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Giraldeli AL, Silva AFM, Silva GSD, Araújo LDS, Baccin LC, Ghirardello GA, Victoria Filho R. Herbicides in the initial growth and chlorophyll indices of sugarcane in pre-sprouted seedlings. J Environ Sci Health B 2024; 59:223-232. [PMID: 38526555 DOI: 10.1080/03601234.2024.2331946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
The aim of the present study was to assess the selectivity of herbicides applied in the pre and post-planting of pre-sprouted seedlings (PSS). The experiment was conducted in a greenhouse, using a completely randomized design, with nine treatments and four repetitions. The IACSP95-5000 cultivar was used. The treatments consisted of herbicides applied in five doses as follows: in pre-planting: sulfentrazone, diclosulam, imazapic, and imazapyr, in post-planting: ethoxysulfuron, halosulfuron, 2,4-D and MSMA, and a control treatment without herbicide. Injury symptoms were assessed at 7, 15, 30, 45, 60, 75, and 90 days after application (DAA), height, diameter, number of tillers, chlorophyll A, B, and total chlorophyll at 30, 60, and 90 DAA, leaf area, shoot and root dry mass at 90 DAA. The post-emergent herbicides were considered selective. Pre-planting herbicides reduced the variables assessed at 90 DAA, observed by linear regression for diclosulam and imazapic, and exponential regression for imazapyr. Treatments with sulfentrazone caused few injury symptoms, with subsequent recovery. In addition, all the variables analyzed were equal to control, with the sulfentrazone considered selective for the IACSP95-5000 cultivar.
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Affiliation(s)
- Ana Ligia Giraldeli
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
- State University of Londrina, Londrina, Brazil
| | - André Felipe Moreira Silva
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
- Crop Pesquisa, Maripá, Brazil
| | - Gustavo Soares da Silva
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
- FMC Agrícola, Paulínia, Brazil
| | - Lucas da Silva Araújo
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
- Instituto Phytus, Formosa, Brazil
| | - Luísa Carolina Baccin
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | | | - Ricardo Victoria Filho
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
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2
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Araujo MAD, Melo AARD, Silva VM, Reis ARD. Selenium enhances ROS scavenging systems and sugar metabolism increasing growth of sugarcane plants. Plant Physiol Biochem 2023; 201:107798. [PMID: 37301189 DOI: 10.1016/j.plaphy.2023.107798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
Selenium (Se) beneficial effect on plants is related to an increase in nitrogen (N) assimilation and its role as an abiotic stress mitigator by reactive oxygen species (ROS) scavenging enhanced by antioxidant metabolism. This study aimed to evaluate sugarcane (Saccharum spp.) growth, photosynthetic and antioxidant responses, and sugar accumulation in response to Se supply. The experimental design was a factorial scheme 2 × 4: two sugarcane varieties (RB96 6928 and RB86 7515) and four Se application rates (0; 5; 10 and 20 μmol L-1) applied as sodium selenate in the nutrient solution. Leaf Se concentration increased under Se application in both varieties. The enzymes SOD (EC 1.15.1.1) and APX (EC 1.11.1.11) showed increase activities under Se application on variety RB96 6928. Nitrate reductase activity increased in both varieties resulting in the conversion of nitrate into higher total amino acids concentration indicating an enhanced N assimilation. This led to an increased concentration of chlorophylls and carotenoids, increased CO2 assimilation rate, stomatal conductance, and internal CO2 concentration. Selenium provided higher starch accumulation and sugar profiles in leaves boosting plant growth. This study shows valuable information regarding the role of Se on growth, photosynthetic process, and sugar accumulation in sugarcane leaves, which could be used for further field experiments. The application rate of 10 μmol Se L-1 was the most adequate for both varieties studied considering the sugar concentration and plant growth.
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Affiliation(s)
| | | | - Vinicius Martins Silva
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), 14884-900 Jaboticabal, SP, Brazil
| | - André Rodrigues Dos Reis
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), Rua Domingos da Costa Lopes 780, 17602-496 Tupã, SP, Brazil.
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3
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Almeida FA, Passamani LZ, Santa-Catarina C, Mooney BP, Thelen JJ, Silveira V. Label-Free Quantitative Phosphoproteomics Reveals Signaling Dynamics Involved in Embryogenic Competence Acquisition in Sugarcane. J Proteome Res 2020; 19:4145-4157. [PMID: 32964716 DOI: 10.1021/acs.jproteome.0c00652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, a label-free quantitative phosphoproteomic analysis was performed to identify and quantify signaling events related to the acquisition of embryogenic competence in sugarcane. Embryogenic and nonembryogenic calli were compared at the multiplication phase, resulting in the identification of 163 phosphoproteins unique to embryogenic calli, 9 unique to nonembryogenic calli, and 51 upregulated and 40 downregulated in embryogenic calli compared to nonembryogenic calli. Data are available via ProteomeXchange with identifier PXD018054. Motif-x analysis revealed the enrichment of [xxxpSPxxx], [RxxpSxxx], and [xxxpSDxxx] motifs, which are predicted phosphorylation sites for several kinases related to stress responses. The embryogenic-related phosphoproteins (those unique and upregulated in embryogenic calli) identified in the present study are related to abscisic acid-induced signaling and abiotic stress response; they include OSK3, ABF1, LEAs, and RD29Bs. On the other hand, the nonembryogenic-related phosphoproteins EDR1 and PP2Ac-2 are negative regulators of abscisic acid signaling, suggesting a relationship between phosphoproteins involved in the abscisic acid and stress responses in the acquisition of embryogenic competence. Moreover, embryogenic-related phosphoproteins associated with epigenetic modifications, such as HDA6, HDA19, and TOPLESS, and with RNA metabolism, including AGO1, DEAH5, SCL30, UB2C, and SR45, were identified to play potential roles in embryogenic competence. These results reveal novel phosphorylation sites for several proteins and identify potential candidate biomarkers for the acquisition of embryogenic competence in sugarcane.
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Affiliation(s)
- Felipe A Almeida
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Lucas Z Passamani
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual, CBB-UENF, Campos dos Goytacazes 28013-602, Rio de Janeiro, Brazil
| | - Brian P Mooney
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Jay J Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, 65211 Columbia, Missouri, United States
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, Rio de Janeiro, Brazil.,Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Av. Alberto Lamego, 2000, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
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Liu X, Yin Z, Liu Y, Li Z, Yan M, Que Y, Xu L, Zhou D. The complete mitochondrial genome of sugarcane ( Saccharum spp.) variety FN15. Mitochondrial DNA B Resour 2020; 5:2163-2165. [PMID: 33366953 PMCID: PMC7510754 DOI: 10.1080/23802359.2020.1768926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022]
Abstract
The complete mitogenome of Saccharum spp. hybrid FN15 was successfully sequenced. It contains two distinct circular chromosomes, Chromosome 1 and Chromosome 2. The former is 301,533 bp in length with the GC content of 43.90%, and 7.12% of genome (21,468 nucleotides) are coding DNA while 92.88% of genome (280,065 nucleotides) are intergenic region. The latter is 144,744 bp in length with the GC content of 43.57%, and 8.20% of genome (11,865 nucleotides) are coding DNA and 91.80% of genome (132,879 nucleotides) are intergenic region. Besides, Chromosome 1 contains 22 protein-coding genes (four atp genes, three ccm genes, three cox genes, one mat gene, one mtt gene, six nad genes and four rps genes), and 21 non-coding genes (15 tRNA and six rRNAs), whereas in Chromosome 2, there are 13 protein-coding genes (two atp genes, one ccm gene, one cob gene, one cox gene, one rpl gene, four nad genes and three rps genes) and five tRNA genes. Maximum Likelihood phylogenetic analysis demonstrated that FN15 is close with S. spp. hybrid ROC22, S. officinarum Khon Kaen 3 and S. bicolor species. This complete mitochondrial genome will provide essential DNA molecular data for further phylogenetic and evolutionary analysis for Saccharum.
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Affiliation(s)
- Xiaolan Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Ze Yin
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Ying Liu
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China
| | - Zhu Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, College of Hunan Province, Xiangtan, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dinggang Zhou
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan, China.,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture/National Engineering Research Center for Sugarcane, Ministry of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-polluted Soils, College of Hunan Province, Xiangtan, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan CKK, Staňková H, Batley J, Šimková H, Doležel J, Edwards D. An efficient approach to BAC based assembly of complex genomes. Plant Methods 2016; 12:2. [PMID: 26793268 PMCID: PMC4719536 DOI: 10.1186/s13007-016-0107-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/08/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. RESULTS We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. CONCLUSIONS We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.
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Affiliation(s)
- Paul Visendi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, P. O. Box 30197, Nairobi, 00100 Kenya
| | | | - Satomi Hayashi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Agnieszka A. Golicz
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Philipp E. Bayer
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Pradeep Ruperao
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Bhavna Hurgobin
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Juan Montenegro
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chon-Kit Kenneth Chan
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Helena Staňková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jacqueline Batley
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - David Edwards
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
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8
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Silva KI, Sales CRG, Marchiori PER, Silveira NM, Machado EC, Ribeiro RV. Short-term physiological changes in roots and leaves of sugarcane varieties exposed to H2O2 in root medium. J Plant Physiol 2015; 177:93-99. [PMID: 25703773 DOI: 10.1016/j.jplph.2015.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
The aim of this study was to evaluate the differential sensitivity of sugarcane genotypes to H2O2 in root medium. As a hypothesis, the drought tolerant genotype would be able to minimize the oxidative damage and maintain the water transport from roots to shoots, reducing the negative effects on photosynthesis. The sugarcane genotypes IACSP94-2094 (drought tolerant) and IACSP94-2101 (drought sensitive) were grown in a growth chamber and exposed to three levels of H2O2 in nutrient solution: control; 3 mmol L(-1) and 80 mmol L(-1). Leaf gas exchange, photochemical activity, root hydraulic conductance (Lr) and antioxidant metabolism in both roots and leaves were evaluated after 15 min of treatment with H2O2. Although, root hydraulic conductance, stomatal aperture, apparent electron transport rate and instantaneous carboxylation efficiency have been reduced by H2O2 in both genotypes, IACSP94-2094 presented higher values of those variables as compared to IACSP94-2101. There was a significant genotypic variation in relation to the physiological responses of sugarcane to increasing H2O2 in root tissues, being root changes associated with modifications in plant shoots. IACSP94-2094 presented a root antioxidant system more effective against H2O2 in root medium, regardless H2O2 concentration. Under low H2O2 concentration, water transport and leaf gas exchange of IACSP94-2094 were less affected as compared to IACSP94-2101. Under high H2O2 concentration, the lower sensitivity of IACSP94-2094 was associated with increases in superoxide dismutase activity in roots and leaves and increases in catalase activity in roots. In conclusion, we propose a general model of sugarcane reaction to H2O2, linking root and shoot physiological responses.
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Affiliation(s)
- Karina I Silva
- Graduate Program in Tropical and Subtropical Agriculture, Agronomic Institute (IAC), Campinas, SP, Brazil; Laboratory of Plant Physiology "Coaracy M. Franco", Center R&D in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Cristina R G Sales
- Graduate Program in Tropical and Subtropical Agriculture, Agronomic Institute (IAC), Campinas, SP, Brazil; Laboratory of Plant Physiology "Coaracy M. Franco", Center R&D in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Paulo E R Marchiori
- Graduate Program in Tropical and Subtropical Agriculture, Agronomic Institute (IAC), Campinas, SP, Brazil; Laboratory of Plant Physiology "Coaracy M. Franco", Center R&D in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Neidiquele M Silveira
- Graduate Program in Tropical and Subtropical Agriculture, Agronomic Institute (IAC), Campinas, SP, Brazil; Laboratory of Plant Physiology "Coaracy M. Franco", Center R&D in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Eduardo C Machado
- Laboratory of Plant Physiology "Coaracy M. Franco", Center R&D in Ecophysiology and Biophysics, IAC, Campinas, SP, Brazil
| | - Rafael V Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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9
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Calderan-Rodrigues MJ, Jamet E, Bonassi MBCR, Guidetti-Gonzalez S, Begossi AC, Setem LV, Franceschini LM, Fonseca JG, Labate CA. Cell wall proteomics of sugarcane cell suspension cultures. Proteomics 2014; 14:738-49. [PMID: 24436144 DOI: 10.1002/pmic.201300132] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 11/10/2013] [Accepted: 12/01/2013] [Indexed: 12/21/2022]
Abstract
The use of cell walls to produce cellulosic ethanol from sugarcane bagasse is a new challenge. A better knowledge of proteins involved in cell wall remodelling is essential to improve the saccharification processes. Cell suspension cultures were used for this first cell wall proteomics study of sugarcane. Proteins extracted from cell walls were identified using an adapted protocol. They were extracted using 0.2 M CaCl2 and 2 M LiCl after purification of cell walls. The proteins were then identified by the innovative nanoACQUITY UPLC MS/MS technology and bioinformatics using the translated SUCEST EST cluster database of sugarcane. The experiments were reproduced three times. Since Sorghum bicolor is the closest plant with a fully sequenced genome, homologous proteins were searched for to complete the annotation of proteins, that is, prediction of subcellular localization and functional domains. Altogether, 69 different proteins predicted to be secreted were identified among 377 proteins. The reproducibility of the experiments is discussed. These proteins were distributed into eight functional classes. Oxidoreductases such as peroxidases were well represented, whereas glycoside hydrolases were scarce. This work provides information about the proteins that could be manipulated through genetic transformation, to increase second-generation ethanol production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba-SP, Brazil
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10
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Pierre JS, Rae AL, Bonnett GD. Abiotic Limits for Germination of Sugarcane Seed in Relation to Environmental Spread. Trop Plant Biol 2014; 7:100-110. [PMID: 25485029 PMCID: PMC4245482 DOI: 10.1007/s12042-014-9141-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/08/2014] [Indexed: 06/04/2023]
Abstract
Sugarcane is a vegetatively propagated crop and hence the production of seed and its fate in the environment has not been studied. The recent development of genetically modified sugarcane, with the aim of commercial production, requires a research effort to understand sugarcane reproductive biology. This study contributes to this understanding by defining the abiotic limits for sugarcane seed germination. Using seed from multiple genetic crosses, germination was measured under different light regimes (light and dark), temperatures (from 18 °C to 42 °C) and water potentials (from 0 MPa to -1 MPa); cardinal temperatures and base water potential of germination were estimated based on the rates of germination. We found that sugarcane seed could germinate over a broad range of temperatures (from 11 °C to 42 °C) with optima ranging from 27 °C to 36 °C depending on source of seed. Water potentials below -0.5 MPa halved the proportion of seed that germinated. By comparing these limits to the environmental conditions in areas where sugarcane grows and has the potential to produce seed, water, but not temperature, will be the main limiting factor for germination. This new information can be taken into account when evaluating any risk of weediness during the assessment of GM sugarcane.
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Affiliation(s)
- J. S. Pierre
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, Qld 4067 Australia
| | - A. L. Rae
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, Qld 4067 Australia
| | - G. D. Bonnett
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, Qld 4067 Australia
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11
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Grativol C, Regulski M, Bertalan M, McCombie WR, da Silva FR, Neto AZ, Vicentini R, Farinelli L, Hemerly AS, Martienssen RA, Ferreira PCG. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. Plant J 2014; 79:162-72. [PMID: 24773339 PMCID: PMC4458261 DOI: 10.1111/tpj.12539] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 05/21/2023]
Abstract
Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.
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Affiliation(s)
- Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Michael Regulski
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Marcelo Bertalan
- Institute of Biological Psychiatry Mental Health Center, Sct. Hans MHS - Capital Region of Denmark Boserupvej, DK-4000 Roskilde, Denmark
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Felipe Rodrigues da Silva
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724, USA
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
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