration of phenotype in Arabidopsis cuc2cuc3 mutant by sugarcane CUC2 gene. BMC Plant Biol 2022; 22:47. [PMID: 35065620 PMCID: PMC8783490 DOI: 10.1186/s12870-022-03440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. RESULTS Here, we have identified the CUP-SHAPED COTYLEDON (CUC) genes in sugarcane and named SsCUC2 (for the orthologous gene of CUC1 and CUC2) and SsCUC3. The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of CUC genes showed that most of the CUC3 genes were accompanied by an intron gain during eudicot divergence. Besides, the study of SsCUCs expression in the RNA-seq obtained during different stages of ovule development revealed that SsCUCs express in developing young tissues, and the expression of SsCUC2 is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the cuc2cuc3 mutant phenotype of Arabidopsis (eudicot). CONCLUSIONS This study further supports that CUC2 has diverged in CUC1 and CUC2 during the evolution of monocots and eudicots from ancestral plants. The functional analysis of CUC expression patterns during sugarcane ovule development and ectopic expression of SsCUC2 in Arabidopsis showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane CUC genes. Our results reveal the crucial functional role of CUC genes in sugarcane.
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Affiliation(s)
- Mohammad Aslam
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Zeyuan She
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Bello Hassan Jakada
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Beenish Fakher
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Joseph G Greaves
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Maokai Yan
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Yingzhi Chen
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China
| | - Ping Zheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yan Cheng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China
| | - Yuan Qin
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004, Nanning, Guangxi, China.
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, 350002, Fuzhou, Fujian, China.
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14
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Li Z, Wang G, Liu X, Wang Z, Zhang M, Zhang J. Genome-wide identification and expression profiling of DREB genes in Saccharum spontaneum. BMC Genomics 2021; 22:456. [PMID: 34139993 PMCID: PMC8212459 DOI: 10.1186/s12864-021-07799-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background The dehydration-responsive element-binding proteins (DREBs) are important transcription factors that interact with a DRE/CRT (C-repeat) sequence and involve in response to multiple abiotic stresses in plants. Modern sugarcane are hybrids from the cross between Saccharum spontaneum and Saccharum officinarum, and the high sugar content is considered to the attribution of S. officinaurm, while the stress tolerance is attributed to S. spontaneum. To understand the molecular and evolutionary characterization and gene functions of the DREBs in sugarcane, based on the recent availability of the whole genome information, the present study performed a genome-wide in silico analysis of DREB genes and transcriptome analysis in the polyploidy S. spontaneum. Results Twelve DREB1 genes and six DREB2 genes were identified in S. spontaneum genome and all proteins contained a conserved AP2/ERF domain. Eleven SsDREB1 allele genes were assumed to be originated from tandem duplications, and two of them may be derived after the split of S. spontaneum and the proximal diploid species sorghum, suggesting tandem duplication contributed to the expansion of DREB1-type genes in sugarcane. Phylogenetic analysis revealed that one DREB2 gene was lost during the evolution of sugarcane. Expression profiling showed different SsDREB genes with variable expression levels in the different tissues, indicating seven SsDREB genes were likely involved in the development and photosynthesis of S. spontaneum. Furthermore, SsDREB1F, SsDREB1L, SsDREB2D, and SsDREB2F were up-regulated under drought and cold condition, suggesting that these four genes may be involved in both dehydration and cold response in sugarcane. Conclusions These findings demonstrated the important role of DREBs not only in the stress response, but also in the development and photosynthesis of S. spontaneum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07799-5.
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Affiliation(s)
- Zhen Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Xihui Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, 530004, Guangxi, China.
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15
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Umeda M, Sakaigaichi T, Tanaka M, Tarumoto Y, Adachi K, Hattori T, Hayano M, Takahashi H, Tamura Y, Kimura T, Mori M. Detection of a major QTL related to smut disease resistance inherited from a Japanese wild sugarcane using GRAS-Di technology. Breed Sci 2021; 71:365-374. [PMID: 34776743 PMCID: PMC8573549 DOI: 10.1270/jsbbs.20137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/23/2021] [Indexed: 06/13/2023]
Abstract
Smut disease of sugarcane causes considerable yield losses and the use of resistant varieties is the best control practice. Our group identified a Japanese wild sugarcane with highly smut disease resistance named 'Iriomote8'. In this study, we conducted QTL analysis for smut disease resistance using a mapping population derived from a resistant variety 'Yaenoushie', in which resistance is inherited from 'Iriomote8'. We identified 4813 non-redundant markers using GRAS-Di technology and developed a linkage map of mapping parents. We evaluated smut disease resistance of the mapping population by the inoculation test. Consequently, a large number of clones did not show the disease symptoms and the distribution of smut disease incidence tended to be "L shaped". Composite interval mapping detected an identical QTL for indices of smut disease incidence with a markedly high LOD score (26.6~45.6) at the end of linkage group 8 of 'Yaenoushie'. This QTL explained approximately 50% of the cases of smut disease incidence. In the mapping population, there were no correlations between the indices of smut disease incidence and other agronomic traits. In conclusion, this QTL could be used for marker-assisted selection to significantly improve smut disease resistance without negative effects on other agronomic traits.
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Affiliation(s)
- Makoto Umeda
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Takeo Sakaigaichi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Miyakonojo Research Station, 6651-2 Yokoichi-cho, Miyakonojo, Miyazaki 885-0091, Japan
| | - Minoru Tanaka
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Central Region Agricultural Research Center, Tsukuba Headquarters, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Yusuke Tarumoto
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Katsuki Adachi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- Kubota Corporation, Agri-Solution Department, 1-2-47 Shikitsuhigashi, Naniwa-ku, Osaka 556-8601, Japan
| | - Taiichiro Hattori
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Kyushu Okinawa Agricultural Research Center, Headquarters, 2421 Suya, Koshi, Kumamoto 861-1192, Japan
| | - Michiko Hayano
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
- NARO Institute for Agro-Environmental Science, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan
| | - Hiroyuki Takahashi
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Yasuaki Tamura
- NARO Kyushu Okinawa Agricultural Research Center, Tanegashima Sugarcane Breeding Site, 1742-1 Anno, Nishinoomote, Kagoshima 891-3102, Japan
| | - Tatsuro Kimura
- Toyota Motor Corporation, Agriculture & Biotechnology Business Division, 1 Toyota-cho, Toyota, Aichi 471-8571, Japan
| | - Masaaki Mori
- Toyota Motor Corporation, Environmental Affairs Division, 1-4-18 Koraku, Bunkyo-ku, Tokyo 112-8701, Japan
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Wang Z, Ren H, Xu F, Lu G, Cheng W, Que Y, Xu L. Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection. Plants (Basel) 2021; 10:322. [PMID: 33567504 DOI: 10.3390/plants10020322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/22/2022]
Abstract
Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.
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Aono AH, Pimenta RJG, Garcia ALB, Correr FH, Hosaka GK, Carrasco MM, Cardoso-Silva CB, Mancini MC, Sforça DA, dos Santos LB, Nagai JS, Pinto LR, Landell MGDA, Carneiro MS, Balsalobre TW, Quiles MG, Pereira WA, Margarido GRA, de Souza AP. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. Front Plant Sci 2021; 12:668623. [PMID: 34305969 PMCID: PMC8294386 DOI: 10.3389/fpls.2021.668623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.
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Affiliation(s)
- Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo José Gonzaga Pimenta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Guilherme Kenichi Hosaka
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Marishani Marin Carrasco
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Melina Cristina Mancini
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - James Shiniti Nagai
- Faculty of Medicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Thiago Willian Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Marcos Gonçalves Quiles
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (Unifesp), São José dos Campos, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira de Souza,
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Sun T, Cen G, You C, Lou W, Wang Z, Su W, Wang W, Li D, Que Y, Su Y. ScAOC1, an allene oxide cyclase gene, confers defense response to biotic and abiotic stresses in sugarcane. Plant Cell Rep 2020; 39:1785-1801. [PMID: 33001313 DOI: 10.1007/s00299-020-02606-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE An allene oxide cyclase gene which is involved in defense against biotic and abiotic stresses was cloned and characterized in sugarcane. Allene oxide cyclase (AOC), a key enzyme in jasmonate acid (JA) biosynthesis, affects the stereoisomerism and biological activity of JA molecules, and plays an important role in plant stress resistance. In this study, four SsAOC alleles (SsAOC1-SsAOC4), which shared similar gene structure and were located on Chr1A, Chr1B, Chr1C, and Chr1D, respectively, were mined from sugarcane wild species Saccharum spontaneum, and a homologous gene ScAOC1 (GenBank Accession Number: MK674849) was cloned from sugarcane hybrid variety Yacheng05-179 inoculated with Sporisorium scitamineum for 48 h. ScAOC1 and SsAOC1-SsAOC4 were alkaline, unstable, hydrophilic, and non-secretory proteins, which possess the same set of conserved motifs and were clustered into one group in the phylogenetic analysis. ScAOC1 was expressed in all sugarcane tissues, but with different levels. After infection by S. scitamineum, the transcripts of ScAOC1 were increased significantly both in the smut-susceptible (ROC22) and resistant (Yacheng05-179) varieties, but its transcripts were more accumulated and lasted for a longer period in the smut-resistant variety than in the smut-susceptible one. ScAOC1 was down-regulated under MeJA and NaCl treatments, but up-regulated under SA, ABA, PEG, and cold stresses. Transiently overexpressing ScAOC1 gene into Nicotiana benthamiana leaves regulated the responses of N. benthamiana to two pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. Furthermore, prokaryotic expression analysis showed overexpression of ScAOC1 in Escherichia coli BL21 could enhance its tolerance to NaCl, mannitol, and cold stimuli. These results indicated that ScAOC1 may play an active role in response to biotic and abiotic stresses in sugarcane.
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Affiliation(s)
- Tingting Sun
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guangli Cen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Wenyue Lou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Wenju Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Damei Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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19
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Yang H, Wang T, Yu X, Yang Y, Wang C, Yang Q, Wang X. Enhanced sugar accumulation and regulated plant hormone signalling genes contribute to cold tolerance in hypoploid Saccharum spontaneum. BMC Genomics 2020; 21:507. [PMID: 32698760 PMCID: PMC7376677 DOI: 10.1186/s12864-020-06917-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane varieties. RESULTS A hypoploid clone 12-23 (2n = 54) and hyperploid clone 15-28 (2n = 92) of S. spontaneum were analysed under cold stress from morphological, physiological, and transcriptomic perspectives. Compared with clone 15-28, clone 12-23 plants had lower plant height, leaf length, internode length, stem diameter, and leaf width; depressed stomata and prominent bristles and papillae; and thick leaves with higher bulliform cell groups and thicker adaxial epidermis. Compared with clone 15-28, clone 12-23 showed significantly lower electrical conductivity, significantly higher water content, soluble protein content, and superoxide dismutase activity, and significantly higher soluble sugar content and peroxidase activity. Under cold stress, the number of upregulated genes and downregulated genes of clone 12-23 was higher than clone 15-28, and many stress response genes and pathways were affected and enriched to varying degrees, particularly sugar and starch metabolic pathways and plant hormone signalling pathways. Under cold stress, the activity of 6-phosphate glucose trehalose synthase, trehalose phosphate phosphatase, and brassinosteroid-signalling kinase and the content of trehalose and brassinosteroids of clone 12-23 increased. CONCLUSIONS Compared with hyperploid clone 15-28, hypoploid clone 12-23 maintained a more robust osmotic adjustment system through sugar accumulation and hormonal regulation, which resulted in stronger cold tolerance.
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Affiliation(s)
- Hongli Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Tianju Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.,Chuxiong normal university, Chuxiong, 675000, Yunnan Province, PR China
| | - Xinghua Yu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.,Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan Province, PR China
| | - Yang Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Chunfang Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China
| | - Qinghui Yang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.
| | - Xianhong Wang
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, PR China.
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20
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Hu W, Hua X, Zhang Q, Wang J, Shen Q, Zhang X, Wang K, Yu Q, Lin YR, Ming R, Zhang J. New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics. BMC Plant Biol 2018; 18:270. [PMID: 30404601 PMCID: PMC6222987 DOI: 10.1186/s12870-018-1495-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/22/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The SWEET (Sugars Will Eventually be Exported Transporters) gene family is a recently identified group of sugar transporters that play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction, nectar secretion, and reproductive tissue development. However, little information on Saccharum SWEET is available for this crop with a complex genetic background. RESULTS In this study, 22 SWEET genes were identified from Saccharum spontaneum Bacterial Artificial Chromosome libraries sequences. Phylogenetic analyses of SWEETs from 11 representative plant species showed that gene expansions of the SWEET family were mainly caused by the recent gene duplication in dicot plants, while these gene expansions were attributed to the ancient whole genome duplication (WGD) in monocot plant species. Gene expression profiles were obtained from RNA-seq analysis. SWEET1a and SWEET2s had higher expression levels in the transitional zone and maturing zone than in the other analyzed zones. SWEET1b was mainly expressed in the leaf tissues and the mature zone of the leaf of both S. spontaneum and S. officinarum, and displayed a peak in the morning and was undetectable in both sclerenchyma and parenchyma cells from the mature stalks of S. officinarum. SsSWEET4a\4b had higher expression levels than SWEET4c and were mainly expressed in the stems of seedlings and mature plants. SWEET13s are recently duplicated genes, and the expression of SWEET13s dramatically increased from the maturing to mature zones. SWEET16b's expression was not detected in S. officinarum, but displayed a rhythmic diurnal expression pattern. CONCLUSIONS Our study revealed the gene evolutionary history of SWEETs in Saccharum and SWEET1b was found to be a sucrose starvation-induced gene involved in the sugar transportation in the high photosynthetic zones. SWEET13c was identified as the key player in the efflux of sugar transportation in mature photosynthetic tissues. SWEET4a\4b were found to be mainly involved in sugar transportation in the stalk. SWEET1a\2a\4a\4b\13a\16b were suggested to be the genes contributing to the differences in sugar contents between S. spontaneum and S. officinarum. Our results are valuable for further functional analysis of SWEET genes and utilization of the SWEET genes for genetic improvement of Saccharum for biofuel production.
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Affiliation(s)
- Weichang Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Agronomy Department, University of Florida, Gainesville, FL 32610 USA
| | - Qiaochu Shen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Kai Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, 100 Taiwan
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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21
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Yu F, Wang P, Li X, Huang Y, Wang Q, Luo L, Jing Y, Liu X, Deng Z, Wu J, Yang Y, Chen R, Zhang M, Xu L. Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization. Mol Cytogenet 2018; 11:35. [PMID: 29977338 PMCID: PMC5992832 DOI: 10.1186/s13039-018-0387-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022] Open
Abstract
Background Interspecific hybridization is an effective strategy for germplasm innovation in sugarcane. Nobilization refers to the breeding theory of development and utilization of wild germplasm. Saccharum spontaneum is the main donor of resistance and adaptive genes in the nobilization breeding process. Chromosome transfer in sugarcane is complicated; thus, research of different inheritance patterns can provide guidance for optimal sugarcane breeding. Results Through chromosome counting and genomic in situ hybridization, we found that six clones with 80 chromosomes were typical S. officinarum and four other clones with more than 80 chromosomes were interspecific hybrids between S. officinarum and S. spontaneum. These data support the classical view that S. officinarum is characterized by 2n = 80. In addition, genomic in situ hybridization showed that five F1 clones were products of a 2n + n transmission and one F1 clone was the product of an n + n transmission in clear pedigree noble hybrids between S. officinarum and S. spontaneum. Interestingly, Yacheng 75–408 and Yacheng 75–409 were the sibling lines of the F1 progeny from the same parents but with different genetic transmissions. Conclusions This is the first clear evidence of Loethers, Crystallina, Luohanzhe, Vietnam Niuzhe, and Nanjian Guozhe were typical S. officinarum by GISH. Furthermore, for the first time, we identified the chromosome transmission of six F1 hybrids between S. officinarum and S. spontaneum. These findings may provide a theoretical basis for germplasm innovation in sugarcane breeding and guidance for further sugarcane nobilization. Electronic supplementary material The online version of this article (10.1186/s13039-018-0387-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Wang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueting Li
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongji Huang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Ling Luo
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanfen Jing
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Xinlong Liu
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Zuhu Deng
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China.,4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Jiayun Wu
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yongqing Yang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rukai Chen
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- 4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Liangnian Xu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
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22
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Meng Z, Zhang Z, Yan T, Lin Q, Wang Y, Huang W, Huang Y, Li Z, Yu Q, Wang J, Wang K. Comprehensively Characterizing the Cytological Features of Saccharum spontaneum by the Development of a Complete Set of Chromosome-Specific Oligo Probes. Front Plant Sci 2018; 9:1624. [PMID: 30459801 PMCID: PMC6232525 DOI: 10.3389/fpls.2018.01624] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/18/2018] [Indexed: 05/04/2023]
Abstract
Chromosome-specific identification is a powerful technique in the study of genome structure and evolution. However, there is no reliable cytogenetic marker to unambiguously identify each of the chromosomes in sugarcane (Saccharum spp., Poaceae), which has a complex genome with a high level of ploidy and heterozygosity. In this study, we developed a set of oligonucleotide (oligo)-based probes through bioinformatic design and massive synthetization. These probes produced a clear and bright single signal in each of the chromosomes and their eight homologous chromosomes in the ancient species Saccharum spontaneum (2n = 8x = 64). Thus, they can be used as reliable markers to robustly label each of the chromosomes in S. spontaneum. We then obtained the karyotype data and established a nomenclature based on chromosomal sizes for the eight chromosomes of the octoploid S. spontaneum. In addition, we also found that the 45S and 5S rDNAs demonstrated high copy number variations among different homologous chromosomes, indicating a rapid evolution of the highly repeated sequence after polyploidization. Our fluorescence in situ hybridization (FISH) assay also demonstrated that these probes could be used as cross-species markers between or within the genera of Sorghum and Saccharum. By comparing FISH analyses, we discovered that several chromosome rearrangement events occurred in S. spontaneum, which might have contributed to the basic chromosome number reduction from 10 in sorghum to 8 in sugarcane. Consistent identification of individual chromosomes makes molecular cytogenetic study possible in sugarcane and will facilitate fine chromosomal structure and karyotype evolution of the genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiliang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianying Yan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingfang Lin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiyuan Huang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongji Huang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhanjie Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingyi Yu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Texas A&M AgriLife Research, The Texas A&M University System, Dallas, TX, United States
| | - Jianping Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Kai Wang, ;
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Dong G, Shen J, Zhang Q, Wang J, Yu Q, Ming R, Wang K, Zhang J. Development and Applications of Chromosome-Specific Cytogenetic BAC-FISH Probes in S. spontaneum. Front Plant Sci 2018; 9:218. [PMID: 29535742 PMCID: PMC5834487 DOI: 10.3389/fpls.2018.00218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Saccharum spontaneum is a major Saccharum species that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescence in situ hybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identify S. spontaneum individual chromosomes and study the relationship between S. spontaneum and other related species. We screened low-copy BACs as probes from the sequences of a high coverage of S. spontaneum BAC library based on BLAST search of the sorghum genome. In total, we isolated 49 positive BAC clones, and identified 27 BAC clones that can give specific signals on the S. spontaneum chromosomes. Of the 27 BAC probes, 18 were confirmed to be able to discriminate the eight basic chromosomes of S. spontaneum. Moreover, BAC-24, BAC-66, BAC-78, BAC-69, BAC-71, BAC-73, and BAC-77 probes were used to construct physical maps of chromosome 1 and chromosome 2 of S. spontaneum, which indicated synteny in Sb01 between S. spontaneum and sorghum. Furthermore, we found that BAC-14 and BAC-19 probes, corresponding to the sorghum chromosomes 2 and 8, respectively, localized to different arms of the same S. spontaneum chromosome, suggesting that there was an inter-chromosomal rearrangement event between S. spontaneum and sorghum. Our study provides the first set of chromosome-specific cytogenetic markers in Saccharum and is critical for future advances in cytogenetics and genome sequencing studies in Saccharum.
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Affiliation(s)
- Guangrui Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiao Shen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qing Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Qingyi Yu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Texas A&M AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, United States
| | - Kai Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Jisen Zhang,
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Hansda A, Kumar V, Anshumali. Cu-resistant Kocuria sp. CRB15: a potential PGPR isolated from the dry tailing of Rakha copper mine. 3 Biotech 2017; 7:132. [PMID: 28593515 DOI: 10.1007/s13205-017-0757-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/30/2017] [Indexed: 10/19/2022] Open
Abstract
Rhizobacteria may enhance biomass production and heavy metal tolerance of plants under stress conditions. The present study was carried out for isolation of metal-resistant bacteria that can be further utilized for phytoremediation process. A potential metal-resistant strain CRB15 was isolated from rhizospheric region of Saccharum spontaneum that was found to be resistant against Cu (6.29 mM), Zn (3.25 mM), Pb (1.5 mM), Ni (1.25 mM), and Cd (0.25 mM). SEM analysis was performed for evaluation of morphological changes on bacterial isolate. FTIR analysis observed the change in wavenumbers after the addition of Cu. 16S rDNA sequence analysis showed that CRB15 isolate matched best with genus of Kocuria and was named as Kocuria sp. CRB15. The isolate Kocuria sp. CRB15 was a potential plant growth-promoting rhizobacterium as it had a high IAA (46 µg ml-1), P solubilisation (39.37 µg ml-1), ammonia production (30.46 µmol ml-1), and hydrogen cyanide production capacity. Root-shoot elongation assay conducted on Brassica nigra under lab conditions with strain CRB15 demonstrated positive effects of strain CRB15 in root and shoot elongation of Cu-treated seedlings. This study proved the Kocuria sp. CRB15 a potential PGPR for bacterial-assisted phytoremediation.
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Iqtedar M, Nadeem M, Naeem H, Abdullah R, Naz S, Qurat ul Ain Syed, Kaleem A. Bioconversion potential of Trichoderma viride HN1 cellulase for a lignocellulosic biomass Saccharum spontaneum. Nat Prod Res 2014; 29:1012-9. [PMID: 25346145 DOI: 10.1080/14786419.2014.971320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The industrialisation of lignocellulose conversion is impeded by expensive cellulase enzymes required for saccharification in bioethanol production. Current research undertakes cellulase production from pretreated Saccharum spontaneum through Trichoderma viride HN1 under submerged fermentation conditions. Pretreatment of substrate with 2% NaOH resulted in 88% delignification. Maximum cellulase production (2603 ± 16.39 U/mL/min carboxymethyl cellulase and 1393 ± 25.55 U/mL/min FPase) was achieved at 6% substrate at pH 5.0, with 5% inoculum, incubated at 35°C for 120 h of fermentation period. Addition of surfactant, Tween 80 and metal ion Mn(+2), significantly enhanced cellulase yield. This study accounts proficient cellulase yield through process optimisation by exploiting cheaper substrate to escalate their commercial endeavour.
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Affiliation(s)
- Mehwish Iqtedar
- a Department of Biotechnology , Lahore College for Women University , Lahore , Pakistan
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Sateesh L, Rodhe AV, Naseeruddin S, Yadav KS, Prasad Y, Rao LV. Simultaneous Cellulase Production, Saccharification and Detoxification Using Dilute Acid Hydrolysate of S. spontaneum with Trichoderma reesei NCIM 992 and Aspergillus niger. Indian J Microbiol 2012; 52:258-62. [PMID: 23729891 DOI: 10.1007/s12088-011-0184-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 04/08/2011] [Indexed: 10/18/2022] Open
Abstract
Bioethanol production from lignocellulosic materials has several limitations. One aspect is the high production cost of cellulases used for saccharification of substrate and inhibition of fermenting yeast due to inhibitors released in acid hydrolysis. In the present work we have made an attempt to achieve simultaneous cellulases production, saccharification and detoxification using dilute acid hydrolysate of Saccharum spontaneum with and without addition of nutrients, supplemented with acid hydrolyzed biomass prior to inoculation in one set and after 3 days of inoculation in another set. Organisms used were T. reesei NCIM 992, and Aspergillus niger isolated in our laboratory. Cellulase yield obtained was 0.8 IU/ml on fourth day with T. reesei. Sugars were found to increase from fourth to fifth day, when hydrolysate was supplemented with nutrients and acid hydrolyzed biomass followed by inoculation with T. reesei. Phenolics were also found to decrease by 67%.
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