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Healey AL, Garsmeur O, Lovell JT, Shengquiang S, Sreedasyam A, Jenkins J, Plott CB, Piperidis N, Pompidor N, Llaca V, Metcalfe CJ, Doležel J, Cápal P, Carlson JW, Hoarau JY, Hervouet C, Zini C, Dievart A, Lipzen A, Williams M, Boston LB, Webber J, Keymanesh K, Tejomurthula S, Rajasekar S, Suchecki R, Furtado A, May G, Parakkal P, Simmons BA, Barry K, Henry RJ, Grimwood J, Aitken KS, Schmutz J, D'Hont A. The complex polyploid genome architecture of sugarcane. Nature 2024; 628:804-810. [PMID: 38538783 PMCID: PMC11041754 DOI: 10.1038/s41586-024-07231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024]
Abstract
Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
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Affiliation(s)
- A L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - O Garsmeur
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - J T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Shengquiang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - A Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - C B Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - N Piperidis
- Sugar Research Australia, Te Kowai, Queensland, Australia
| | - N Pompidor
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - V Llaca
- Corteva Agriscience, Johnston, IA, USA
| | - C J Metcalfe
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - P Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - J W Carlson
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Y Hoarau
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- ERCANE, Sainte-Clotilde, La Réunion, France
| | - C Hervouet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Zini
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Dievart
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - A Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - L B Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - J Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Tejomurthula
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - S Rajasekar
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - R Suchecki
- CSIRO Agriculture and Food, Urrbrae, South Australia, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - G May
- Corteva Agriscience, Johnston, IA, USA
| | | | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - K Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, Queensland, Australia
| | - J Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - K S Aitken
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - J Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - A D'Hont
- CIRAD, UMR AGAP Institut, Montpellier, France.
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Maniero RA, Koltun A, Vitti M, Factor BG, de Setta N, Câmara AS, Lima JE, Figueira A. Identification and functional characterization of the sugarcane ( Saccharum spp.) AMT2-type ammonium transporter ScAMT3;3 revealed a presumed role in shoot ammonium remobilization. FRONTIERS IN PLANT SCIENCE 2023; 14:1299025. [PMID: 38098795 PMCID: PMC10720369 DOI: 10.3389/fpls.2023.1299025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023]
Abstract
Sugarcane (Saccharum spp.) is an important crop for sugar and bioethanol production worldwide. To maintain and increase sugarcane yields in marginal areas, the use of nitrogen (N) fertilizers is essential, but N overuse may result in the leaching of reactive N to the natural environment. Despite the importance of N in sugarcane production, little is known about the molecular mechanisms involved in N homeostasis in this crop, particularly regarding ammonium (NH4 +), the sugarcane's preferred source of N. Here, using a sugarcane bacterial artificial chromosome (BAC) library and a series of in silico analyses, we identified an AMMONIUM TRANSPORTER (AMT) from the AMT2 subfamily, sugarcane AMMONIUM TRANSPORTER 3;3 (ScAMT3;3), which is constitutively and highly expressed in young and mature leaves. To characterize its biochemical function, we ectopically expressed ScAMT3;3 in heterologous systems (Saccharomyces cerevisiae and Arabidopsis thaliana). The complementation of triple mep mutant yeast demonstrated that ScAMT3;3 is functional for NH3/H+ cotransport at high availability of NH4 + and under physiological pH conditions. The ectopic expression of ScAMT3;3 in the Arabidopsis quadruple AMT knockout mutant restored the transport capacity of 15N-NH4 + in roots and plant growth under specific N availability conditions, confirming the role of ScAMT3;3 in NH4 + transport in planta. Our results indicate that ScAMT3;3 belongs to the low-affinity transport system (Km 270.9 µM; Vmax 209.3 µmol g-1 root DW h-1). We were able to infer that ScAMT3;3 plays a presumed role in NH4 + source-sink remobilization in the shoots via phloem loading. These findings help to shed light on the functionality of a novel AMT2-type protein and provide bases for future research focusing on the improvement of sugarcane yield and N use efficiency.
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Affiliation(s)
- Rodolfo A. Maniero
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Alessandra Koltun
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marielle Vitti
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Bruna G. Factor
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Amanda S. Câmara
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Joni E. Lima
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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Meng Z, Wang F, Xie Q, Li R, Shen H, Li H. Reconstruction of karyotypic evolution in Saccharum spontaneum species by comparative oligo-FISH mapping. BMC PLANT BIOLOGY 2022; 22:599. [PMID: 36539690 PMCID: PMC9764494 DOI: 10.1186/s12870-022-04008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. RESULTS In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012-46 (x = 9, hexaploid) and AP85-441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. CONCLUSIONS Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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4
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Senthilkumar S, Vinod KK, Parthiban S, Thirugnanasambandam P, Lakshmi Pathy T, Banerjee N, Sarath Padmanabhan TS, Govindaraj P. Identification of potential MTAs and candidate genes for juice quality- and yield-related traits in Saccharum clones: a genome-wide association and comparative genomic study. Mol Genet Genomics 2022; 297:635-654. [PMID: 35257240 DOI: 10.1007/s00438-022-01870-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/06/2022] [Indexed: 11/30/2022]
Abstract
Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop.
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Affiliation(s)
- Shanmugavel Senthilkumar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Selvaraj Parthiban
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | | | - Thalambedu Lakshmi Pathy
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - Nandita Banerjee
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh, 226002, India
| | | | - P Govindaraj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
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Yu F, Zhao X, Chai J, Ding X, Li X, Huang Y, Wang X, Wu J, Zhang M, Yang Q, Deng Z, Jiang J. Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. THE NEW PHYTOLOGIST 2022; 233:1953-1965. [PMID: 34874076 DOI: 10.1111/nph.17905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species. Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligo-based chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus. We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species. We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.
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Affiliation(s)
- Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Xinwang Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jin Chai
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueer Ding
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Xianhong Wang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Muqing Zhang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Qinghui Yang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
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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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7
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Pompidor N, Charron C, Hervouet C, Bocs S, Droc G, Rivallan R, Manez A, Mitros T, Swaminathan K, Glaszmann JC, Garsmeur O, D’Hont A. Three founding ancestral genomes involved in the origin of sugarcane. ANNALS OF BOTANY 2021; 127:827-840. [PMID: 33637991 PMCID: PMC8103802 DOI: 10.1093/aob/mcab008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. METHODS To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. KEY RESULTS The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. CONCLUSIONS This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.
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Affiliation(s)
- Nicolas Pompidor
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Carine Charron
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurore Manez
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Jean-Christophe Glaszmann
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- For correspondence. E-mail
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8
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Voss-Fels KP, Wei X, Ross EM, Frisch M, Aitken KS, Cooper M, Hayes BJ. Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1493-1511. [PMID: 33587151 DOI: 10.1007/s00122-021-03785-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 01/27/2021] [Indexed: 05/14/2023]
Abstract
Simulations highlight the potential of genomic selection to substantially increase genetic gain for complex traits in sugarcane. The success rate depends on the trait genetic architecture and the implementation strategy. Genomic selection (GS) has the potential to increase the rate of genetic gain in sugarcane beyond the levels achieved by conventional phenotypic selection (PS). To assess different implementation strategies, we simulated two different GS-based breeding strategies and compared genetic gain and genetic variance over five breeding cycles to standard PS. GS scheme 1 followed similar routines like conventional PS but included three rapid recurrent genomic selection (RRGS) steps. GS scheme 2 also included three RRGS steps but did not include a progeny assessment stage and therefore differed more fundamentally from PS. Under an additive trait model, both simulated GS schemes achieved annual genetic gains of 2.6-2.7% which were 1.9 times higher compared to standard phenotypic selection (1.4%). For a complex non-additive trait model, the expected annual rates of genetic gain were lower for all breeding schemes; however, the rates for the GS schemes (1.5-1.6%) were still greater than PS (1.1%). Investigating cost-benefit ratios with regard to numbers of genotyped clones showed that substantial benefits could be achieved when only 1500 clones were genotyped per 10-year breeding cycle for the additive genetic model. Our results show that under a complex non-additive genetic model, the success rate of GS depends on the implementation strategy, the number of genotyped clones and the stage of the breeding program, likely reflecting how changes in QTL allele frequencies change additive genetic variance and therefore the efficiency of selection. These results are encouraging and motivate further work to facilitate the adoption of GS in sugarcane breeding.
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Affiliation(s)
- Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Giessen, Germany
| | - Karen S Aitken
- Agriculture and Food, CSIRO, QBP, St. Lucia, QLD, 4067, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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9
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Aono AH, Costa EA, Rody HVS, Nagai JS, Pimenta RJG, Mancini MC, Dos Santos FRC, Pinto LR, Landell MGDA, de Souza AP, Kuroshu RM. Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. Sci Rep 2020; 10:20057. [PMID: 33208862 PMCID: PMC7676261 DOI: 10.1038/s41598-020-77063-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and for sugarcane, brown rust resistance is a desirable characteristic due to the large economic impact of the disease. Although marker-assisted selection for rust resistance has been successful, the genes involved are still unknown, and the associated regions vary among cultivars, thus restricting methodological generalization. We used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes. We established a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning. We identified 14,540 SNPs, which led to a mean prediction accuracy of 50% when using different models. We also tested feature selection algorithms to increase predictive accuracy, resulting in a reduced dataset with more explanatory power for rust phenotypes. As a result of this approach, we achieved an accuracy of up to 95% with a dataset of 131 SNPs related to brown rust QTL regions and auxiliary genes. Therefore, our novel strategy has the potential to assist studies of the genomic organization of brown rust resistance in sugarcane.
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Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Estela Araujo Costa
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Hugo Vianna Silva Rody
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - James Shiniti Nagai
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Ricardo José Gonzaga Pimenta
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Melina Cristina Mancini
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, SP, Brazil
| | | | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Department of Plant Biology, Institute of Biology (IB), University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (UNIFESP), São José dos Campos, SP, Brazil.
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10
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Ma P, Zhang X, Chen L, Zhao Q, Zhang Q, Hua X, Wang Z, Tang H, Yu Q, Zhang M, Ming R, Zhang J. Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum. BMC PLANT BIOLOGY 2020; 20:422. [PMID: 32928111 PMCID: PMC7488781 DOI: 10.1186/s12870-020-02599-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. RESULTS In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. CONCLUSIONS SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.
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Affiliation(s)
- Panpan Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lanping Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qian Zhao
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Muqing Zhang
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
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11
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You Q, Yang X, Peng Z, Islam MS, Sood S, Luo Z, Comstock J, Xu L, Wang J. Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2829-2845. [PMID: 31321474 DOI: 10.1007/s00122-019-03391-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/05/2019] [Indexed: 05/13/2023]
Abstract
An Axiom Sugarcane100K SNP array has been designed and successfully utilized to construct the sugarcane genetic map and to identify the QTLs associated with SCYLV resistance. To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single-nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single-dose (SD) SNPs and 68,648 low-dosage (33,277 SD and 35,371 double dose) SNPs from two datasets, respectively, were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This array was used to genotype 469 sugarcane clones, including one F1 population derived from the cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3482 SD SNP markers spanning 3336 cM, a map for IND81-146 with 1513 SD SNP markers spanning 2615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3651 cM. Quantitative trait loci (QTL) analysis identified 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease-resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high-throughput genotyping in highly polyploid sugarcane.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | | | - Sushma Sood
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jack Comstock
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350001, Fujian, China.
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12
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Nascimento LC, Yanagui K, Jose J, Camargo ELO, Grassi MCB, Cunha CP, Bressiani JA, Carvalho GMA, Carvalho CR, Prado PF, Mieczkowski P, Pereira GAG, Carazzolle MF. Unraveling the complex genome of Saccharum spontaneum using Polyploid Gene Assembler. DNA Res 2019; 26:205-216. [PMID: 30768175 PMCID: PMC6589550 DOI: 10.1093/dnares/dsz001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/21/2019] [Indexed: 12/01/2022] Open
Abstract
The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencing.
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Affiliation(s)
- Leandro Costa Nascimento
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Laboratório Central de Tecnologias de Alto Desempenho (LaCTAD), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Karina Yanagui
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliana Jose
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Eduardo L O Camargo
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Biocelere Agroindustrial Ltda, GranBio Investimentos S.A., Campinas, SP, Brazil
| | - Maria Carolina B Grassi
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Camila P Cunha
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisas em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | | | - Guilherme M A Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Paula F Prado
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gonçalo A G Pereira
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e bioEnergia (LGE), Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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13
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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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14
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Zhang J, Zhang Q, Li L, Tang H, Zhang Q, Chen Y, Arrow J, Zhang X, Wang A, Miao C, Ming R. Recent polyploidization events in three Saccharum founding species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:264-274. [PMID: 29878497 PMCID: PMC6330536 DOI: 10.1111/pbi.12962] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/21/2018] [Accepted: 06/04/2018] [Indexed: 05/07/2023]
Abstract
The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F1 individuals derived from S. officinarumLA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole-genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole-genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long-standing hypothesis and clarified the timing of speciation and whole-genome duplication events in Saccharum.
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Affiliation(s)
- Jisen Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Qing Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Leiting Li
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Haibao Tang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhanChina
| | - Yang Chen
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Jie Arrow
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Xingtan Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Aiqin Wang
- State Key Lab for Conservation and Utilization of Subtropical Agro‐biological ResourcesGuangxi UniversityNanningChina
| | - Chenyong Miao
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ray Ming
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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15
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Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet 2018; 50:1565-1573. [DOI: 10.1038/s41588-018-0237-2] [Citation(s) in RCA: 288] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/15/2018] [Indexed: 01/13/2023]
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16
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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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17
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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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18
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Mancini MC, Cardoso-Silva CB, Sforça DA, Pereira de Souza A. "Targeted Sequencing by Gene Synteny," a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region. FRONTIERS IN PLANT SCIENCE 2018; 9:397. [PMID: 29643861 PMCID: PMC5882829 DOI: 10.3389/fpls.2018.00397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/12/2018] [Indexed: 05/25/2023]
Abstract
Sugarcane exhibits a complex genome mainly due to its aneuploid nature and high ploidy level, and sequencing of its genome poses a great challenge. Closely related species with well-assembled and annotated genomes can be used to help assemble complex genomes. Here, a stable quantitative trait locus (QTL) related to sugar accumulation in sorghum was successfully transferred to the sugarcane genome. Gene sequences related to this QTL were identified in silico from sugarcane transcriptome data, and molecular markers based on these sequences were developed to select bacterial artificial chromosome (BAC) clones from the sugarcane variety SP80-3280. Sixty-eight BAC clones containing at least two gene sequences associated with the sorghum QTL were sequenced using Pacific Biosciences (PacBio) technology. Twenty BAC sequences were found to be related to the syntenic region, of which nine were sufficient to represent this region. The strategy we propose is called "targeted sequencing by gene synteny," which is a simpler approach to understanding the genome structure of complex genomic regions associated with traits of interest.
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Affiliation(s)
- Melina C. Mancini
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | | | - Danilo A. Sforça
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering, University of Campinas, Campinas, Brazil
- Departament Plant Biology, Biology Institute, University of Campinas, Campinas, Brazil
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19
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Thirugnanasambandam PP, Hoang NV, Henry RJ. The Challenge of Analyzing the Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:616. [PMID: 29868072 PMCID: PMC5961476 DOI: 10.3389/fpls.2018.00616] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 05/04/2023]
Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
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Affiliation(s)
- Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Prathima P. Thirugnanasambandam,
| | - Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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20
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Wang HB, Chen PH, Yang YQ, D'Hont A, Lu YH. Molecular insights into the origin of the brown rust resistance gene Bru1 among Saccharum species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2431-2443. [PMID: 28821913 DOI: 10.1007/s00122-017-2968-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Analysis of 387 sugarcane clones using Bru 1 diagnostic markers revealed two possible sources of Bru 1 in Chinese cultivars: one from Saccharum spontaneum and another from Saccharum robustum of New Guinea. Sugarcane brown rust (SBR) is an important fungal disease in many sugarcane production areas around the world, and can cause considerable yield losses in susceptible sugarcane cultivars. One major SBR resistance gene, named Bru1, initially identified from cultivar R570, was shown to be a major SBR resistance source in most of the sugarcane producing areas of the world. In this study, by using the two Bru1-associated markers, R12H16 and 9O20-F4, we surveyed the presence of Bru1 in a Chinese sugarcane germplasm collection of 387 clones, consisting of 228 hybrid cultivars bred by different Chinese sugarcane breeding establishments, 54 exotic hybrid cultivars introduced from other countries and 105 clones of sugarcane ancestral species. The Bru1-bearing haplotype was detected in 43.4% of Chinese sugarcane cultivars, 20.4% of exotic hybrid cultivars, and only 3.8% of ancestral species. Among the 33 Chinese cultivars for which phenotypes of resistance to SBR were available, Bru1 was present in 69.2% (18/26) of the resistant clones. Analyses of the allelic sequence variations of R12H16 and 9O20-F4 suggested two possible sources of Bru1 in Chinese cultivars: one from S. spontaneum and another from S. robustum of New Guinea. In addition, we developed an improved Bru1 diagnostic marker, 9O20-F4-HaeIII, which can eliminate all the false results of 9O20-F4-RsaI observed among S. spontaneum, as well as a new dominant Bru1 diagnostic marker, R12E03-2, from the BAC ShCIR12E03. Our results provide valuable information for further efforts of breeding SBR-resistant varieties, searching new SBR resistance sources and cloning of Bru1 in sugarcane.
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Affiliation(s)
- Heng-Bo Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | - Ping-Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China
| | | | - Yun-Hai Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of Ministry of Agriculture for Sugarcane Biology and Genetic Breeding, College of Crop Science, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, People's Republic of China.
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21
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Vilela MDM, Del Bem LE, Van Sluys MA, de Setta N, Kitajima JP, Cruz GMQ, Sforça DA, de Souza AP, Ferreira PCG, Grativol C, Cardoso-Silva CB, Vicentini R, Vincentz M. Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum. Genome Biol Evol 2017; 9:266-278. [PMID: 28082603 PMCID: PMC5381655 DOI: 10.1093/gbe/evw293] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 12/23/2022] Open
Abstract
Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.
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Affiliation(s)
- Mariane de Mendonça Vilela
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Luiz Eduardo Del Bem
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC (UFABC), São Bernardo do Campo, SP, Brazil
| | | | | | - Danilo Augusto Sforça
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Parque Califórnia, Campos dos Goytacazes, RJ, Brazil
| | - Claudio Benicio Cardoso-Silva
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
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22
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Racedo J, Gutiérrez L, Perera MF, Ostengo S, Pardo EM, Cuenya MI, Welin B, Castagnaro AP. Genome-wide association mapping of quantitative traits in a breeding population of sugarcane. BMC PLANT BIOLOGY 2016; 16:142. [PMID: 27342657 PMCID: PMC4921039 DOI: 10.1186/s12870-016-0829-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/14/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. Previous sugarcane genome-wide association analyses (GWAS) have found few molecular markers associated with relevant traits at plant-cane stage. The aim of this study was to establish an appropriate GWAS to find molecular markers associated with yield related traits consistent across harvesting seasons in a breeding population. Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY) and sugar content (SC) at two locations during three successive crop cycles. GWAS mapping was applied within a novel mixed-model framework accounting for population structure with Principal Component Analysis scores as random component. RESULTS A total of 43 markers significantly associated with CY in plant-cane, 42 in first ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were associated with CY in 2 years. Additionally, 38 significant associations for SC were detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker-trait association was found significant for the 3 years of the study, while twelve markers presented association for 2 years. In the multi-QTL model several markers with large allelic substitution effect were found. Sequences of four DArT markers showed high similitude and e-value with coding sequences of Sorghum bicolor, confirming the high gene microlinearity between sorghum and sugarcane. CONCLUSIONS In contrast with other sugarcane GWAS studies reported earlier, the novel methodology to analyze multi-QTLs through successive crop cycles used in the present study allowed us to find several markers associated with relevant traits. Combining existing phenotypic trial data and genotypic DArT and TRAP marker characterizations within a GWAS approach including population structure as random covariates may prove to be highly successful. Moreover, sequences of DArT marker associated with the traits of interest were aligned in chromosomal regions where sorghum QTLs has previously been reported. This approach could be a valuable tool to assist the improvement of sugarcane and better supply sugarcane demand that has been projected for the upcoming decades.
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Affiliation(s)
- Josefina Racedo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Lucía Gutiérrez
- />Departamento de Biometría, Estadística y Cómputos, Facultad de Agronomía, Universidad de la República, Garzón 780, 12900 Montevideo, Uruguay
- />Agronomy Department, University of Wisconsin – Madison, 1575 Linden Dr., Madison, WI 53706 USA
| | - María Francisca Perera
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Santiago Ostengo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Esteban Mariano Pardo
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - María Inés Cuenya
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Bjorn Welin
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
| | - Atilio Pedro Castagnaro
- />Estación Experimental Agroindustrial Obispo Colombres (EEAOC)- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Av. William Cross 3150, Las Talitas, T4101XAC Tucumán Argentina
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23
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Zhang J, Sharma A, Yu Q, Wang J, Li L, Zhu L, Zhang X, Chen Y, Ming R. Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics 2016; 17:446. [PMID: 27287040 PMCID: PMC4902974 DOI: 10.1186/s12864-016-2817-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 06/07/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum, 10-20 % S. spontaneum, and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. RESULTS To investigate the origin and evolution of haplotypes in the Bru1 genomic regions in sugarcane cultivars, we identified two BAC clones from S. spontaneum and four from S. officinarum and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from S. officinarum, two from S. spontaneum and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33.7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitor genomes. Tajima's D analysis revealed that S. spontaneum hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. CONCLUSIONS This is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from S. spontaneum. Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of S. spontaneum and S. officinarum haplotype in Saccharum hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in Saccharum hybrids after hybridization. The combined minimum difference at 19.5 % among homologous chromosomes in S. officinarum would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid Saccharum genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.
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Affiliation(s)
- Jisen Zhang
- />FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
- />College of Life Sciences, Fujian Normal University, Fuzhou, 350108 China
- />Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Anupma Sharma
- />Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX 75252 USA
| | - Qingyi Yu
- />FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
- />Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX 75252 USA
| | - Jianping Wang
- />FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
- />Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL 32610 USA
| | - Leiting Li
- />Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- />College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095 China
| | - Lin Zhu
- />Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- />College of Plant Science, Jilin University, Changchun, Jilin 130062 China
| | - Xingtan Zhang
- />FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
| | - Youqiang Chen
- />College of Life Sciences, Fujian Normal University, Fuzhou, 350108 China
| | - Ray Ming
- />FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China
- />Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Singh RK, Banerjee N, Khan MS, Yadav S, Kumar S, Duttamajumder SK, Lal RJ, Patel JD, Guo H, Zhang D, Paterson AH. Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping. Mol Genet Genomics 2016; 291:1363-77. [DOI: 10.1007/s00438-016-1190-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
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Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane. PLoS One 2015; 10:e0134586. [PMID: 26226299 PMCID: PMC4520453 DOI: 10.1371/journal.pone.0134586] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/10/2015] [Indexed: 11/29/2022] Open
Abstract
Histones are the main structural components of the nucleosome, hence targets of many regulatory proteins that mediate processes involving changes in chromatin. The functional outcome of many pathways is “written” in the histones in the form of post-translational modifications that determine the final gene expression readout. As a result, modifications, alone or in combination, are important determinants of chromatin states. Histone modifications are accomplished by the addition of different chemical groups such as methyl, acetyl and phosphate. Thus, identifying and characterizing these modifications and the proteins related to them is the initial step to understanding the mechanisms of gene regulation and in the future may even provide tools for breeding programs. Several studies over the past years have contributed to increase our knowledge of epigenetic gene regulation in model organisms like Arabidopsis, yet this field remains relatively unexplored in crops. In this study we identified and initially characterized histones H3 and H4 in the monocot crop sugarcane. We discovered a number of histone genes by searching the sugarcane ESTs database. The proteins encoded correspond to canonical histones, and their variants. We also purified bulk histones and used them to map post-translational modifications in the histones H3 and H4 using mass spectrometry. Several modifications conserved in other plants, and also novel modified residues, were identified. In particular, we report O-acetylation of serine, threonine and tyrosine, a recently identified modification conserved in several eukaryotes. Additionally, the sub-nuclear localization of some well-studied modifications (i.e., H3K4me3, H3K9me2, H3K27me3, H3K9ac, H3T3ph) is described and compared to other plant species. To our knowledge, this is the first report of histones H3 and H4 as well as their post-translational modifications in sugarcane, and will provide a starting point for the study of chromatin regulation in this crop.
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Aitken KS, McNeil MD, Berkman PJ, Hermann S, Kilian A, Bundock PC, Li J. Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane. BMC PLANT BIOLOGY 2014; 14:190. [PMID: 25059596 PMCID: PMC4222257 DOI: 10.1186/s12870-014-0190-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/14/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the genome. We have used the genetic map of a sugarcane cultivar to generate a consensus genetic map to increase genome coverage for comparison to the sorghum genome. We have utilized the recently developed sugarcane DArT array to increase the marker density within the genetic map. The sequence of these DArT markers plus SNP and EST-SSR markers was then used to form a bridge to the sorghum genomic sequence by BLAST alignment to start to unravel the complex genomic architecture of sugarcane. RESULTS Comparative mapping revealed that certain sugarcane chromosomes show greater levels of synteny to sorghum than others. On a macrosyntenic level a good collinearity was observed between sugarcane and sorghum for 4 of the 8 homology groups (HGs). These 4 HGs were syntenic to four sorghum chromosomes with from 98% to 100% of these chromosomes covered by these linked markers. Four major chromosome rearrangements were identified between the other four sugarcane HGs and sorghum, two of which were condensations of chromosomes reducing the basic chromosome number of sugarcane from x = 10 to x = 8. This macro level of synteny was transferred to other members within the Poaceae family such as maize to uncover the important evolutionary relationships that exist between sugarcane and these species. CONCLUSIONS Comparative mapping of sugarcane to the sorghum genome has revealed new information on the genome structure of sugarcane which will help guide identification of important genes for use in sugarcane breeding. Furthermore of the four major chromosome rearrangements identified in this study, three were common to maize providing some evidence that chromosome reduction from a common paleo-ancestor of both maize and sugarcane was driven by the same translocation events seen in both species.
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Affiliation(s)
- Karen S Aitken
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Meredith D McNeil
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Paul J Berkman
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
| | - Scott Hermann
- BSES Limited, 50 Meiers Road, Indooroopilly, Brisbane 4068, QLD, Australia
| | - Andrzej Kilian
- Diversity Arrays P/L, 1 Wilf Crane Crescent, Yarralumla, Canberra 2600, ACT, Australia
| | - Peter C Bundock
- Southern Cross University, Ctr Plant Conservation Genetics, Lismore 2480, NSW, Australia
| | - Jingchuan Li
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane 4067, QLD, Australia
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de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GMQ, Del Bem LE, Vicentini R, Nogueira FTS, Campos RA, Nunes SL, Turrini PCG, Vieira AP, Ochoa Cruz EA, Corrêa TCS, Hotta CT, de Mello Varani A, Vautrin S, da Trindade AS, de Mendonça Vilela M, Lembke CG, Sato PM, de Andrade RF, Nishiyama MY, Cardoso-Silva CB, Scortecci KC, Garcia AAF, Carneiro MS, Kim C, Paterson AH, Bergès H, D'Hont A, de Souza AP, Souza GM, Vincentz M, Kitajima JP, Van Sluys MA. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 2014; 15:540. [PMID: 24984568 PMCID: PMC4122759 DOI: 10.1186/1471-2164-15-540] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/19/2014] [Indexed: 01/24/2023] Open
Abstract
Background Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marie-Anne Van Sluys
- Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil.
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de Souza MCP, Silva JN, Almeida C. Differential detection of transposable elements between Saccharum species. Genet Mol Biol 2013; 36:408-12. [PMID: 24130449 PMCID: PMC3795168 DOI: 10.1590/s1415-47572013005000030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/03/2013] [Indexed: 11/22/2022] Open
Abstract
Cultivars of sugarcane (Saccharum) are hybrids between species S. officinarum (x = 10, 2n = 8x = 80) and S. spontaneum (x = 8, 2n = 5 – 16x = 40 – 128). These accessions have 100 to 130 chromosomes, 80–85% of which are derived from S. officinarum, 10–15% from S. spontaneum, and 5–10% are possible recombinants between the two genomes. The aim of this study was to analyze the repetition of DNA sequences in S. officinarum and S. spontaneum. For this purpose, genomic DNA from S. officinarum was digested with restriction enzymes and the fragments cloned. Sixty-eight fragments, approximately 500 bp, were cloned, sequenced and had their identity analyzed in NCBI, and in the rice, maize, and sorghum genome databases using BLAST. Twelve clones containing partial transposable elements, one single-copy control, one DNA repetitive clone control and two genome controls were analyzed by DNA hybridization on membrane, using genomic probes from S. officinarum and S. spontaneum. The hybridization experiment revealed that six TEs had a similar repetitive DNA pattern in the genomes of S. officinarum and S. spontaneum, while six TEs were more abundant in the genome of S. officinarum. We concluded that the species S. officinarum and S. spontaneum have differential accumulation LTR retrotransposon families, suggesting distinct insertion or modification patterns.
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Moyle RL, Birch RG. Diversity of sequences and expression patterns among alleles of a sugarcane loading stem gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1775-82. [PMID: 23546592 DOI: 10.1007/s00122-013-2091-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/21/2013] [Indexed: 05/13/2023]
Abstract
Modern sugarcane cultivars are highly polyploid and aneuploid hybrids, which are propagated as clones. Their complex genome structure comprises 100-130 chromosomes and 10-13 hom(e)ologous copies of most loci. There is preliminary evidence of very high heterozygosity, with implications for genetic improvement approaches ranging from marker-assisted selection to transgenics. Here, we report that sugarcane cultivar Q200 has at least nine alleles at the Loading Stem Gene (ScLSG) locus. Exon-intron structure is identical and the predicted protein products show at least 92 % identity, across sugarcane alleles and the Sorghum homologue Sb07g027880. There is substantial variation in the 5' UTR and promoter regions including numerous allele-specific nucleotide polymorphisms, insertions and deletions. We developed an allele-specific qRT-PCR method to undertake the first compelling test of allele-specific expression in polyploid sugarcane. Seven alleles distinguished by this method all showed peak expression in the sucrose-loading zone of the stem, but there was apparent variability in expression patterns across other tissues. The ScLSG2 and ScLSG5 alleles appear promising for specificity of expression in stems, relative to leaf, meristem, emerging shoot and root tissues. Within the stem, there was activity in parenchyma, vascular and rind tissues. This expression pattern is of interest in basic research and biotechnology aimed at enhanced sucrose content, engineering value-added products, and manipulation of stem biomass composition.
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Affiliation(s)
- Richard L Moyle
- Hines Plant Science Building, University of Queensland, Brisbane 4072, Australia
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de Siqueira Ferreira S, Nishiyama MY, Paterson AH, Souza GM. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. Genome Biol 2013; 14:210. [PMID: 23805917 PMCID: PMC3707038 DOI: 10.1186/gb-2013-14-6-210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
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Affiliation(s)
- Savio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF, Lengelle J, Baurens FC, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs S. The banana genome hub. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat035. [PMID: 23707967 PMCID: PMC3662865 DOI: 10.1093/database/bat035] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/
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Affiliation(s)
- Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier F-34398, France.
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Zhang J, Arro J, Chen Y, Ming R. Haplotype analysis of sucrose synthase gene family in three Saccharum species. BMC Genomics 2013; 14:314. [PMID: 23663250 PMCID: PMC3668173 DOI: 10.1186/1471-2164-14-314] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 04/29/2013] [Indexed: 11/10/2022] Open
Abstract
Background Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugarcane cultivars are complex hybrids derived mainly from crosses among its progenitor species, S. officinarum and S. spontanuem, and to a lesser degree, S. robustom. Atypical of higher plants, sugarcane stores its photoassimilates as sucrose rather than as starch in its parenchymous stalk cells. In the sugar biosynthesis pathway, sucrose synthase (SuSy, UDP-glucose: D-fructose 2-a-D-glucosyltransferase, EC 2.4.1.13) is a key enzyme in the regulation of sucrose accumulation and partitioning by catalyzing the reversible conversion of sucrose and UDP into UDP-glucose and fructose. However, little is known about the sugarcane SuSy gene family members and hence no definitive studies have been reported regarding allelic diversity of SuSy gene families in Saccharum species. Results We identified and characterized a total of five sucrose synthase genes in the three sugarcane progenitor species through gene annotation and PCR haplotype analysis by analyzing 70 to 119 PCR fragments amplified from intron-containing target regions. We detected all but one (i.e. ScSuSy5) of ScSuSy transcripts in five tissue types of three Saccharum species. The average SNP frequency was one SNP per 108 bp, 81 bp, and 72 bp in S. officinarum, S. robustom, and S. spontanuem respectively. The average shared SNP is 15 between S. officinarum and S. robustom, 7 between S. officinarum and S. spontanuem , and 11 between S. robustom and S. spontanuem. We identified 27, 35, and 32 haplotypes from the five ScSuSy genes in S. officinarum, S. robustom, and S. spontanuem respectively. Also, 12, 11, and 9 protein sequences were translated from the haplotypes in S. officinarum, S. robustom, S. spontanuem, respectively. Phylogenetic analysis showed three separate clusters composed of SbSuSy1 and SbSuSy2, SbSuSy3 and SbSuSy5, and SbSuSy4. Conclusions The five members of the SuSy gene family evolved before the divergence of the genera in the tribe Andropogoneae at least 12 MYA. Each ScSuSy gene showed at least one non-synonymous substitution in SNP haplotypes. The SNP frequency is the lowest in S. officinarum, intermediate in S. robustum, and the highest in S. spontaneum, which may reflect the timing of the two rounds of whole genome duplication in these octoploids. The higher rate of shared SNP frequency between S. officinarum and S. robustum than between S. officinarum and in S. spontaneum confirmed that the speciation event separating S. officinarum and S. robustum occurred after their common ancestor diverged from S. spontaneum. The SNP and haplotype frequencies in three Saccharum species provide fundamental information for designing strategies to sequence these autopolyploid genomes.
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Affiliation(s)
- Jisen Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou 350108, China
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Ortiz-Morea FA, Vicentini R, Silva GF, Silva EM, Carrer H, Rodrigues AP, Nogueira FT. Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2307-20. [PMID: 23564956 PMCID: PMC3654421 DOI: 10.1093/jxb/ert089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth.
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Affiliation(s)
- Fausto A. Ortiz-Morea
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- These authors contributed equally to this work
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
- These authors contributed equally to this work
| | - Geraldo F.F. Silva
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Eder M. Silva
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Helaine Carrer
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
| | - Ana P. Rodrigues
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
| | - Fabio T.S. Nogueira
- Centro de Biotecnologia Agricola (CEBTEC), Escola Superior de Agricultura ‘Luiz de Queiroz’, (ESALQ)/USP, Piracicaba, SP, Brazil
- Laboratory of Molecular Genetics of Plant Development, Department of Genetics, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr.,17 s/n. CEP 18618–970 Botucatu, SP, Brazil
- To whom correspondence should be addressed.
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Jung JH, Fouad WM, Vermerris W, Gallo M, Altpeter F. RNAi suppression of lignin biosynthesis in sugarcane reduces recalcitrance for biofuel production from lignocellulosic biomass. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:1067-76. [PMID: 22924974 DOI: 10.1111/j.1467-7652.2012.00734.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Sugarcane is a prime bioethanol feedstock. Currently, sugarcane ethanol is produced through fermentation of the sucrose, which can easily be extracted from stem internodes. Processes for production of biofuels from the abundant lignocellulosic sugarcane residues will boost the ethanol output from sugarcane per land area. However, unlocking the vast amount of chemical energy stored in plant cell walls remains expensive primarily because of the intrinsic recalcitrance of lignocellulosic biomass. We report here the successful reduction in lignification in sugarcane by RNA interference, despite the complex and highly polyploid genome of this interspecific hybrid. Down-regulation of the sugarcane caffeic acid O-methyltransferase (COMT) gene by 67% to 97% reduced the lignin content by 3.9% to 13.7%, respectively. The syringyl/guaiacyl ratio in the lignin was reduced from 1.47 in the wild type to values ranging between 1.27 and 0.79. The yields of directly fermentable glucose from lignocellulosic biomass increased up to 29% without pretreatment. After dilute acid pretreatment, the fermentable glucose yield increased up to 34%. These observations demonstrate that a moderate reduction in lignin (3.9% to 8.4%) can reduce the recalcitrance of sugarcane biomass without compromising plant performance under controlled environmental conditions.
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Affiliation(s)
- Je Hyeong Jung
- Agronomy Department, University of Florida, IFAS, Gainesville, FL, USA
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Manetti ME, Rossi M, Cruz GMQ, Saccaro NL, Nakabashi M, Altebarmakian V, Rodier-Goud M, Domingues D, D’Hont A, Van Sluys MA. Mutator System Derivatives Isolated from Sugarcane Genome Sequence. TROPICAL PLANT BIOLOGY 2012; 5:233-243. [PMID: 22905278 PMCID: PMC3418495 DOI: 10.1007/s12042-012-9104-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I-IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12042-012-9104-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M. E. Manetti
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Rossi
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - G. M. Q. Cruz
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - N. L. Saccaro
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Nakabashi
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - V. Altebarmakian
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
| | - M. Rodier-Goud
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - D. Domingues
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - A. D’Hont
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - M. A. Van Sluys
- Departamento de Botânica-IB-USP, GaTE Lab, Brasil, Rua do Matão, 277, 05508-900 São Paulo, SP Brazil
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Costet L, Le Cunff L, Royaert S, Raboin LM, Hervouet C, Toubi L, Telismart H, Garsmeur O, Rousselle Y, Pauquet J, Nibouche S, Glaszmann JC, Hoarau JY, D'Hont A. Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:825-36. [PMID: 22572763 DOI: 10.1007/s00122-012-1875-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/19/2012] [Indexed: 05/07/2023]
Abstract
Modern sugarcane cultivars (Saccharum spp., 2n = 100-130) are high polyploid, aneuploid and of interspecific origin. A major gene (Bru1) conferring resistance to brown rust, caused by the fungus Puccinia melanocephala, has been identified in cultivar R570. We analyzed 380 modern cultivars and breeding materials covering the worldwide diversity with 22 molecular markers genetically linked to Bru1 in R570 within a 8.2 cM segment. Our results revealed a strong LD in the Bru1 region and strong associations between most of the markers and rust resistance. Two PCR markers, that flank the Bru1-bearing segment, were found completely associated with one another and only in resistant clones representing efficient molecular diagnostic for Bru1. On this basis, Bru1 was inferred in 86 % of the 194 resistant sugarcane accessions, revealing that it constitutes the main source of brown rust resistance in modern cultivars. Bru1 PCR diagnostic markers should be particularly useful to identify cultivars with potentially alternative sources of resistance to diversify the basis of brown rust resistance in breeding programs.
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Affiliation(s)
- L Costet
- Cirad, UMR PVBMT, Saint-Pierre, 97410, La Réunion, France
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Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W, Jordão H, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AAF, Vieira MLC. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 2012; 13:51. [PMID: 22742069 PMCID: PMC3443450 DOI: 10.1186/1471-2156-13-51] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/13/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. RESULTS The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. CONCLUSIONS Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
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Affiliation(s)
- Alessandra C Palhares
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Taislene B Rodrigues-Morais
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Douglas S Domingues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Present address: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, 86047-902, Londrina, Brazil
| | - Walter Maccheroni
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Hamilton Jordão
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Thiago G Marconi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Marcelo Mollinari
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Rodrigo Gazaffi
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Antonio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
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Cesarino I, Araújo P, Sampaio Mayer JL, Paes Leme AF, Mazzafera P. Enzymatic activity and proteomic profile of class III peroxidases during sugarcane stem development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 55:66-76. [PMID: 22551762 DOI: 10.1016/j.plaphy.2012.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/21/2012] [Indexed: 05/11/2023]
Abstract
Class III peroxidases are present as large multigene families in all land plants. This large number of genes together with the diversity of processes catalyzed by peroxidases suggests possible functional specialization of each isoform. However, assigning a precise role for each individual peroxidase gene has continued to be a major bottleneck. Here we investigated the enzyme activity and translational profile of class III peroxidases during stem development of sugarcane as a first step in the estimation of physiological functions of individual isoenzymes. Internodes at three different developmental stages (young, developing and mature) were divided into pith (inner tissue) and rind (outer tissue) fractions. The rind of mature internodes presented the highest enzymatic activity and thus could be considered the ideal tissue for the discovery of peroxidase gene function. In addition, activity staining of 2DE gels revealed different isoperoxidase profiles and protein expression regulation among different tissue fractions. In-gel tryptic digestion of excised spots followed by peptide sequencing by LC-MS/MS positively matched uncharacterized peroxidases in the sugarcane database SUCEST. Multiple spots matching the same peroxidase gene were found, which reflects the generation of more than one isoform from a particular gene by post-translational modifications. The identified sugarcane peroxidases appear to be monocot-specific sequences with no clear ortholog in dicot model plant Arabidopsis thaliana.
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Affiliation(s)
- Igor Cesarino
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970 Campinas, SP, Brazil
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Figueira TRES, Okura V, Rodrigues da Silva F, Jose da Silva M, Kudrna D, Ammiraju JSS, Talag J, Wing R, Arruda P. A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome. BMC Res Notes 2012; 5:185. [PMID: 22524198 PMCID: PMC3419638 DOI: 10.1186/1756-0500-5-185] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 04/23/2012] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n = 80 chromosomes while S. spontaneum has 2n = 40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80% S. officinaram and 5-20% S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome. RESULTS A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs. CONCLUSION The SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.
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Affiliation(s)
- Thais Rezende e Silva Figueira
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Vagner Okura
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | | | - Marcio Jose da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Jetty SS Ammiraju
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-875, Brazil
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Domingues DS, Cruz GMQ, Metcalfe CJ, Nogueira FTS, Vicentini R, de S Alves C, Van Sluys MA. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics 2012; 13:137. [PMID: 22507400 PMCID: PMC3352295 DOI: 10.1186/1471-2164-13-137] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 04/16/2012] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. RESULTS Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. CONCLUSIONS Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.
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Affiliation(s)
- Douglas S Domingues
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Rod. Celso Garcia Cid (PR-445), km375, 86047-902 Londrina, Brazil
| | - Guilherme MQ Cruz
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
| | - Cushla J Metcalfe
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
| | - Fabio TS Nogueira
- Depto. de Genética, Inst. de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000 Botucatu, Brazil
| | - Renato Vicentini
- Systems Biology Laboratory, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, Brazil
| | - Cristiane de S Alves
- Depto. de Genética, Inst. de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000 Botucatu, Brazil
| | - Marie-Anne Van Sluys
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
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Guignon V, Droc G, Alaux M, Baurens FC, Garsmeur O, Poiron C, Carver T, Rouard M, Bocs S. Chado controller: advanced annotation management with a community annotation system. ACTA ACUST UNITED AC 2012; 28:1054-6. [PMID: 22285827 PMCID: PMC3315714 DOI: 10.1093/bioinformatics/bts046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form Contact:valentin.guignon@cirad.fr; stephanie.sidibe-bocs@cirad.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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de Setta N, Metcalfe CJ, Cruz GMQ, Ochoa EA, Van Sluys MA. Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Parisod C, Senerchia N. Responses of Transposable Elements to Polyploidy. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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