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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. FRONTIERS IN PLANT SCIENCE 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] [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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Moura Dias H, Vieira AP, de Jesus EM, de Setta N, Barros G, Van Sluys MA. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 2023; 11:e14973. [PMID: 37214086 PMCID: PMC10194071 DOI: 10.7717/peerj.14973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/07/2023] [Indexed: 05/24/2023] Open
Abstract
De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
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Affiliation(s)
| | | | | | - Nathalia de Setta
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
- Universidade Federal do ABC, Sao Bernardo do Campo, Sao Paulo, Brazil
| | - Gesiele Barros
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. Int J Mol Sci 2022; 23:ijms231911603. [PMID: 36232906 PMCID: PMC9569758 DOI: 10.3390/ijms231911603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.
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Dinesh Babu KS, Janakiraman V, Palaniswamy H, Kasirajan L, Gomathi R, Ramkumar TR. A short review on sugarcane: its domestication, molecular manipulations and future perspectives. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2623-2643. [PMID: 36159774 PMCID: PMC9483297 DOI: 10.1007/s10722-022-01430-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/11/2022] [Indexed: 06/16/2023]
Abstract
Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.
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Affiliation(s)
| | - Vardhana Janakiraman
- Department of Biotechnology, Vels Institute of Science, Technology & Advanced studies (VISTAS), Chennai, TN 600117 India
| | - Harunipriya Palaniswamy
- Tissue Culture Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Lakshmi Kasirajan
- Genomics Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Raju Gomathi
- Plant Physiology Laboratory, Division of Crop Production, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Thakku R. Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL 32611 USA
- Department of Biological Sciences, Delaware State University, Dover, DE 19001 USA
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Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system. Mol Genet Genomics 2022; 297:1403-1421. [PMID: 35879567 DOI: 10.1007/s00438-022-01929-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
KEY MESSAGE Nitrate uptake in sugarcane roots is regulated at the transcriptional and posttranscriptional levels based on the physiological status of the plant and is likely a determinant mechanism for discrimination against nitrate. Sugarcane (Saccharum spp.) is one of the most suitable energy crops for biofuel feedstock, but the reduced recovery of nitrogen (N) fertilizer by sugarcane roots increases the crop carbon footprint. The low nitrogen use efficiency (NUE) of sugarcane has been associated with the significantly low nitrate uptake, which limits the utilization of the large amount of nitrate available in agricultural soils. To understand the regulation of nitrate uptake in sugarcane roots, we identified the major canonical nitrate transporter genes (NRTs-NITRATE TRANSPORTERS) and then determined their expression profiles in roots under contrasting N conditions. Correlation of gene expression with 15N-nitrate uptake revealed that under N deprivation or inorganic N (ammonium or nitrate) supply in N-sufficient roots, the regulation of ScNRT2.1 and ScNRT3.1 expression is the predominant mechanism for the modulation of the activity of the nitrate high-affinity transport system. Conversely, in N-deficient roots, the induction of ScNRT2.1 and ScNRT3.1 transcription is not correlated with the marked repression of nitrate uptake in response to nitrate resupply or high N provision, which suggested the existence of a posttranscriptional regulatory mechanism. Our findings suggested that high-affinity nitrate uptake is regulated at the transcriptional and presumably at the posttranscriptional levels based on the physiological N status and that the regulation of NRT2.1 and NRT3.1 activity is likely a determinant mechanism for the discrimination against nitrate uptake observed in sugarcane roots, which contributes to the low NUE in this crop species.
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de Oliveira LP, Navarro BV, de Jesus Pereira JP, Lopes AR, Martins MCM, Riaño-Pachón DM, Buckeridge MS. Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane. Sci Rep 2022; 12:7516. [PMID: 35525890 PMCID: PMC9079074 DOI: 10.1038/s41598-022-11508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.
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Affiliation(s)
- Lauana Pereira de Oliveira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Bruno Viana Navarro
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - João Pedro de Jesus Pereira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | | | - Marina C M Martins
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Centro de Energia Nuclear na Agricultura, Evolutiva e de Sistemas, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
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7
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Venail J, da Silva Santos PH, Manechini JR, Alves LC, Scarpari M, Falcão T, Romanel E, Brito M, Vicentini R, Pinto L, Jackson SD. Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2035-2049. [PMID: 34893811 PMCID: PMC8982381 DOI: 10.1093/jxb/erab539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/09/2021] [Indexed: 05/21/2023]
Abstract
Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.
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Affiliation(s)
- Julien Venail
- School of Life Sciences, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | | | - Joao Ricardo Manechini
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | - Maximiliano Scarpari
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, São Paulo, Brazil
| | - Thais Falcão
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Elisson Romanel
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Michael Brito
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, São Paulo, Brazil
| | - Renato Vicentini
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucia Pinto
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, São Paulo, Brazil
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Ramasamy M, Damaj MB, Vargas-Bautista C, Mora V, Liu J, Padilla CS, Irigoyen S, Saini T, Sahoo N, DaSilva JA, Mandadi KK. A Sugarcane G-Protein-Coupled Receptor, ShGPCR1, Confers Tolerance to Multiple Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:745891. [PMID: 35295863 PMCID: PMC8919185 DOI: 10.3389/fpls.2021.745891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Sugarcane (Saccharum spp.) is a prominent source of sugar and serves as bioenergy/biomass feedstock globally. Multiple biotic and abiotic stresses, including drought, salinity, and cold, adversely affect sugarcane yield. G-protein-coupled receptors (GPCRs) are components of G-protein-mediated signaling affecting plant growth, development, and stress responses. Here, we identified a GPCR-like protein (ShGPCR1) from sugarcane and energy cane (Saccharum spp. hybrids) and characterized its function in conferring tolerance to multiple abiotic stresses. ShGPCR1 protein sequence contained nine predicted transmembrane (TM) domains connected by four extracellular and four intracellular loops, which could interact with various ligands and heterotrimeric G proteins in the cells. ShGPCR1 sequence displayed other signature features of a GPCR, such as a putative guanidine triphosphate (GTP)-binding domain, as well as multiple myristoylation and protein phosphorylation sites, presumably important for its biochemical function. Expression of ShGPCR1 was upregulated by drought, salinity, and cold stresses. Subcellular imaging and calcium (Ca2+) measurements revealed that ShGPCR1 predominantly localized to the plasma membrane and enhanced intracellular Ca2+ levels in response to GTP, respectively. Furthermore, constitutive overexpression of ShGPCR1 in sugarcane conferred tolerance to the three stressors. The stress-tolerance phenotype of the transgenic lines corresponded with activation of multiple drought-, salinity-, and cold-stress marker genes, such as Saccharum spp. LATE EMBRYOGENESIS ABUNDANT, DEHYDRIN, DROUGHT RESPONSIVE 4, GALACTINOL SYNTHASE, ETHYLENE RESPONSIVE FACTOR 3, SALT OVERLY SENSITIVE 1, VACUOLAR Na+/H+ ANTIPORTER 1, NAM/ATAF1/2/CUC2, COLD RESPONSIVE FACTOR 2, and ALCOHOL DEHYDROGENASE 3. We suggest that ShGPCR1 plays a key role in conferring tolerance to multiple abiotic stresses, and the engineered lines may be useful to enhance sugarcane production in marginal environments with fewer resources.
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Affiliation(s)
- Manikandan Ramasamy
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Mona B. Damaj
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | | | - Victoria Mora
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Jiaxing Liu
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Carmen S. Padilla
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Sonia Irigoyen
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Tripti Saini
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Jorge A. DaSilva
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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Shabbir R, Javed T, Afzal I, Sabagh AE, Ali A, Vicente O, Chen P. Modern Biotechnologies: Innovative and Sustainable Approaches for the Improvement of Sugarcane Tolerance to Environmental Stresses. AGRONOMY 2021; 11:1042. [DOI: 10.3390/agronomy11061042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Sugarcane (Saccharum spp.) is one of the most important industrial cash crops, contributing to the world sugar industry and biofuel production. It has been cultivated and improved from prehistoric times through natural selection and conventional breeding and, more recently, using the modern tools of genetic engineering and biotechnology. However, the heterogenicity, complex poly-aneuploid genome and susceptibility of sugarcane to different biotic and abiotic stresses represent impediments that require us to pay greater attention to the improvement of the sugarcane crop. Compared to traditional breeding, recent advances in breeding technologies (molecular marker-assisted breeding, sugarcane transformation, genome-editing and multiple omics technologies) can potentially improve sugarcane, especially against environmental stressors. This article will focus on efficient modern breeding technologies, which provide crucial clues for the engineering of sugarcane cultivars resistant to environmental stresses.
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10
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Fanelli A, Rancour DM, Sullivan M, Karlen SD, Ralph J, Riaño-Pachón DM, Vicentini R, Silva TDF, Ferraz A, Hatfield RD, Romanel E. Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall. FRONTIERS IN PLANT SCIENCE 2021; 12:626168. [PMID: 33995431 PMCID: PMC8117936 DOI: 10.3389/fpls.2021.626168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 05/11/2023]
Abstract
The purification of hydroxycinnamic acids [p-coumaric acid (pCA) and ferulic acid (FA)] from grass cell walls requires high-cost processes. Feedstocks with increased levels of one hydroxycinnamate in preference to the other are therefore highly desirable. We identified and conducted expression analysis for nine BAHD acyltransferase ScAts genes from sugarcane. The high conservation of AT10 proteins, together with their similar gene expression patterns, supported a similar role in distinct grasses. Overexpression of ScAT10 in maize resulted in up to 75% increase in total pCA content. Mild hydrolysis and derivatization followed by reductive cleavage (DFRC) analysis showed that pCA increase was restricted to the hemicellulosic portion of the cell wall. Furthermore, total FA content was reduced up to 88%, resulting in a 10-fold increase in the pCA/FA ratio. Thus, we functionally characterized a sugarcane gene involved in pCA content on hemicelluloses and generated a C4 plant that is promising for valorizing pCA production in biorefineries.
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Affiliation(s)
- Amanda Fanelli
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | | | - Michael Sullivan
- U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI, United States
| | - Steven D. Karlen
- Department of Biochemistry, and The Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI, United States
| | - John Ralph
- Department of Biochemistry, and The Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI, United States
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Renato Vicentini
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Tatiane da Franca Silva
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | - André Ferraz
- Laboratório de Ciências da Madeira, Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
| | - Ronald D. Hatfield
- U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, Madison, WI, United States
| | - Elisson Romanel
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, Brazil
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11
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Calderan-Rodrigues MJ, de Barros Dantas LL, Cheavegatti Gianotto A, Caldana C. Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential. FRONTIERS IN PLANT SCIENCE 2021; 12:637166. [PMID: 33679852 PMCID: PMC7935522 DOI: 10.3389/fpls.2021.637166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/27/2021] [Indexed: 05/21/2023]
Abstract
Sugarcane (Saccharum spp.), a C4 grass, has a peculiar feature: it accumulates, gradient-wise, large amounts of carbon (C) as sucrose in its culms through a complex pathway. Apart from being a sustainable crop concerning C efficiency and bioenergetic yield per hectare, sugarcane is used as feedstock for producing ethanol, sugar, high-value compounds, and products (e.g., polymers and succinate), and bioelectricity, earning the title of the world's leading biomass crop. Commercial cultivars, hybrids bearing high levels of polyploidy, and aneuploidy, are selected from a large number of crosses among suitable parental genotypes followed by the cloning of superior individuals among the progeny. Traditionally, these classical breeding strategies have been favoring the selection of cultivars with high sucrose content and resistance to environmental stresses. A current paradigm change in sugarcane breeding programs aims to alter the balance of C partitioning as a means to provide more plasticity in the sustainable use of this biomass for metabolic engineering and green chemistry. The recently available sugarcane genetic assemblies powered by data science provide exciting perspectives to increase biomass, as the current sugarcane yield is roughly 20% of its predicted potential. Nowadays, several molecular phenotyping tools can be applied to meet the predicted sugarcane C potential, mainly targeting two competing pathways: sucrose production/storage and biomass accumulation. Here we discuss how molecular phenotyping can be a powerful tool to assist breeding programs and which strategies could be adopted depending on the desired final products. We also tackle the advances in genetic markers and mapping as well as how functional genomics and genetic transformation might be able to improve yield and saccharification rates. Finally, we review how "omics" advances are promising to speed up plant breeding and reach the unexplored potential of sugarcane in terms of sucrose and biomass production.
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Affiliation(s)
| | | | | | - Camila Caldana
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Camila Caldana,
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12
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Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Plant Proteomics and Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:51-66. [DOI: 10.1007/978-3-030-80352-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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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. FRONTIERS IN PLANT SCIENCE 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] [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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15
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Shibao PYT, Santos-Júnior CD, Santiago AC, Mohan C, Miguel MC, Toyama D, Vieira MAS, Narayanan S, Figueira A, Carmona AK, Schiermeyer A, Soares-Costa A, Henrique-Silva F. Sugarcane cystatins: From discovery to biotechnological applications. Int J Biol Macromol 2020; 167:676-686. [PMID: 33285201 DOI: 10.1016/j.ijbiomac.2020.11.185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
Abstract
Phytocystatins are tight-binding cysteine protease inhibitors produced by plants. The first phytocystatin described was isolated from Oryza sativa and, since then, cystatins from several plant species were reported, including from sugarcane. Sugarcane cystatins were unraveled in Sugarcane EST project database, after sequencing of cDNA libraries from various sugarcane tissues at different developmental stages and six sugarcane cystatins were cloned, expressed and characterized (CaneCPI-1 to CaneCPI-6). These recombinant proteins were produced in different expression systems and inhibited several cysteine proteases, including human cathepsins B and L, which can be involved in pathologies, such as cancer. In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal localization, and genomic organization. We also present protein docking of CaneCPI-5 in the active site of human cathepsin B, insights about canecystatins structures; recombinant expression in different systems, comparison of their inhibitory activities against human cysteine cathepsins B, K, L, S, V, falcipains from Plasmodium falciparum and a cathepsin L-like from the sugarcane weevil Sphenophorus levis; and enlighten their potential and current applications in agriculture and health.
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Affiliation(s)
- Priscila Yumi Tanaka Shibao
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Célio Dias Santos-Júnior
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | | | - Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mariana Cardoso Miguel
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Subramonian Narayanan
- Genetic Transformation Laboratory, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Adriana K Carmona
- Department of Biophysics, Federal University of São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
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16
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Diniz AL, da Silva DIR, Lembke CG, Costa MDBL, ten-Caten F, Li F, Vilela RD, Menossi M, Ware D, Endres L, Souza GM. Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci 2020; 21:ijms21239124. [PMID: 33266228 PMCID: PMC7729667 DOI: 10.3390/ijms21239124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023] Open
Abstract
The ability to expand crop plantations without irrigation is a major goal to increase agriculture sustainability. To achieve this end, we need to understand the mechanisms that govern plant growth responses under drought conditions. In this study, we combined physiological, transcriptomic, and genomic data to provide a comprehensive picture of drought and recovery responses in the leaves and roots of sugarcane. Transcriptomic profiling using oligoarrays and RNA-seq identified 2898 (out of 21,902) and 46,062 (out of 373,869) transcripts as differentially expressed, respectively. Co-expression analysis revealed modules enriched in photosynthesis, small molecule metabolism, alpha-amino acid metabolism, trehalose biosynthesis, serine family amino acid metabolism, and carbohydrate transport. Together, our findings reveal that carbohydrate metabolism is coordinated with the degradation of amino acids to provide carbon skeletons to the tricarboxylic acid cycle. This coordination may help to maintain energetic balance during drought stress adaptation, facilitating recovery after the stress is alleviated. Our results shed light on candidate regulatory elements and pave the way to biotechnology strategies towards the development of drought-tolerant sugarcane plants.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Danielle Izilda Rodrigues da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Maximiller Dal-Bianco Lamas Costa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Forrest Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
| | - Romel Duarte Vilela
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Marcelo Menossi
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil;
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Lauricio Endres
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Correspondence:
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17
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da Silva MF, Gonçalves MC, Brito MDS, Medeiros CN, Harakava R, Landell MGDA, Pinto LR. Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes. PLoS One 2020; 15:e0241493. [PMID: 33166323 PMCID: PMC7652275 DOI: 10.1371/journal.pone.0241493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.
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Affiliation(s)
- Marcel Fernando da Silva
- Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias (FCAV) Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, São Paulo, Brazil
| | | | - Michael dos Santos Brito
- Departamento de Ciência e Tecnologia, Instituto de Ciência e Tecnologia da Universidade Federal de São Paulo, São José dos Campos, São Paulo, Brazil
| | | | - Ricardo Harakava
- Crop Protection Research Centre, Instituto Biológico, São Paulo, Brazil
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18
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Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, Jeżowski S, Barry K, Chae WB, Juvik JA, Gifford J, Oladeinde A, Yamada T, Grimwood J, Putnam NH, De Vega J, Barth S, Klaas M, Hodkinson T, Li L, Jin X, Peng J, Yu CY, Heo K, Yoo JH, Ghimire BK, Donnison IS, Schmutz J, Hudson ME, Sacks EJ, Moose SP, Swaminathan K, Rokhsar DS. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 2020; 11:5442. [PMID: 33116128 PMCID: PMC7595124 DOI: 10.1038/s41467-020-18923-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/19/2020] [Indexed: 02/05/2023] Open
Abstract
Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.
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Affiliation(s)
- Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Adam M Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Brandon T James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Guohong Albert Wu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Mohammad B Belaffif
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Hongxu Dong
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adam Barling
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Jessica R Holmes
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Jessica E Mattick
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Siyao Liu
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Genetics, Curriculum of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Kerrie Farrar
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Katarzyna Głowacka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Stanisław Jeżowski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Won Byoung Chae
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Environmental Horticulture, Dankook University, Cheonan, 31116, Republic of Korea
| | - John A Juvik
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Justin Gifford
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adebosola Oladeinde
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, 10-chōme-3 Kita 11 Jōnishi, Kita-ku, Sapporo, Hokkaido, 060-0811, Japan
| | - Jane Grimwood
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Nicholas H Putnam
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Jose De Vega
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, NR4 7UZ, UK
| | - Susanne Barth
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Manfred Klaas
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Trevor Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, D2, Dublin, Ireland
| | - Laigeng Li
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032, China
| | - Xiaoli Jin
- Department of Agronomy, Zhejiang University, Hangzhou, 310058, China
| | - Junhua Peng
- HuaZhi Rice Biotech Company, Changsha, 410125, Hunan, China
| | - Chang Yeon Yu
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Ji Hye Yoo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Bimal Kumar Ghimire
- Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea
| | - Iain S Donnison
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Erik J Sacks
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Stephen P Moose
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA. .,Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan. .,Chan-Zuckerberg BioHub, 499 Illinois St, San Francisco, CA, 94158, USA.
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Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq. Int J Mol Sci 2020; 21:ijms21217934. [PMID: 33114621 PMCID: PMC7672567 DOI: 10.3390/ijms21217934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/16/2022] Open
Abstract
Some metals are beneficial to plants and contribute to critical physiological processes. Some metals, however, are not. The presence of aluminum ions (Al3+) can be very toxic, especially in acidic soils. Considerable parts of the world's arable land are acidic in nature; mechanistically elucidating a plant's response to aluminum stress is critical to mitigating this stress and improving the quality of plants. To identify the genes involved in sugarcane response to aluminum stress, we generated 372 million paired-end RNA sequencing reads from the roots of CTC-2 and RB855453, which are two contrasting cultivars. Data normalization resulted in 162,161 contigs (contiguous sequences) and 97,335 genes from a de novo transcriptome assembly (trinity genes). A total of 4858 and 1307 differently expressed genes (DEGs) for treatment versus control were identified for the CTC-2 and RB855453 cultivars, respectively. The DEGs were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and downregulated in RB855453 (sensitive cultivar). Here, we present the first root transcriptome of sugarcane under aluminum stress. The results and conclusions of this study are a crucial launch pad for future genetic and genomic studies of sugarcane. The transcriptome analysis shows that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with lateral root formation and activation of redox enzymes. We also present a hypothetical model for aluminum tolerance in the CTC-2 cultivar.
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Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Crit Rev Biotechnol 2020; 40:865-880. [PMID: 32508157 DOI: 10.1080/07388551.2020.1765730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
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Affiliation(s)
- Ramaswamy Manimekalai
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Gayathri Suresh
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Hemaprabha Govinda Kurup
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Selvi Athiappan
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Mallikarjuna Kandalam
- Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA
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21
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Selvi A, Devi K, Manimekalai R, Prathima PT. Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought. 3 Biotech 2020; 10:236. [PMID: 32399386 PMCID: PMC7203378 DOI: 10.1007/s13205-020-02226-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.
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Affiliation(s)
- A. Selvi
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - K. Devi
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - R. Manimekalai
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - P. T. Prathima
- Biotechnology Section, Division of Crop Improvement, Indian Council of Agricultural Research- Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
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22
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Plant Cell Wall Proteins and Development. Int J Mol Sci 2020; 21:ijms21082731. [PMID: 32326416 PMCID: PMC7215729 DOI: 10.3390/ijms21082731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
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23
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Gallinari RH, Coletta RD, Araújo P, Menossi M, Nery MF. Bringing to light the molecular evolution of GUX genes in plants. Genet Mol Biol 2020; 43:e20180208. [PMID: 32232316 PMCID: PMC7198009 DOI: 10.1590/1678-4685-gmb-2018-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/06/2019] [Indexed: 11/30/2022] Open
Abstract
Hemicellulose and cellulose are essential polysaccharides for plant development and major components of cell wall. They are also an important energy source for the production of ethanol from plant biomass, but their conversion to fermentable sugars is hindered by the complex structure of cell walls. The glucuronic acid substitution of xylan (GUX) enzymes attach glucuronic acid to xylan, a major component of hemicellulose, decreasing the efficiency of enzymes used for ethanol production. Since loss-of-function gux mutants of Arabidopsis thaliana enhance enzyme accessibility and cell wall digestion without adverse phenotypes, GUX genes are potential targets for genetically improving energy crops. However, comprehensive identification of GUX in important species and their evolutionary history are largely lacking. Here, we identified putative GUX proteins using hidden Markov model searches with the GT8 domain and a GUX-specific motif, and inferred the phylogenetic relationship of 18 species with Maximum likelihood and Bayesian approaches. Each species presented a variable number of GUX, and their evolution can be explained by a mixture of divergent, concerted and birth-and-death evolutionary models. This is the first broad insight into the evolution of GUX gene family in plants and will potentially guide genetic and functional studies in species used for biofuel production.
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Affiliation(s)
- Rafael Henrique Gallinari
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Rafael Della Coletta
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Pedro Araújo
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Marcelo Menossi
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
| | - Mariana Freitas Nery
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Campinas, SP, Brazil
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24
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Souza GM, Van Sluys MA, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL, Oliveira MDM, Ferreira SDS, Nishiyama MY, ten-Caten F, Ragagnin GT, Andrade PDM, de Souza RF, Nicastro GG, Pandya R, Kim C, Guo H, Durham AM, Carneiro MS, Zhang J, Zhang X, Zhang Q, Ming R, Schatz MC, Davidson B, Paterson AH, Heckerman D. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience 2019; 8:giz129. [PMID: 31782791 PMCID: PMC6884061 DOI: 10.1093/gigascience/giz129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/23/2019] [Accepted: 10/08/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
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Affiliation(s)
- Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Hayan Lee
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CACA94598, United States of America
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP 13418-900, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Jonas Weissmann Gaiarsa
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Mauro de Medeiros Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Sávio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, SP05503-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Geovani Tolfo Ragagnin
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Pablo de Morais Andrade
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Gianlucca Gonçalves Nicastro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Ravi Pandya
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
- Department of Crop Science, Chungnam National University, 99 Daehak Ro Yuseong Gu, Deajeon,34134, South Korea
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - Alan Mitchell Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão, 1010, São Paulo, SP 05508-090, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Washington Luis km 235, Araras, SP 13.565-905, Brazil
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 201 W. Gregory Dr. Urbana, Urbana, Illinois 61801, United States of America
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Departments of Computer Science and Biology, Johns Hopkins University, 3400 North Charles Street,Baltimore, MD 21218-2608, United States of America
| | - Bob Davidson
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - David Heckerman
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
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25
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Diniz AL, Ferreira SS, Ten-Caten F, Margarido GRA, Dos Santos JM, Barbosa GVDS, Carneiro MS, Souza GM. Genomic resources for energy cane breeding in the post genomics era. Comput Struct Biotechnol J 2019; 17:1404-1414. [PMID: 31871586 PMCID: PMC6906722 DOI: 10.1016/j.csbj.2019.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023] Open
Abstract
Sugarcane is one of the most sustainable energy crops among cultivated crops presenting the highest tonnage of cultivated plants. Its high productivity of sugar, bioethanol and bioelectricity make it a promising green alternative to petroleum. Furthermore, the myriad of products that can be derived from sugarcane biomass has been driving breeding programs towards varieties with a higher yield of fiber and a more vigorous and sustainable performance: the energy cane. Here we provide an overview of the energy cane including plant description, breeding efforts, types, and end-uses. In addition, we describe recently published genomic resources for the development of this crop, discuss current knowledge of cell wall metabolism, bioinformatic tools and databases available for the community.
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Affiliation(s)
- Augusto L Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Sávio S Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo 05508-090, SP, Brazil
| | - Felipe Ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
| | - Gabriel R A Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba 13418-900, SP, Brazil
| | - João M Dos Santos
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Geraldo V de S Barbosa
- Departamento de Fitotecnia e Fitossanidade, Centro de Ciências Agrárias, Universidade Federal de Alagoas, BR 104 Norte, km 85, Rio Largo 571000-000, AL, Brazil
| | - Monalisa S Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera km 174, Araras 13600-970, SP, Brazil
| | - Glaucia M Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil
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26
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Begcy K, Mariano ED, Lembke CG, Zingaretti SM, Souza GM, Araújo P, Menossi M. Overexpression of an evolutionarily conserved drought-responsive sugarcane gene enhances salinity and drought resilience. ANNALS OF BOTANY 2019; 124:691-700. [PMID: 31125059 PMCID: PMC6821327 DOI: 10.1093/aob/mcz044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/07/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Improving drought adaptation is more pressing for crops such as sugarcane, rice, wheat and maize, given the high dependence of these crops on irrigation. One option for enhancing adaptation to water limitation in plants is by transgenic approaches. An increasing number of genes that are associated with mechanisms used by plants to cope with water scarcity have been discovered. Genes encoding proteins with unknown functions comprise a relevant fraction of the genes that are modulated by drought. We characterized a gene in response to environmental stresses to gain insight into the unknown fraction of the sugarcane genome. Scdr2 (Sugarcane drought-responsive 2) encodes a small protein and shares highly conserved sequences within monocots, dicots, algae and fungi. METHODS Plants overexpressing the Scdr2 sugarcane gene were examined in response to salinity and drought. Measurements of the gas exchange parameters, germination rate, water content, dry mass and oxidative damage were performed. Seeds as well as juvenile plants were used to explore the resilience level of the transgenic plants when compared with wild-type plants. KEY RESULTS Overexpression of Scdr2 enhanced germination rates in tobacco seeds under drought and salinity conditions. Juvenile transgenic plants overexpressing Scdr2 and subjected to drought and salinity stresses showed higher photosynthesis levels, internal CO2 concentration and stomatal conductance, reduced accumulation of hydrogen peroxide in the leaves, no penalty for photosystem II and faster recovery after submission to both stress conditions. Respiration was not strongly affected by both stresses in the Scdr2 transgenic plants, whereas wild-type plants exhibited increased respiration rates. CONCLUSIONS Scdr2 is involved in the response mechanism to abiotic stresses. Higher levels of Scdr2 enhanced resilience to salinity and drought, and this protection correlated with reduced oxidative damage. Scdr2 confers, at the physiological level, advantages to climate limitations. Therefore, Scdr2 is a potential target for improving sugarcane resilience to abiotic stress.
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Affiliation(s)
- Kevin Begcy
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Regensburg, Germany
| | - Eduardo D Mariano
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- Present address: Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, Brazil
| | - Carolina G Lembke
- Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sonia Marli Zingaretti
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Glaucia M Souza
- Laboratório de Transdução de Sinal, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro Araújo
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- For correspondence. E-mail
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27
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Righetto GL, Sriranganadane D, Halabelian L, Chiodi CG, Elkins JM, Massirer KB, Gileadi O, Menossi M, Couñago RM. The C-Terminal Domains SnRK2 Box and ABA Box Have a Role in Sugarcane SnRK2s Auto-Activation and Activity. FRONTIERS IN PLANT SCIENCE 2019; 10:1105. [PMID: 31620147 PMCID: PMC6759772 DOI: 10.3389/fpls.2019.01105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Resistance to drought stress is fundamental to plant survival and development. Abscisic acid (ABA) is one of the major hormones involved in different types of abiotic and biotic stress responses. ABA intracellular signaling has been extensively explored in Arabidopsis thaliana and occurs via a phosphorylation cascade mediated by three related protein kinases, denominated SnRK2s (SNF1-related protein kinases). However, the role of ABA signaling and the biochemistry of SnRK2 in crop plants remains underexplored. Considering the importance of the ABA hormone in abiotic stress tolerance, here we investigated the regulatory mechanism of sugarcane SnRK2s-known as stress/ABA-activated protein kinases (SAPKs). The crystal structure of ScSAPK10 revealed the characteristic SnRK2 family architecture, in which the regulatory SnRK2 box interacts with the kinase domain αC helix. To study sugarcane SnRK2 regulation, we produced a series of mutants for the protein regulatory domains SnRK2 box and ABA box. Mutations in ScSAPK8 SnRK2 box aimed at perturbing its interaction with the protein kinase domain reduced protein kinase activity in vitro. On the other hand, mutations to ScSAPK ABA box did not impact protein kinase activity but did alter the protein autophosphorylation pattern. Taken together, our results demonstrate that both SnRK2 and ABA boxes might play a role in sugarcane SnRK2 function.
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Affiliation(s)
- Germanna Lima Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution, and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - Dev Sriranganadane
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, Brazil
| | - Levon Halabelian
- Structural Genomics Consortium, MaRS Centre, Toronto, ON, Canada
| | - Carla G. Chiodi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, Brazil
| | - Jonathan M. Elkins
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, Brazil
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Katlin B. Massirer
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, Brazil
| | - Opher Gileadi
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution, and Bioagents, Institute of Biology, State University of Campinas, Campinas, Brazil
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, Brazil
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Ali A, Khan M, Sharif R, Mujtaba M, Gao SJ. Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2019; 8:E344. [PMID: 31547331 PMCID: PMC6784093 DOI: 10.3390/plants8090344] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022]
Abstract
Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world's sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops.
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Affiliation(s)
- Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mehran Khan
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan, Punjab 32200, Pakistan
| | - Rahat Sharif
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Muhammad Mujtaba
- Institute of Biotechnology, Ankara University, Ankara 06110, Turkey
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Salvato F, Loziuk P, Kiyota E, Daneluzzi GS, Araújo P, Muddiman DC, Mazzafera P. Label-Free Quantitative Proteomics of Enriched Nuclei from Sugarcane (Saccharum ssp) Stems in Response to Drought Stress. Proteomics 2019; 19:e1900004. [PMID: 31172662 DOI: 10.1002/pmic.201900004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/31/2019] [Indexed: 11/09/2022]
Abstract
Drought is considered the major abiotic stress limiting crop productivity. This study seeks to identify proteins involved in the drought response in sugarcane stems submitted to drought stress. The integration of nuclei enrichment sample preparation with the shotgun proteomic approach results in great coverage of the sugarcane stem proteome with 5381 protein groups identified. A total of 1204 differentially accumulated proteins are detected in response to drought, among which 586 and 618 are increased and reduced in abundance, respectively. A total of 115 exclusive proteins are detected, being 41 exclusives of drought-stressed plants and 74 exclusives of control plants. In the control plants, most of these proteins are related to cell wall metabolism, indicating that drought affects negatively the cell wall metabolism. Also, 37 transcription factors (TFs) are identified, which are low abundant nuclear proteins and are differentially accumulated in response to drought stress. These TFs are associated to protein domains such as leucine-rich (bZIP), C2H2, NAC, C3H, LIM, Myb-related, heat shock factor (HSF) and auxin response factor (ARF). Increased abundance of chromatin remodeling and RNA processing proteins are also observed. It is suggested that these variations result from an imbalance of protein synthesis and degradation processes induced by drought.
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Affiliation(s)
- Fernanda Salvato
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13081, Brazil
| | - Philip Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Eduardo Kiyota
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13081, Brazil
| | - Gabriel Silva Daneluzzi
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418, Brazil
| | - Pedro Araújo
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13081, Brazil
| | - David C Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Paulo Mazzafera
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13081, Brazil.,Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418, Brazil
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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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31
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Figueiredo R, Araújo P, Llerena JPP, Mazzafera P. Suberin and hemicellulose in sugarcane cell wall architecture and crop digestibility: A biotechnological perspective. Food Energy Secur 2019. [DOI: 10.1002/fes3.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Raquel Figueiredo
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
| | - Pedro Araújo
- Department of Genetics, Evolution and Bioagents Institute of Biology State University of Campinas Campinas Brazil
| | - Juan Pablo P. Llerena
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
| | - Paulo Mazzafera
- Department of Plant Biology Institute of Biology State University of Campinas Campinas Brazil
- Department of Crop Science College of Agriculture Luiz de Queiroz University of São Paulo Piracicaba Brazil
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Fonseca JG, Calderan-Rodrigues MJ, de Moraes FE, Cataldi TR, Jamet E, Labate CA. Cell Wall Proteome of Sugarcane Young and Mature Leaves and Stems. Proteomics 2019; 18. [PMID: 29274249 DOI: 10.1002/pmic.201700129] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 10/25/2017] [Indexed: 11/07/2022]
Abstract
By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it is possible to address unique characteristics in each of them. Four-month-old leaves show a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to 4-month-old internodes. It is possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which is assumed to be linked to cuticle formation. The data generated enrich the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants.
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Affiliation(s)
- Juliana G Fonseca
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria J Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Fabrício E de Moraes
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Thaís R Cataldi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet Tolosan, France
| | - Carlos A Labate
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
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Singh P, Singh SN, Tiwari AK, Pathak SK, Singh AK, Srivastava S, Mohan N. Integration of sugarcane production technologies for enhanced cane and sugar productivity targeting to increase farmers' income: strategies and prospects. 3 Biotech 2019; 9:48. [PMID: 30729072 DOI: 10.1007/s13205-019-1568-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
The idea of doubling the farmers' income in next 5 years has been slated by the Government of India. The specific target of increasing sugarcane farmers' income could be achieved by developing cost-effective technologies, transferring them from laboratory to land, educating the farmers and creating a linkage between all stakeholders. Consistent efforts shall be required to harness all possible sources for increasing farmer's income in and outside the agriculture sector with respect to improvement in sugarcane and sugar productivity, enhancement in resource use efficiency and adopting various other ways and means including intercropping, management of pests and diseases, use of biotechnological tools and minimizing post-harvest deterioration. The advances in sugarcane biotechnology could become remarkable in the coming years, both in terms of improving productivity as well as increasing the value and utility of this crop substantially. In future, genetically modified sugarcane varieties with increased resistance to different biotic and abiotic stresses would serve more towards sugarcane crop improvement. Any possibility of enhancement in the income of sugarcane farmers shall also be dependent upon the profitability and sustainability of the sugar industry. Integration of sugarcane production technologies for improvement in farm productivity, diversified sugarcane production system, reduced cost of cultivation along with increased processing plant efficiency and diversification to produce value added products shall ensure smooth and higher payment to the farmers. Development of low-cost technologies to convert "waste to resource" on a smaller scale shall also help the farmers to increase their income further. This paper focuses on possible measures to be taken up in each aspects of sugarcane cultivation including biotechnological approaches to achieve the goal of enhancing the income of sugarcane farmers substantially, particularly in the sub-tropical region of India.
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Grativol C, Thiebaut F, Sangi S, Montessoro P, Santos WDS, Hemerly AS, Ferreira PC. A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 2019; 7:e6080. [PMID: 30648010 PMCID: PMC6331000 DOI: 10.7717/peerj.6080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
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Affiliation(s)
- Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Flavia Thiebaut
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Sangi
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Patricia Montessoro
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Walaci da Silva Santos
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo C.G. Ferreira
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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Budzinski IGF, de Moraes FE, Cataldi TR, Franceschini LM, Labate CA. Network Analyses and Data Integration of Proteomics and Metabolomics From Leaves of Two Contrasting Varieties of Sugarcane in Response to Drought. FRONTIERS IN PLANT SCIENCE 2019; 10:1524. [PMID: 31850025 PMCID: PMC6892781 DOI: 10.3389/fpls.2019.01524] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/01/2019] [Indexed: 05/11/2023]
Abstract
Uncovering the molecular mechanisms involved in the responses of crops to drought is crucial to understand and enhance drought tolerance mechanisms. Sugarcane (Saccharum spp.) is an important commercial crop cultivated mainly in tropical and subtropical areas for sucrose and ethanol production. Usually, drought tolerance has been investigated by single omics analysis (e.g. global transcripts identification). Here we combine label-free quantitative proteomics and metabolomics data (GC-TOF-MS), using a network-based approach, to understand how two contrasting commercial varieties of sugarcane, CTC15 (tolerant) and SP90-3414 (susceptible), adjust their leaf metabolism in response to drought. To this aim, we propose the utilization of regularized canonical correlation analysis (rCCA), which is a modification of classical CCA, and explores the linear relationships between two datasets of quantitative variables from the same experimental units, with a threshold set to 0.99. Light curves revealed that after 4 days of drought, the susceptible variety had its photosynthetic capacity already significantly reduced, while the tolerant variety did not show major reduction. Upon 12 days of drought, photosynthesis in the susceptible plants was completely reduced, while the tolerant variety was at a third of its rate under control conditions. Network analysis of proteins and metabolites revealed that different biological process had a stronger impact in each variety (e.g. translation in CTC15, generation of precursor metabolites, response to stress and energy in SP90-3414). Our results provide a reference data set and demonstrate that rCCA can be a powerful tool to infer experimentally metabolite-protein or protein-metabolite associations to understand plant biology.
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Overexpression of ScMYBAS1 alternative splicing transcripts differentially impacts biomass accumulation and drought tolerance in rice transgenic plants. PLoS One 2018; 13:e0207534. [PMID: 30517137 PMCID: PMC6281192 DOI: 10.1371/journal.pone.0207534] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/01/2018] [Indexed: 02/05/2023] Open
Abstract
Drought is the most significant environmental stress for agricultural production worldwide, and tremendous efforts have been made to improve crop yield under the increasing water scarcity. Transcription factors are major players in the regulation of water stress-related genes in plants. Recently, different MYB transcription factors were characterized for their involvement in drought response. A sugarcane R2R3-MYB gene (ScMYBAS1) and its four alternative forms of transcript (ScMYAS1-2, ScMYBAS1-3, ScMYBAS1-4 and ScMYBAS1-5) were identified in this study. The subcellular localization, in Nicotiniana benthamiana, of the TFs fused in frame with GFP revealed that ScMYBAS1-2-GFP and ScMYBAS1-3-GFP were observed in the nucleus. The overexpression of ScMYBAS1-2 and ScMYBAS1-3 spliced transcripts in rice promoted change in plant growth under both well-watered and drought conditions. The ScMYBAS1-2 and ScMYBAS1-3 transgenic lines revealed a higher relative water content (RWC) compared to the wild type before maximum stress under drought conditions. The ScMYBAS1-2 transgenic lines showed a reduction in biomass (total dry weight). Conversely, ScMYBAS1-3 showed an increased biomass (total dry weight) relative to the wild-type. The overexpression of ScMYBAS1-3 in rice transgenic lines showed involvement with drought tolerance and biomass and, for this reason, was considered a good target for plant transformation, particularly for use in developing genotypes with drought tolerance and biomass accumulation.
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Cia MC, de Carvalho G, Azevedo RA, Monteiro-Vitorello CB, Souza GM, Nishiyama-Junior MY, Lembke CG, Antunes de Faria RSDC, Marques JPR, Melotto M, Camargo LEA. Novel Insights Into the Early Stages of Ratoon Stunting Disease of Sugarcane Inferred from Transcript and Protein Analysis. PHYTOPATHOLOGY 2018; 108:1455-1466. [PMID: 29969065 DOI: 10.1094/phyto-04-18-0120-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite of the importance of ratoon stunting disease, little is known on the responses of sugarcane to its causal agent, the vascular bacterial endophyte Leifsonia xyli subsp. xyli. The transcriptome and proteome of young plants of a susceptible cultivar with no symptoms of stunting but with relative low and high bacterial titers were compared at 30 and 60 days after inoculation. Increased bacterial titers were associated with alterations in the expression of 267 cDNAs and in the abundance of 150 proteins involved in plant growth, hormone metabolism, signal transduction and defense responses. Some alterations are predicted to benefit the pathogen, such as the up-regulation of genes involved in the synthesis of methionine. Also, genes and proteins of the cell division cycle were all down-regulated in plants with higher titers at both times. It is hypothesized that the negative effects on cell division related to increased bacterial titers is cumulative over time and its modulation by other host and environmental factors results in the stunting symptom.
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Affiliation(s)
- Mariana Cicarelli Cia
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Giselle de Carvalho
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Ricardo Antunes Azevedo
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Claudia Barros Monteiro-Vitorello
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Glaucia Mendes Souza
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Milton Yutaka Nishiyama-Junior
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Carolina Gimiliani Lembke
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Raphael Severo da Cunha Antunes de Faria
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - João Paulo Rodrigues Marques
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Maeli Melotto
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
| | - Luis Eduardo Aranha Camargo
- First, second, third, fourth, eighth, ninth, and eleventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil; fifth and seventh authors: Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, São Paulo, SP, Brazil; sixth author: Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, Av. Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil; and tenth author: Department of Plant Sciences, University of California, Davis 95616
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Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, D'Hont A. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nat Commun 2018; 9:2638. [PMID: 29980662 PMCID: PMC6035169 DOI: 10.1038/s41467-018-05051-5] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/13/2018] [Indexed: 01/31/2023] Open
Abstract
Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
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Affiliation(s)
- Olivier Garsmeur
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Gaetan Droc
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Bernard Potier
- SASRI (South African Sugarcane Research Institute), Mount Edgecombe, 4300, South Africa
| | - Karen Aitken
- CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia, QLD, 4067, Australia
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - Guillaume Martin
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Carine Charron
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Laurent Costet
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
| | - Nabila Yahiaoui
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | - David Sims
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA
| | | | | | - Andrzej Kilian
- Diversity Arrays Technology, Yarralumla, ACT, 2600, Australia
| | - Agnes Chan
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | | | - Hélène Bergès
- INRA-CNRGV, 31326, Toulouse, Castanet-Tolosan, France
| | - Blake Simmons
- JBEI Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jean Christophe Glaszmann
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | | | - Robert Henry
- QAAFI (Queensland Alliance for Agriculture and Food Innovation), University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA.,Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Angélique D'Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France. .,AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France.
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Khan MS, Kumar S, Singh RK, Singh J, Duttamajumder SK, Kapur R. Characterization of leaf transcriptome, development and utilization of unigenes-derived microsatellite markers in sugarcane ( Saccharum sp. hybrid). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:665-682. [PMID: 30042621 PMCID: PMC6041238 DOI: 10.1007/s12298-018-0563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 05/14/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
Sugarcane (Saccharum species hybrid) is the major source of sugar (> 80% sugar) in the world and is cultivated in more than 115 countries. It has recently gained attention as a source of biofuel (ethanol). Due to genomic complexity, the development of new genomic resources is imperative in understanding the gene regulation and function, and to fine tune the genetic improvement of sugarcane. In this study, a cDNA library was constructed from mature leaves so as to develop ESTs resources which were further compared with nucleotide and protein databases to explore the functional identity of sugarcane genes. The non-redundant ESTs (unigenes) were categorized into 18 metabolic functions. The major categories were bioenergetics and photosynthesis (4%), cell metabolism (5%), development related protein (3%), membrane-related, mobile genetic elements (5%), signal transduction (2%), DNA (1%), RNA (1%) and protein (2%) metabolism, other metabolic processes (3%), transcription factors (1%), transport (4%) and proteins related to stress/defense (4%). From 540 unique ESTs, 212 simple sequence repeats were identified, of which 206 were from 463 singlets and six were mined from 77 contig sequences. A total of 540 unique EST sequences were used for SSR search of which 97 (17.9%) contained specified SSR motifs, generating 212 unique SSRs. The genes characterized in this study and the EST-derived microsatellite markers identified from the cDNA library will enrich genomic resources for association- and linkage-mapping studies in sugarcane.
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Affiliation(s)
- Mohammad Suhail Khan
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, U.P. 226002 India
| | - Sanjeev Kumar
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, U.P. 226002 India
| | - Ram Kewal Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, U.P. 226002 India
- Present Address: Division of Crop Science, Indian Council of Agricultural Research, Dr. Rajendra Prasad Road, Krishi Bhawan, New Delhi, 110 001 India
| | - Jyotsnendra Singh
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, U.P. 226002 India
| | | | - Raman Kapur
- ICAR-Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow, U.P. 226002 India
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40
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Melo PM, El Chamy Maluf S, Azevedo MF, Paschoalin T, Budu A, Bagnaresi P, Henrique-Silva F, Soares-Costa A, Gazarini ML, Carmona AK. Inhibition of Plasmodium falciparum cysteine proteases by the sugarcane cystatin CaneCPI-4. Parasitol Int 2018; 67:233-236. [DOI: 10.1016/j.parint.2017.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/03/2017] [Accepted: 12/25/2017] [Indexed: 10/18/2022]
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Ukoskit K, Posudsavang G, Pongsiripat N, Chatwachirawong P, Klomsa-Ard P, Poomipant P, Tragoonrung S. Detection and validation of EST-SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping. Genomics 2018; 111:1-9. [PMID: 29608956 DOI: 10.1016/j.ygeno.2018.03.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 01/17/2023]
Abstract
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis. Association analysis was performed on a set of 200 accessions, based on the mixed linear model. Validation of the EST-SSR markers using association mapping within the target QTL genomic regions identified two EST-SSR markers showing a putative relationship with uridine diphosphate (UDP) glycosyltransferase, and beta-amylase, which are associated with pol and sugar yield. These functional markers can be used for marker-assisted selection of sugarcane.
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Affiliation(s)
- Kittipat Ukoskit
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand.
| | - Ganlayarat Posudsavang
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand
| | - Nattapat Pongsiripat
- Department of Biotechnology, Thammasat University, (Rangsit Campus) Klong Luang, Pathum Thani 12121, Thailand
| | - Prasert Chatwachirawong
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, (Kamphaengsean Campus), Nakhon Pathom, 73140, Thailand
| | - Peeraya Klomsa-Ard
- Mitr Phol Innovation and Research Centre, 399 Moo 1, Chumphae-Phukiao Rd. Khoksa-at, Phu Khiao, Chaiyaphum 36110, Thailand
| | - Patthinun Poomipant
- Institute of Food Research and Product Development, Kasetsart University, P.O. Box 1043, Kasetsart, Chatuchak, Bangkok 10903, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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42
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Hoang NV, Furtado A, Thirugnanasambandam PP, Botha FC, Henry RJ. De novo assembly and characterizing of the culm-derived meta-transcriptome from the polyploid sugarcane genome based on coding transcripts. Heliyon 2018; 4:e00583. [PMID: 29862346 PMCID: PMC5968133 DOI: 10.1016/j.heliyon.2018.e00583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/02/2018] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
Sugarcane biomass has been used for sugar, bioenergy and biomaterial production. The majority of the sugarcane biomass comes from the culm, which makes it important to understand the genetic control of biomass production in this part of the plant. A meta-transcriptome of the culm was obtained in an earlier study by using about one billion paired-end (150 bp) reads of deep RNA sequencing of samples from 20 diverse sugarcane genotypes and combining de novo assemblies from different assemblers and different settings. Although many genes could be recovered, this resulted in a large combined assembly which created the need for clustering to reduce transcript redundancy while maintaining gene content. Here, we present a comprehensive analysis of the effect of different assembly settings and clustering methods on de novo assembly, annotation and transcript profiling focusing especially on the coding transcripts from the highly polyploid sugarcane genome. The new coding sequence-based transcript clustering resulted in a better representation of transcripts compared to the earlier approach, having 121,987 contigs, which included 78,052 main and 43,935 alternative transcripts. About 73%, 67%, 61% and 10% of the transcriptome was annotated against the NCBI NR protein database, GO terms, orthologous groups and KEGG orthologies, respectively. Using this set for a differential gene expression analysis between the young and mature sugarcane culm tissues, a total of 822 transcripts were found to be differentially expressed, including key transcripts involved in sugar/fiber accumulation in sugarcane. In the context of the lack of a whole genome sequence for sugarcane, the availability of a well annotated culm-derived meta-transcriptome through deep sequencing provides useful information on coding genes specific to the sugarcane culm and will certainly contribute to understanding the process of carbon partitioning, and biomass accumulation in the sugarcane culm.
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Affiliation(s)
- Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
- Sugar Research Australia, Indooroopilly, Queensland, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, 4072, Australia
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43
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Kandel R, Yang X, Song J, Wang J. Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:151. [PMID: 29503654 PMCID: PMC5821101 DOI: 10.3389/fpls.2018.00151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/29/2018] [Indexed: 05/07/2023]
Abstract
Lignocellulosic biomass has become an emerging feedstock for second-generation bioethanol production. Sugarcane (Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features viz. fast growth rate and abilities for high tillering, ratooning, and photosynthesis. Energy cane, an ideal type of sugarcane, has been bred specifically as a biomass crop. In this review, we described (1) biomass potentials of sugarcane and its underlying genetics, (2) challenges associated with biomass improvement such as large and complex genome, narrow gene pool in existing commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass improvement, and (4) mining candidate genes controlling biomass in genomic databases. We extensively reviewed databases for biomass-related genes and their usefulness in biofuel generation. This review provides valuable resources for sugarcane breeders, geneticists, and broad scientific communities involved in bioenergy production.
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Affiliation(s)
- Ramkrishna Kandel
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Jian Song
- Agronomy Department, University of Florida, Gainesville, FL, United States
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems, Fujian Agriculture and Forestry University, Fuzhou, China
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44
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Thirugnanasambandam PP, Hoang NV, Furtado A, Botha FC, Henry RJ. Association of variation in the sugarcane transcriptome with sugar content. BMC Genomics 2017; 18:909. [PMID: 29178834 PMCID: PMC5702190 DOI: 10.1186/s12864-017-4302-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/14/2017] [Indexed: 01/01/2023] Open
Abstract
Background Sugarcane is a major crop of the tropics cultivated mainly for its high sucrose content. The crop is genetically less explored due to its complex polyploid genome. Sucrose synthesis and accumulation are complex processes influenced by physiological, biochemical and genetic factors, and the growth environment. The recent focus on the crop for fibre and biofuel has led to a renewed interest on understanding the molecular basis of sucrose and biomass traits. This transcriptome study aimed to identify genes that are associated with and differentially regulated during sucrose synthesis and accumulation in the mature stage of sugarcane. Patterns of gene expression in high and low sugar genotypes as well as mature and immature culm tissues were studied using RNA-Seq of culm transcriptomes. Results In this study, 28 RNA-Seq libraries from 14 genotypes of sugarcane differing in their sucrose content were used for studying the transcriptional basis of sucrose accumulation. Differential gene expression studies were performed using SoGI (Saccharum officinarum Gene Index, 3.0), SAS (sugarcane assembled sequences) of sugarcane EST database (SUCEST) and SUGIT, a sugarcane Iso-Seq transcriptome database. In total, about 34,476 genes were found to be differentially expressed between high and low sugar genotypes with the SoGI database, 20,487 genes with the SAS database and 18,543 genes with the SUGIT database at FDR < 0.01, using the Baggerley’s test. Further, differential gene expression analyses were conducted between immature (top) and mature (bottom) tissues of the culm. The DEGs were functionally annotated using GO classification and the genes consistently associated with sucrose accumulation were identified. Conclusions The large number of DEGs may be due to the large number of genes that influence sucrose content or are regulated by sucrose content. These results indicate that apart from being a primary metabolite and storage and transport sugar, sucrose may serve as a signalling molecule that regulates many aspects of growth and development in sugarcane. Further studies are needed to confirm if sucrose regulates the expression of the identified DEGs or vice versa. The DEGs identified in this study may lead to identification of genes/pathways regulating sucrose accumulation and/or regulated by sucrose levels in sugarcane. We propose identifying the master regulators of sucrose if any in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4302-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prathima P Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Nam V Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.,College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | | | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St Lucia, QLD, 4072, Australia.
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45
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Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane. Mol Genet Genomics 2017; 292:1323-1340. [PMID: 28699001 DOI: 10.1007/s00438-017-1349-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/04/2017] [Indexed: 01/13/2023]
Abstract
Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.
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Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/06/2017] [Indexed: 05/20/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
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Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
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47
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Santiago A, Khan Z, Miguel M, Gironda C, Soares-Costa A, Pelá V, Leite A, Edwardson J, Buzalaf M, Henrique-Silva F. A New Sugarcane Cystatin Strongly Binds to Dental Enamel and Reduces Erosion. J Dent Res 2017; 96:1051-1057. [DOI: 10.1177/0022034517712981] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cystatin B was recently identified as an acid-resistant protein in acquired enamel pellicle; it could therefore be included in oral products to protect against caries and erosion. However, human recombinant cystatin is very expensive, and alternatives to its use are necessary. Phytocystatins are reversible inhibitors of cysteine peptidases that are found naturally in plants. In plants, they have several biological and physiological functions, such as the regulation of endogenous processes, defense against pathogens, and response to abiotic stress. Previous studies performed by our research group have reported high inhibitory activity and potential agricultural and medical applications of several sugarcane cystatins, including CaneCPI-1, CaneCPI-2, CaneCPI-3, and CaneCPI-4. In the present study, we report the characterization of a novel sugarcane cystatin, named CaneCPI-5. This cystatin was efficiently expressed in Escherichia coli, and inhibitory assays demonstrated that it was a potent inhibitor of human cathepsins B, K, and L ( Ki = 6.87, 0.49, and 0.34 nM, respectively). The ability of CaneCPI-5 to bind to dental enamel was evaluated using atomic force microscopy. Its capacity to protect against initial enamel erosion was also tested in vitro via changes in surface hardness. CaneCPI-5 showed a very large force of interaction with enamel (e.g., compared with mucin and casein) and significantly reduced initial enamel erosion. These results suggest that the inclusion of CaneCPIs in dental products might confer protection against enamel erosion.
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Affiliation(s)
- A.C. Santiago
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Z.N. Khan
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - M.C. Miguel
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - C.C. Gironda
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - A. Soares-Costa
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - V.T. Pelá
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - A.L. Leite
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - J.M. Edwardson
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - M.A.R. Buzalaf
- Laboratory of Biochemistry, Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - F. Henrique-Silva
- Laboratory of Molecular Biology, Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
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48
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Hoang NV, Furtado A, Mason PJ, Marquardt A, Kasirajan L, Thirugnanasambandam PP, Botha FC, Henry RJ. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing. BMC Genomics 2017; 18:395. [PMID: 28532419 PMCID: PMC5440902 DOI: 10.1186/s12864-017-3757-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 05/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms. RESULTS The sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes. CONCLUSIONS The transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.
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Affiliation(s)
- Nam V Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Patrick J Mason
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia
| | - Annelie Marquardt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Lakshmi Kasirajan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Prathima P Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.,Sugar Research Australia, Indooroopilly, QLD, 4068, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, St. Lucia, QLD, 4072, Australia.
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49
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Cunha CP, Roberto GG, Vicentini R, Lembke CG, Souza GM, Ribeiro RV, Machado EC, Lagôa AMMA, Menossi M. Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening. Sci Rep 2017; 7:43364. [PMID: 28266527 PMCID: PMC5339719 DOI: 10.1038/srep43364] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
The effects of ethephon as a sugarcane ripener are attributed to ethylene. However, the role of this phytohormone at the molecular level is unknown. We performed a transcriptome analysis combined with the evaluation of sucrose metabolism and hormone profiling of sugarcane plants sprayed with ethephon or aminoethoxyvinylglycine (AVG), an ethylene inhibitor, at the onset of ripening. The differential response between ethephon and AVG on sucrose level and sucrose synthase activity in internodes indicates ethylene as a potential regulator of sink strength. The correlation between hormone levels and transcriptional changes suggests ethylene as a trigger of multiple hormone signal cascades, with approximately 18% of differentially expressed genes involved in hormone biosynthesis, metabolism, signalling, and response. A defence response elicited in leaves favoured salicylic acid over the ethylene/jasmonic acid pathway, while the upper internode was prone to respond to ethylene with strong stimuli on ethylene biosynthesis and signalling genes. Besides, ethylene acted synergistically with abscisic acid, another ripening factor, and antagonistically with gibberellin and auxin. We identified potential ethylene target genes and characterized the hormonal status during ripening, providing insights into the action of ethylene at the site of sucrose accumulation. A molecular model of ethylene interplay with other hormones is proposed.
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Affiliation(s)
- Camila P. Cunha
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Guilherme G. Roberto
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Renato Vicentini
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Carolina G. Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000, São Paulo, Brasil
| | - Glaucia M. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-000, São Paulo, Brasil
| | - Rafael V. Ribeiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
| | - Eduardo C. Machado
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Ana M. M. A. Lagôa
- Centro de Ecofisiologia e Biofísica, Instituto Agronômico de Campinas, 13001-970, Campinas, Brasil
| | - Marcelo Menossi
- Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brasil
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50
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Balsalobre TWA, da Silva Pereira G, Margarido GRA, Gazaffi R, Barreto FZ, Anoni CO, Cardoso-Silva CB, Costa EA, Mancini MC, Hoffmann HP, de Souza AP, Garcia AAF, Carneiro MS. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics 2017; 18:72. [PMID: 28077090 PMCID: PMC5225503 DOI: 10.1186/s12864-016-3383-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. RESULTS We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. CONCLUSIONS This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane.
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Affiliation(s)
- Thiago Willian Almeida Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Guilherme da Silva Pereira
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Rodrigo Gazaffi
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Fernanda Zatti Barreto
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Carina Oliveira Anoni
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Cláudio Benício Cardoso-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Estela Araújo Costa
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Melina Cristina Mancini
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Hermann Paulo Hoffmann
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Avenida Monteiro Lobato 255, Campinas, CEP 13083-862 São Paulo Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Avenida Candido Rondon 400, Campinas, CEP 13083-875 São Paulo Brazil
| | - Antonio Augusto Franco Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias 11, Piracicaba, CEP 13418-900 São Paulo Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, Araras, CEP 13600-970 São Paulo Brazil
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