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Ishikawa C, Date Y, Umeda M, Tarumoto Y, Okubo M, Morimitsu Y, Tamura Y, Nishiba Y, Ono H. A Data-Driven Approach to Sugarcane Breeding Programs with Agronomic Characteristics and Amino Acid Constituent Profiling. Metabolites 2024; 14:243. [PMID: 38668371 PMCID: PMC11052186 DOI: 10.3390/metabo14040243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Sugarcane (Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane yield. However, other constituents in sugarcane remain largely unutilized in sugarcane breeding programs. This study aims to establish a data-driven approach to analyze agronomic characteristics from breeding programs. This approach also determines a correlation between agronomic characteristics and free amino acid composition to make breeding programs more efficient. Sugarcane was sampled in clones in the later stage of breeding selection and cultivars from experimental fields on Tanegashima Island. Principal component analysis and hierarchical cluster analysis using agronomic characteristics revealed the diversity and variability of each sample, and the data-driven approach classified cultivars and clones into three groups based on yield type. A comparison of free amino acid constituents between these groups revealed significant differences in amino acids such as asparagine and glutamine. This approach dealing with a large volume of data on agronomic characteristics will be useful for assessing the characteristics of potential clones under selection and accelerating breeding programs.
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Affiliation(s)
- Chiaki Ishikawa
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yasuhiro Date
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan; (Y.D.); (H.O.)
| | - Makoto Umeda
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Yusuke Tarumoto
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Megumi Okubo
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Yasujiro Morimitsu
- Institute for Human Life Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan;
| | - Yasuaki Tamura
- Western Region Agricultural Research Center (Kinki, Chugoku and Shikoku Regions), National Agriculture and Food Research Organization, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan;
| | - Yoichi Nishiba
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 2421 Suya, Koshi, Kumamoto 861-1192, Japan;
| | - Hiroshi Ono
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan; (Y.D.); (H.O.)
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Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. PLANT METHODS 2023; 19:112. [PMID: 37865785 PMCID: PMC10589961 DOI: 10.1186/s13007-023-01091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript libraries. However, the value of including libraries of differing sizes has not been established. METHODS A comprehensive transcriptome of the leaves of Jojoba (Simmondsia chinensis) was generated from two different PacBio library preparations: standard workflow (SW) and long workflow (LW). RESULTS The importance of using both transcript groups in the analysis was demonstrated by the high proportion of unique sequences (74.6%) that were not shared between the groups. A total of 37.8% longer transcripts were only detected in the long dataset. The completeness of the combined transcriptome was indicated by the presence of 98.7% of genes predicted in the jojoba male reference genome. The high coverage of the transcriptome was further confirmed by BUSCO analysis showing the presence of 96.9% of the genes from the core viridiplantae_odb10 lineage. The high-quality isoforms post Cd-Hit merged dataset of the two workflows had a total of 167,866 isoforms. Most of the transcript isoforms were protein-coding sequences (71.7%) containing open reading frames (ORFs) ≥ 100 amino acids (aa). Alternative splicing and intron retention were the basis of most transcript diversity when analysed at the whole genome level and by specific analysis of the apetala2 gene families. CONCLUSION This suggests the need to specifically target the capture of longer transcripts to provide more comprehensive genome coverage in plant transcriptome analysis and reveal the high level of alternative splicing.
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Affiliation(s)
- Othman Al-Dossary
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Ardashir KharabianMasouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Ibrahim Al-Mssallem
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
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Niazi R, Parveen G, Noman M, Mukhtar N, Hadayat N, Sami A, Khaliq B, Shrestha J, Ullah I. Comparative expression analysis of sucrose phosphate synthase gene family in a low and high sucrose Pakistani sugarcane cultivars. PeerJ 2023; 11:e15832. [PMID: 37719124 PMCID: PMC10503496 DOI: 10.7717/peerj.15832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/11/2023] [Indexed: 09/19/2023] Open
Abstract
Sugarcane is the world's largest cultivated crop by biomass and is the main source of sugar and biofuel. Sucrose phosphate synthase (SPS) enzymes are directly involved in the synthesis of sucrose. Here, we analyzed and compared one of the important gene families involved in sucrose metabolism in a high and low sucrose sugarcane cultivar. A comprehensive in silico analysis of the SoSPS family displayed their phylogenetic relationship, gene and protein structure, miRNA targets, protein interaction network (PPI), gene ontology and collinearity. This was followed by a spatial expression analysis in two different sugarcane varieties. The phylogenetic reconstruction distributed AtSPS, ZmSPS, OsSPS, SoSPS and SbSPS into three main groups (A, B, C). The regulatory region of SoSPS genes carries ABRE, ARE, G-box, and MYC as the most dominant cis-regulatory elements. The PPI analysis predicted a total of 14 unique proteins interacting with SPS. The predominant expression of SPS in chloroplast clearly indicates that they are the most active in the organelle which is the hub of photosynthesis. Similarly, gene ontology attributed SPS to sucrose phosphate synthase and glucosyl transferase molecular functions, as well as sucrose biosynthetic and disaccharide biological processes. Overall, the expression of SPS in CPF252 (high sucrose variety) was higher in leaf and culm as compared to that of CPF 251 (low sucrose variety). In brief, this study adds to the present literature about sugarcane, sucrose metabolism and role of SPS in sucrose metabolism thereby opening up further avenues of research in crop improvement.
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Affiliation(s)
- Robi Niazi
- Department of Botany, Women University Swabi, Swabi, Khyber Pakhtun Khwa, Pakistan
| | - Gulnaz Parveen
- Department of Botany, Women University Swabi, Swabi, Khyber Pakhtun Khwa, Pakistan
| | - Muhammad Noman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center Islamabad Pakistan, Islamabad, Capital, Pakistan
| | - Naila Mukhtar
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Naila Hadayat
- Department of Botany, Division of Science & Technology, University of Education, Lahor
| | - Amtul Sami
- Health Biotechnology, Women University Swabi, Swabi, Khyber Pakhtun Khwan, Pakistan
| | - Binish Khaliq
- Department of Botany, University of Okara, Okara, Punjab, Pakistan
| | - Jiban Shrestha
- Nepal Agricultural Research Council, National Plant Breeding and Genetics Research Centre, Khumaltar, Lalitpur, Nepal
| | - Irfan Ullah
- Department of Zoology, Karakaram International University, Ghizer, Gilgit, Pakistan
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de Souza TA, Rodrigues GCS, de Souza PHN, Abreu LS, Pereira LCO, da Silva MS, Tavares JF, Scotti L, Scotti MT. Mass Spectrometry-Based Investigation of Sugarcane Exposed to Five Different Pesticides. Life (Basel) 2023; 13:life13041034. [PMID: 37109563 PMCID: PMC10145413 DOI: 10.3390/life13041034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/01/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The use of agrochemicals has become a standard practice worldwide to ensure the productivity and quality of sugarcane crops. This study aimed to analyze the metabolic changes in sugarcane culms treated with five different nematicides. The experimental design was randomized in blocks, and agro-industrial and biometric variables were evaluated. The samples were extracted and then analyzed using LC-MS, LC-MS/MS, and LC-HRMS. The data obtained were submitted to statistical methods (PCA and PLS). Fragmentation patterns, retention time, and UV absorptions of the main features were analyzed. The plantations treated with carbosulfan (T4) obtained higher agricultural productivity and total recoverable sugar (TRS), while the use of benfuracarb (T3) was associated with lower growth and lower TRS. Statistical analysis revealed the contribution of the features at m/z 353 and m/z 515, assigned as chlorogenic acids, which discriminated the groups. The MS profile also supported the occurrence of flavonoids (C-glycosides and O-glycosides) in the samples.
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Affiliation(s)
- Thalisson A de Souza
- Multi-User Laboratory for Characterization and Analysis, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Gabriela C S Rodrigues
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Pedro H N de Souza
- Miriri Alimentos e Bioenergia S/A, Fazenda Miriri, Zona Rural, Santa Rita 58300-970, PB, Brazil
| | - Lucas S Abreu
- Department of Organic Chemistry, Fluminense Federal University, Niteroi 24220-900, RJ, Brazil
| | - Laiane C O Pereira
- Multi-User Laboratory for Characterization and Analysis, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Marcelo S da Silva
- Multi-User Laboratory for Characterization and Analysis, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Josean F Tavares
- Multi-User Laboratory for Characterization and Analysis, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Luciana Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Marcus Tullius Scotti
- Laboratory of Cheminformatics, Program of Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
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Fallah N, Pang Z, Dong F, Zhou Y, Lin W, Fabrice KMA, Hu C, Yuan Z. Niche differentiation modulates metabolites abundance and composition in silicon fertilizer amended soil during sugarcane growth. BMC PLANT BIOLOGY 2022; 22:497. [PMID: 36280810 PMCID: PMC9590199 DOI: 10.1186/s12870-022-03880-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/10/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND As one of the vital crops globally, sugarcane (Saccharum officinarum L.) has been one of model crops for conducting metabolome research. Although many studies have focused on understanding bioactive components in specific sugarcane tissues, crucial questions have been left unanswered about the response of metabolites to niche differentiation such as different sugarcane tissues (leaf, stem and root), and soil regions (rhizosphere and bulk) under silicon (Si) amended soils. Here, nontargeted metabolite profiling method was leveraged to assess the similarities and differences in the abundance and community composition of metabolites in the different sugarcane and soil compartments. Identify the compartment-specific expression patterns of metabolites, and their association with cane agronomic traits and edaphic factors. We also investigated the response of sugarcane agronomic traits and edaphic factors to Si amended soil. RESULTS We found that Si fertilizer exhibited the advantages of overwhelmingly promoting the height and theoretical production of cane, and profoundly increased soil Si content by 24.8 and 27.0%, while soil available potassium (AK) was enhanced by 3.07 and 2.67 folds in the bulk and rhizosphere soils, respectively. It was also noticed that available phosphorus (AP) in the rhizosphere soil tremendously increased by 105.5%. We detected 339 metabolites in 30 samples using LC-MS/MS analyses, 161 of which were classified and annotated, including organooxygen compounds (19.9%), carboxylic acids and derivatives (15.5%), fatty acyls (15.5%), flavonoids (4.4%), phenols (4.4%), and benzene and substituted derivatives (3.7%). In addition, the total percentages covered by these core metabolites in each compartment ranged from 94.0% (bulk soil) to 93.4% (rhizosphere soil), followed by 87.4% (leaf), 81.0% (root) and 80.5% (stem), suggesting that these bioactive compounds may have migrated from the belowground tissues and gradually filtered in various aboveground niches of the plant. We also observed that the variations and enrichment of metabolites abundance and community were compartment-specific. Furthermore, some key bioactive compounds were markedly associated with plant growth parameters and soil edaphic. CONCLUSION Taken together, we hypothesized that Si utilization can exhibit the advantage of enhancing edaphic factors and cane agronomic traits, and variations in metabolites community are tissue-specific.
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Affiliation(s)
- Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Dong
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongmei Zhou
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kabore Manegdebwaoga Arthur Fabrice
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning, 530000, China.
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Perlo V, Furtado A, Botha FC, Margarido GRA, Hodgson‐Kratky K, Choudhary H, Gladden J, Simmons B, Henry RJ. Transcriptome and metabolome integration in sugarcane through culm development. Food Energy Secur 2022. [DOI: 10.1002/fes3.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo São Paulo Brazil
| | - Katrina Hodgson‐Kratky
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
| | - Hemant Choudhary
- Joint BioEnergy Institute Emeryville CA USA
- Sandia National Laboratories Livermore CA USA
| | - John Gladden
- Joint BioEnergy Institute Emeryville CA USA
- Sandia National Laboratories Livermore CA USA
| | | | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation University of Queensland Brisbane Australia
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Perlo V, Margarido GRA, Botha FC, Furtado A, Hodgson-Kratky K, Correr FH, Henry RJ. Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1619-1636. [PMID: 35224663 PMCID: PMC9110458 DOI: 10.1007/s00122-022-04058-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Sugarcane, with its exceptional carbon dioxide assimilation, biomass and sugar yield, has a high potential for the production of bio-energy, bio-plastics and high-value products in the food and pharmaceutical industries. A crucial challenge for long-term economic viability and environmental sustainability is also to optimize the production of biomass composition and carbon sequestration. Sugarcane varieties such as KQ228 and Q253 are highly utilized in the industry. These varieties are characterized by a high early-season sugar content associated with high yield. In order to investigate these correlations, 1,440 internodes were collected and combined to generate a set of 120 samples in triplicate across 24 sugarcane cultivars at five different development stages. Weighted gene co-expression network analysis (WGCNA) was used and revealed for the first time two sets of co-expressed genes with a distinct and opposite correlation between fibre and sugar content. Gene identification and metabolism pathways analysis was used to define these two sets of genes. Correlation analysis identified a large number of interconnected metabolic pathways linked to sugar content and fibre content. Unsupervised hierarchical clustering of gene expression revealed a stronger level of segregation associated with the genotypes than the stage of development, suggesting a dominant genetic influence on biomass composition and facilitating breeding selection. Characterization of these two groups of co-expressed key genes can help to improve breeding program for high fibre, high sugar species or plant synthetic biology.
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Affiliation(s)
- Virginie Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Gabriel R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo, 13418-900 Brazil
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Katrina Hodgson-Kratky
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Fernando H. Correr
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, São Paulo, 13418-900 Brazil
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
- The University of Queensland, Level 2, Queensland Bioscience Precinct [#80], 306 Carmody Road St Lucia, St Lucia, QLD 4072 Australia
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Margarido GRA, Correr FH, Furtado A, Botha FC, Henry RJ. Limited allele-specific gene expression in highly polyploid sugarcane. Genome Res 2022; 32:297-308. [PMID: 34949669 PMCID: PMC8805727 DOI: 10.1101/gr.275904.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/19/2021] [Indexed: 12/04/2022]
Abstract
Polyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole-genome level in the highly polyploid sugarcane genome. Very high depth whole-genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single-copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.
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Affiliation(s)
- Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
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Yuan Z, Dong F, Pang Z, Fallah N, Zhou Y, Li Z, Hu C. Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:921536. [PMID: 35783968 PMCID: PMC9244704 DOI: 10.3389/fpls.2022.921536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 05/02/2023]
Abstract
Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype-genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3'H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
- *Correspondence: Zhaonian Yuan,
| | - Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongmei Zhou
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
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