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Batista LMT, Ribeiro Junior WQ, Ramos MLG, Bufon VB, Sousa RZ, Vinson CC, Deuner S. Effect of Irrigation on Sugarcane Morphophysiology in the Brazilian Cerrado. PLANTS (BASEL, SWITZERLAND) 2024; 13:937. [PMID: 38611467 PMCID: PMC11013474 DOI: 10.3390/plants13070937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Since sugarcane is semi-perennial, it has no escape from water stresses in the Brazilian Cerrado, and consequently, drought impacts plant growth and industrial quality. The objective of this study was to evaluate the morphophysiology and quality of the first ratoon of two sugarcane varieties submitted to irrigated and stressed treatments under field conditions. For the biometric characteristics, in general, significant decreases were observed under the stressed treatment for all periods, and only minor differences were detected between the studied cultivars. Physiological parameters decreased under stressed conditions, but to a different extent between the varieties. RB855536 was able to maintain a greater rate of transpiration. Productivity was reduced by 103 t ha-1 for variety RB855536 and 121 t ha-1 for RB867515, compared to plants with full irrigation during the dry period, but cane quality was similar in both genotypes. Measurements of physiological and morphological parameters may prove useful in the rapid identification of genotypes with greater tolerance to abiotic stress.
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Affiliation(s)
- Laryssa Maria Teles Batista
- Faculty of Agronomy and Veterinary Medicine, University of Brasília, Brasília 70910-900, Brazil; (L.M.T.B.); (C.C.V.)
| | | | - Maria Lucrecia Gerosa Ramos
- Faculty of Agronomy and Veterinary Medicine, University of Brasília, Brasília 70910-900, Brazil; (L.M.T.B.); (C.C.V.)
| | - Vinicius Bof Bufon
- Brazilian Agricultural Research Corporation—(EMBRAPA Meio Ambiente), Jaguariuna 13918-110, Brazil;
| | - Rodrigo Zuketta Sousa
- Brazilian Agricultural Research Corporation—(EMBRAPA Cerrados), Planaltina 73310-970, Brazil;
| | - Christina Cleo Vinson
- Faculty of Agronomy and Veterinary Medicine, University of Brasília, Brasília 70910-900, Brazil; (L.M.T.B.); (C.C.V.)
| | - Sidnei Deuner
- Botany Department, Biology Institute, Federal University of Pelotas, Pelotas 96010-900, Brazil;
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2
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Wei Y, Xu Y, Khan A, Jiang C, Li H, Wu Y, Zhang C, Wang M, Chen J, Zeng L, Zhang M. Analysis of Photosynthetic Characteristics and Screening High Light-Efficiency Germplasm in Sugarcane. PLANTS (BASEL, SWITZERLAND) 2024; 13:587. [PMID: 38475434 DOI: 10.3390/plants13050587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/14/2024]
Abstract
Sugarcane is a globally significant crop for sugar and energy production, and developing high light-efficiency sugarcane varieties is crucial for enhancing yield and quality. However, limited research is available on the screening of sugarcane germplasm with high photosynthetic efficiency, especially with different leaf positions. The present study, conducted in Guangxi, China, aimed to analyze the photosynthetic characteristics of 258 sugarcane varieties at different leaf positions over three consecutive years in field experiments. The results showed significant differences in photosynthetic characteristics among genotypes, years, and leaf positions. Heritability estimates for various photosynthetic parameters ranged from 0.76 to 0.88. Principal component analysis revealed that the first three principal components accounted for over 99% of the cumulative variance. The first component represented photosynthetic efficiency and light utilization, the second focused on electron transfer and reaction center status, and the third was associated with chlorophyll content. Cluster and discriminant analysis classified sugarcane genotypes into three categories: high photosynthetic efficiency (HPE) with 86 genotypes, medium photosynthetic efficiency (MPE) with 60 genotypes, and low photosynthetic efficiency (LPE) with 112 genotypes. Multi-year trials confirmed that HPE sugarcane genotypes had higher single-stem weight and sucrose content. This study provides valuable insights into the photosynthetic physiological characteristics of different sugarcane varieties, which can contribute to further research regarding high yields and sugar breeding.
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Affiliation(s)
- Yibin Wei
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Abdullah Khan
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chunxiu Jiang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Huojian Li
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuling Wu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chi Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Maoyao Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Jun Chen
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Lifang Zeng
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
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3
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Cheesman AW, Brown F, Farha MN, Rosan TM, Folberth GA, Hayes F, Moura BB, Paoletti E, Hoshika Y, Osborne CP, Cernusak LA, Ribeiro RV, Sitch S. Impacts of ground-level ozone on sugarcane production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166817. [PMID: 37673248 DOI: 10.1016/j.scitotenv.2023.166817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/27/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
Sugarcane is a vital commodity crop often grown in (sub)tropical regions which have been experiencing a recent deterioration in air quality. Unlike for other commodity crops, the risk of air pollution, specifically ozone (O3), to this C4 crop has not yet been quantified. Yet, recent work has highlighted both the potential risks of O3 to C4 bioenergy crops, and the emergence of O3 exposure across the tropics as a vital factor determining global food security. Given the large extent, and planned expansion of sugarcane production in places like Brazil to meet global demand for biofuels, there is a pressing need to characterize the risk of O3 to the industry. In this study, we sought to a) derive sugarcane O3 dose-response functions across a range of realistic O3 exposure and b) model the implications of this across a globally important production area. We found a significant impact of O3 on biomass allocation (especially to leaves) and production across a range of sugarcane genotypes, including two commercially relevant varieties (e.g. CTC4, Q240). Using these data, we calculated dose-response functions for sugarcane and combined them with hourly O3 exposure across south-central Brazil derived from the UK Earth System Model (UKESM1) to simulate the current regional impact of O3 on sugarcane production using a dynamic global vegetation model (JULES vn 5.6). We found that between 5.6 % and 18.3 % of total crop productivity is likely lost across the region due to the direct impacts of current O3 exposure. However, impacts depended critically on the substantial differences in O3 susceptibility observed among sugarcane genotypes and how these were implemented in the model. Our work highlights not only the urgent need to fully elucidate the impacts of O3 in this important bioenergetic crop, but the potential implications air quality may have upon tropical food production more generally.
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Affiliation(s)
- Alexander W Cheesman
- College of Science & Engineering and Centre for Tropical Environmental and Sustainability Science, James Cook University, Cairns, Queensland, Australia; Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK.
| | - Flossie Brown
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | - Mst Nahid Farha
- College of Science & Engineering and Centre for Tropical Environmental and Sustainability Science, James Cook University, Cairns, Queensland, Australia; Department of Chemistry, Rajshahi University of Engineering &Technology, Rajshahi 6204, Bangladesh
| | - Thais M Rosan
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | | | - Felicity Hayes
- UK Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, Gwynedd LL57 2UW, UK
| | - Barbara B Moura
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council of Italy (CNR), Sesto Fiorentino, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy
| | - Elena Paoletti
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council of Italy (CNR), Sesto Fiorentino, Italy; Italian Integrated Environmental Research Infrastructures System (ITINERIS), Tito Scalo, 85050 Potenza, Italy
| | - Yasutomo Hoshika
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council of Italy (CNR), Sesto Fiorentino, Italy; Italian Integrated Environmental Research Infrastructures System (ITINERIS), Tito Scalo, 85050 Potenza, Italy
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Lucas A Cernusak
- College of Science & Engineering and Centre for Tropical Environmental and Sustainability Science, James Cook University, Cairns, Queensland, Australia
| | - Rafael V Ribeiro
- Laboratory of Crop Physiology (LCroP), Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Stephen Sitch
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
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4
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Narayan JA, Manoj VM, Nerkar G, Chakravarthi M, Dharshini S, Subramonian N, Premachandran MN, Valarmathi R, Kumar RA, Gomathi R, Surendar KK, Hemaprabha G, Appunu C. Transgenic sugarcane with higher levels of BRK1 showed improved drought tolerance. PLANT CELL REPORTS 2023; 42:1611-1628. [PMID: 37578541 DOI: 10.1007/s00299-023-03056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/25/2023] [Indexed: 08/15/2023]
Abstract
KEY MESSAGE Transgenic sugarcane overexpressing BRK1 showed improved tolerance to drought stress through modulation of actin polymerization and formation of interlocking marginal lobes in epidermal leaf cells, a typical feature associated with BRK1 expression under drought stress. BRICK1 (BRK1) genes promote leaf epidermal cell morphogenesis and division in plants that involves local actin polymerization. Although the changes in actin filament organization during drought have been reported, the role of BRK in stress tolerance remains unknown. In our previous work, the drought-tolerant Erianthus arundinaceus exhibited high levels of the BRK gene expression under drought stress. Therefore, in the present study, the drought-responsive gene, BRK1 from Saccharum spontaneum, was transformed into sugarcane to test if it conferred drought tolerance in the commercial sugarcane cultivar Co 86032. The transgenic lines were subjected to drought stress, and analyzed using physiological parameters for drought stress. The drought-induced BRK1-overexpressing lines of sugarcane exhibited significantly higher transgene expression compared with the wild-type control and also showed improved physiological parameters. In addition, the formation of interlocking marginal lobes in the epidermal leaf cells, a typical feature associated with BRK1 expression, was observed in all transgenic BRK1 lines during drought stress. This is the first report to suggest that BRK1 plays a role in sugarcane acclimation to drought stress and may prove to be a potential candidate in genetic engineering of plants for enhanced biomass production under drought stress conditions.
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Affiliation(s)
- J Ashwin Narayan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - V M Manoj
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - Gauri Nerkar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - M Chakravarthi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, SP, CEP 13565-905, Brazil
| | - S Dharshini
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - N Subramonian
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - M N Premachandran
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Valarmathi
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Arun Kumar
- Division of Crop Production, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - R Gomathi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - K Krisha Surendar
- Deprtament of Plant Physiology, Paddy Breeding Station, Tamil Nadu Agricultural University (TNAU), Tamil Nadu, Coimbatore, 641003, India
| | - G Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India
| | - C Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute (SBI), Tamil Nadu, Coimbatore, 641007, India.
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5
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Kumar R, Sagar V, Verma VC, Kumari M, Gujjar RS, Goswami SK, Kumar Jha S, Pandey H, Dubey AK, Srivastava S, Singh SP, Mall AK, Pathak AD, Singh H, Jha PK, Prasad PVV. Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1225234. [PMID: 37645467 PMCID: PMC10461627 DOI: 10.3389/fpls.2023.1225234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.
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Affiliation(s)
- Rajeev Kumar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Vidya Sagar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Vegetable Research, Varanasi, India
| | | | - Mala Kumari
- Integral Institute of Agriculture Science and Technology, Integral University, Lucknow, India
| | - Ranjit Singh Gujjar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sanjay K. Goswami
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Sudhir Kumar Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research, Kanpur, India
| | - Himanshu Pandey
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Abhishek Kumar Dubey
- Indian Council of Agricultural Research (ICAR)-Research Complex for Eastern Region, Patna, India
| | - Sangeeta Srivastava
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - S. P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashutosh K. Mall
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Ashwini Dutt Pathak
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Sugarcane Research, Lucknow, India
| | - Hemlata Singh
- Department of Botany, Plant Physiology & Biochemistry, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, India
| | - Prakash Kumar Jha
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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6
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Luo T, Liu X, Lakshmanan P. A Combined Genomics and Phenomics Approach is Needed to Boost Breeding in Sugarcane. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0074. [PMID: 37456081 PMCID: PMC10348406 DOI: 10.34133/plantphenomics.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Ting Luo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xiaoyan Liu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia 4067, QLD, Australia
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7
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Contiliani DF, Nebó JFCDO, Ribeiro RV, Landell MGDA, Pereira TC, Ming R, Figueira A, Creste S. Drought-triggered leaf transcriptional responses disclose key molecular pathways underlying leaf water use efficiency in sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1182461. [PMID: 37223790 PMCID: PMC10200899 DOI: 10.3389/fpls.2023.1182461] [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: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Drought is a major constraint to sugarcane (Saccharum spp.) production and improving the water use efficiency (WUE) is a critical trait for the sustainability of this bioenergy crop. The molecular mechanism underlying WUE remains underexplored in sugarcane. Here, we investigated the drought-triggered physiological and transcriptional responses of two sugarcane cultivars contrasting for drought tolerance, 'IACSP97-7065' (sensitive) and 'IACSP94-2094' (tolerant). After 21 days without irrigation (DWI), only 'IACSP94-2094' exhibited superior WUE and instantaneous carboxylation efficiency, with the net CO2 assimilation being less impacted when compared with 'IACSP97-7065'. RNA-seq of sugarcane leaves at 21 DWI revealed a total of 1,585 differentially expressed genes (DEGs) for both genotypes, among which 'IACSP94-2094' showed 617 (38.9%) exclusive transcripts (212 up- and 405 down-regulated). Functional enrichment analyses of these unique DEGs revealed several relevant biological processes, such as photosynthesis, transcription factors, signal transduction, solute transport, and redox homeostasis. The better drought-responsiveness of 'IACSP94-2094' suggested signaling cascades that foster transcriptional regulation of genes implicated in the Calvin cycle and transport of water and carbon dioxide, which are expected to support the high WUE and carboxylation efficiency observed for this genotype under water deficit. Moreover, the robust antioxidant system of the drought-tolerant genotype might serve as a molecular shield against the drought-associated overproduction of reactive oxygen species. This study provides relevant data that may be used to develop novel strategies for sugarcane breeding programs and to understand the genetic basis of drought tolerance and WUE improvement of sugarcane.
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Affiliation(s)
- Danyel F. Contiliani
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Sugarcane Center, Agronomic Institute (IAC), Ribeirão Preto, SP, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | | | - Tiago C. Pereira
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Biology, Faculty of Philosophy, Sciences, and Letters of Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, SP, Brazil
| | - Ray Ming
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Silvana Creste
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Sugarcane Center, Agronomic Institute (IAC), Ribeirão Preto, SP, Brazil
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8
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Global Responses of Autopolyploid Sugarcane Badila ( Saccharum officinarum L.) to Drought Stress Based on Comparative Transcriptome and Metabolome Profiling. Int J Mol Sci 2023; 24:ijms24043856. [PMID: 36835268 PMCID: PMC9966050 DOI: 10.3390/ijms24043856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Sugarcane (Saccharum spp. hybrid) is frequently affected by seasonal drought, which causes substantial declines in quality and yield. To understand the drought resistance mechanisms of S. officinarum, the main species of modern sugarcane, at a molecular level, we carried out a comparative analysis of transcriptome and metabolome profiling of the sugarcane variety Badila under drought stress (DS). Compared with control group (CG) plants, plants exposed to DS had 13,744 (6663 up-regulated and 7081 down-regulated) differentially expressed genes (DEGs). GO and KEGG analysis showed that the DEGs were enriched in photosynthesis-related pathways and most DEGs had down-regulated expression. Moreover, the chlorophyll content, photosynthesis (Photo), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) were sharply decreased under DS. These results indicate that DS has a significant negative influence on photosynthesis in sugarcane. Metabolome analysis identified 166 (37 down-regulated and 129 up-regulated) significantly regulated metabolites (SRMs). Over 50% of SRMs were alkaloids, amino acids and their derivatives, and lipids. The five most significantly enriched KEGG pathways among SRMs were Aminoacyl-tRNA biosynthesis, 2-Oxocarboxylic acid metabolism, Biosynthesis of amino acids, Phenylalanine metabolism, and Arginine and proline metabolism (p < 0.05). Comparing CG with DS for transcriptome and metabolome profiling (T_CG/DS and M_CG/DS, respectively), we found three of the same KEGG-enriched pathways, namely Biosynthesis of amino acids, Phenylalanine metabolism and Arginine and proline metabolism. The potential importance of Phenylalanine metabolism and Arginine and proline metabolism was further analyzed for response to DS in sugarcane. Seven SRMs (five up-regulated and two down-regulated) and 60 DEGs (17 up-regulated and 43 down-regulated) were enriched in Phenylalanine metabolism under DS, of which novel.31261, Sspon.04G0008060-1A, Sspon.04G0008060-2B and Sspon.04G0008060-3C were significantly correlated with 7 SRMs. In Arginine and proline metabolism, eight SRMs (seven up-regulated and one down-regulated) and 63 DEGs (32 up-regulated and 31 down-regulated) were enriched, of which Sspon.01G0026110-1A (OAT) and Sspon.03G0002750-3D (P5CS) were strongly associated with proline (r > 0.99). These findings present the dynamic changes and possible molecular mechanisms of Phenylalanine metabolism as well as Arginine and proline metabolism under DS and provide a foundation for future research and sugarcane improvement.
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9
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de Oliveira LP, Navarro BV, de Jesus Pereira JP, Lopes AR, Martins MCM, Riaño-Pachón DM, Buckeridge MS. Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane. Sci Rep 2022; 12:7516. [PMID: 35525890 PMCID: PMC9079074 DOI: 10.1038/s41598-022-11508-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trehalose-6-phosphate (T6P) is an intermediate of trehalose biosynthesis that plays an essential role in plant metabolism and development. Here, we comprehensively analyzed sequences from enzymes of trehalose metabolism in sugarcane, one of the main crops used for bioenergy production. We identified protein domains, phylogeny, and in silico expression levels for all classes of enzymes. However, post-translational modifications and residues involved in catalysis and substrate binding were analyzed only in trehalose-6-phosphate synthase (TPS) sequences. We retrieved 71 putative full-length TPS, 93 trehalose-6-phosphate phosphatase (TPP), and 3 trehalase (TRE) of sugarcane, showing all their conserved domains, respectively. Putative TPS (Classes I and II) and TPP sugarcane sequences were categorized into well-known groups reported in the literature. We measured the expression levels of the sequences from one sugarcane leaf transcriptomic dataset. Furthermore, TPS Class I has specific N-glycosylation sites inserted in conserved motifs and carries catalytic and binding residues in its TPS domain. Some of these residues are mutated in TPS Class II members, which implies loss of enzyme activity. Our approach retrieved many homo(eo)logous sequences for genes involved in trehalose metabolism, paving the way to discover the role of T6P signaling in sugarcane.
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Affiliation(s)
- Lauana Pereira de Oliveira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Bruno Viana Navarro
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - João Pedro de Jesus Pereira
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | | | - Marina C M Martins
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório de Biologia Computacional, Centro de Energia Nuclear na Agricultura, Evolutiva e de Sistemas, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil. .,Instituto Nacional de Ciência e Tecnologia do Bioetanol, São Paulo, Brazil.
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10
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Oliveira MDS, Rocha SV, Schneider VK, Henrique-Silva F, Soares MR, Soares-Costa A. Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum. PeerJ 2021; 9:e11461. [PMID: 34249482 PMCID: PMC8247702 DOI: 10.7717/peerj.11461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/26/2021] [Indexed: 11/20/2022] Open
Abstract
Background Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils. Methods Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress. Results Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.
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Affiliation(s)
| | - Sâmara Vieira Rocha
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marcio Roberto Soares
- Department of Natural Resources and Environmental Protection/Agrarian Sciences Center, Federal University of São Carlos, Araras, SP, Brazil
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
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11
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Natarajan S, Basnayake J, Lakshmanan P, Fukai S. Genotypic variation in intrinsic transpiration efficiency correlates with sugarcane yield under rainfed and irrigated field conditions. PHYSIOLOGIA PLANTARUM 2021; 172:976-989. [PMID: 32997338 PMCID: PMC8247395 DOI: 10.1111/ppl.13221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 09/19/2020] [Indexed: 06/08/2023]
Abstract
Intrinsic transpiration efficiency (i TE), the ratio of photosynthesis (A) to stomatal conductance (gs ), is considered a useful trait for improving productivity; however, higher i TE with high A is more desirable than that with low gs . This study dissects i TE of 20 sugarcane genotypes to understand its relationship with total dry matter (TDM) and cane yield (TCH) under irrigated and rainfed conditions. Water stress reduced mean A and gs by 56 and 61%, and mean TDM and TCH by 55 and 59%, respectively; however, genotype × irrigation treatment interaction was smaller than genotype variance. Mean i TE increased from 117.4 μmol mol-1 in the irrigated treatment to 130.6 μmol mol-1 in the rainfed treatment. In irrigated conditions, i TE had high heritability (H2 b = 0.67) and significant genetic correlation with TDM (rg = 0.58) and TCH (rg = 0.72). Under water stress, at gs below 0.1 mol m-2 s-1 , non-stomatal limitation to A was evident and i TE had low heritability (H2 b = 0.2). Whereas in the gs range of 0.1-0.4 mol m-2 s-1 , heritability of i TE (H2 b = 0.63) and its genetic correlation with TDM (rg = 0.78) and TCH (rg = 0.75) were maximised. There was significant genotypic variation in photosynthetic capacity (Ac ), and the differences were related to TDM and i TE. Selecting genotypes with higher i TE and Ac could offer potential for improving productivity without the unfavourable effect of low gs .
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Affiliation(s)
- Sijesh Natarajan
- School of Agriculture and Food SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
- Sugar Research AustraliaBrandonQueenslandAustralia
| | | | - Prakash Lakshmanan
- Sugarcane Research InstituteGuangxi Academy of Agricultural SciencesNanningChina
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin (CAGD)College of Resources and Environment, Southwest UniversityChongqingChina
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Shu Fukai
- School of Agriculture and Food SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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12
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Bazzer SK, Purcell LC. Identification of quantitative trait loci associated with canopy temperature in soybean. Sci Rep 2020; 10:17604. [PMID: 33077811 PMCID: PMC7572360 DOI: 10.1038/s41598-020-74614-8] [Citation(s) in RCA: 4] [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: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
A consistent risk for soybean (Glycine max L.) production is the impact of drought on growth and yield. Canopy temperature (CT) is an indirect measure of transpiration rate and stomatal conductance and may be valuable in distinguishing differences among genotypes in response to drought. The objective of this study was to map quantitative trait loci (QTLs) associated with CT using thermal infrared imaging in a population of recombinant inbred lines developed from a cross between KS4895 and Jackson. Heritability of CT was 35% when estimated across environments. QTL analysis identified 11 loci for CT distributed on eight chromosomes that individually explained between 4.6 and 12.3% of the phenotypic variation. The locus on Gm11 was identified in two individual environments and across environments and explained the highest proportion of phenotypic variation (9.3% to 11.5%) in CT. Several of these CT loci coincided with the genomic regions from previous studies associated with canopy wilting, canopy temperature, water use efficiency, and other morpho-physiological traits related with drought tolerance. Candidate genes with biological function related to transpiration, root development, and signal transduction underlie these putative CT loci. These genomic regions may be important resources in soybean breeding programs to improve tolerance to drought.
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Affiliation(s)
- Sumandeep K Bazzer
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA.
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13
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Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions. 3 Biotech 2020; 10:440. [PMID: 33014683 PMCID: PMC7501393 DOI: 10.1007/s13205-020-02416-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.
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14
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Johansson KSL, El-Soda M, Pagel E, Meyer RC, Tõldsepp K, Nilsson AK, Brosché M, Kollist H, Uddling J, Andersson MX. Genetic controls of short- and long-term stomatal CO2 responses in Arabidopsis thaliana. ANNALS OF BOTANY 2020; 126:179-190. [PMID: 32296835 PMCID: PMC7304471 DOI: 10.1093/aob/mcaa065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/09/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS The stomatal conductance (gs) of most plant species decreases in response to elevated atmospheric CO2 concentration. This response could have a significant impact on plant water use in a future climate. However, the regulation of the CO2-induced stomatal closure response is not fully understood. Moreover, the potential genetic links between short-term (within minutes to hours) and long-term (within weeks to months) responses of gs to increased atmospheric CO2 have not been explored. METHODS We used Arabidopsis thaliana recombinant inbred lines originating from accessions Col-0 (strong CO2 response) and C24 (weak CO2 response) to study short- and long-term controls of gs. Quantitative trait locus (QTL) mapping was used to identify loci controlling short- and long-term gs responses to elevated CO2, as well as other stomata-related traits. KEY RESULTS Short- and long-term stomatal responses to elevated CO2 were significantly correlated. Both short- and long-term responses were associated with a QTL at the end of chromosome 2. The location of this QTL was confirmed using near-isogenic lines and it was fine-mapped to a 410-kb region. The QTL did not correspond to any known gene involved in stomatal closure and had no effect on the responsiveness to abscisic acid. Additionally, we identified numerous other loci associated with stomatal regulation. CONCLUSIONS We identified and confirmed the effect of a strong QTL corresponding to a yet unknown regulator of stomatal closure in response to elevated CO2 concentration. The correlation between short- and long-term stomatal CO2 responses and the genetic link between these traits highlight the importance of understanding guard cell CO2 signalling to predict and manipulate plant water use in a world with increasing atmospheric CO2 concentration. This study demonstrates the power of using natural variation to unravel the genetic regulation of complex traits.
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Affiliation(s)
- Karin S L Johansson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Ellen Pagel
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Rhonda C Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Kadri Tõldsepp
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Anders K Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Brosché
- Institute of Technology, University of Tartu, Tartu, Estonia
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Johan Uddling
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Mats X Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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15
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Reyes JAO, Carpentero AS, Santos PJA, Delfin EF. Effects of Water Regime, Genotype, and Formative Stages on the Agro-Physiological Response of Sugarcane ( Saccharum officinarum L.) to Drought. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9050661. [PMID: 32456149 PMCID: PMC7284505 DOI: 10.3390/plants9050661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 05/29/2023]
Abstract
Drought during the formative stages of a plant's growth triggers a sequence of responses to maintain optimal growing conditions, but often at the expense of crop productivity. Two field experiments were conducted to determine the effect of drought on 10 high-yielding sugarcane genotypes at two formative stages (the tillering stage (TS) and stalk elongation (SS)), within 30 days after treatment imposition. The experiments followed a split-plot in a randomized complete block design with three replicates per genotype. Agro-physiological responses to drought were observed to compare the differences in the response of sugarcane during the two formative stages. Drought significantly reduced total chlorophyll content (Chl) and stomatal conductance (Gs) for both formative stages, while significantly increasing total scavenging activity (AOA) and electrolyte leakage (EC). A higher level of Chl was observed in the stalk elongation stage compared to the tillering stage; however, lower AOA coupled with higher EC in the stalk elongation stage suggests higher drought susceptibility. Pearson's correlation analysis revealed a stronger correlation between plant height, internode length, Chl, AOA, EC, and Gs at the tillering stage relative to the stalk elongation stage. Moreover, results from the multivariate analysis indicate the different contribution values of each parameter, supplementing the hypothesized difference in response between the two formative stages. Multivariate analysis clustered the 10 genotypes into groups based on the traits evaluated, suggesting the ability of these traits to detect differences in a sample population. The observed relationship among traits during the two formative stages of sugarcane will be significant in screening and identifying drought-susceptible and drought-tolerant genotypes for variety development studies.
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16
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High-Throughput Phenotyping of Indirect Traits for Early-Stage Selection in Sugarcane Breeding. REMOTE SENSING 2019. [DOI: 10.3390/rs11242952] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
One of the major limitations for sugarcane genetic improvement is the low heritability of yield in the early stages of breeding, mainly due to confounding inter-plot competition effects. In this study, we investigate an indirect selection index (Si), developed based on traits correlated to yield (indirect traits) that were measured using an unmanned aerial vehicle (UAV), to improve clonal assessment in early stages of sugarcane breeding. A single-row early-stage clonal assessment trial, involving 2134 progenies derived from 245 crosses, and a multi-row experiment representative of pure-stand conditions, with an unrelated population of 40 genotypes, were used in this study. Both experiments were screened at several stages using visual, multispectral, and thermal sensors mounted on a UAV for indirect traits, including canopy cover, canopy height, canopy temperature, and normalised difference vegetation index (NDVI). To construct the indirect selection index, phenotypic and genotypic variance-covariances were estimated in the single-row and multi-row experiment, respectively. Clonal selection from the indirect selection index was compared to single-row yield-based selection. Ground observations of stalk number and plant height at six months after planting made from a subset of 75 clones within the single-row experiment were highly correlated to canopy cover (rg = 0.72) and canopy height (rg = 0.69), respectively. The indirect traits had high heritability and strong genetic correlation with cane yield in both the single-row and multi-row experiments. Only 45% of the clones were common between the indirect selection index and single-row yield based selection, and the expected efficiency of correlated response to selection for pure-stand yield based on indirect traits (44%–73%) was higher than that based on single-row yield (45%). These results highlight the potential of high-throughput phenotyping of indirect traits combined in an indirect selection index for improving early-stage clonal selections in sugarcane breeding.
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17
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Mirajkar SJ, Dalvi SG, Ramteke SD, Suprasanna P. Foliar application of gamma radiation processed chitosan triggered distinctive biological responses in sugarcane under water deficit stress conditions. Int J Biol Macromol 2019; 139:1212-1223. [DOI: 10.1016/j.ijbiomac.2019.08.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/04/2019] [Accepted: 08/10/2019] [Indexed: 12/24/2022]
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18
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Furbank RT, Jimenez-Berni JA, George-Jaeggli B, Potgieter AB, Deery DM. Field crop phenomics: enabling breeding for radiation use efficiency and biomass in cereal crops. THE NEW PHYTOLOGIST 2019; 223:1714-1727. [PMID: 30937909 DOI: 10.1111/nph.15817] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/02/2019] [Indexed: 05/21/2023]
Abstract
Plant phenotyping forms the core of crop breeding, allowing breeders to build on physiological traits and mechanistic science to inform their selection of material for crossing and genetic gain. Recent rapid progress in high-throughput techniques based on machine vision, robotics, and computing (plant phenomics) enables crop physiologists and breeders to quantitatively measure complex and previously intractable traits. By combining these techniques with affordable genomic sequencing and genotyping, machine learning, and genome selection approaches, breeders have an opportunity to make rapid genetic progress. This review focuses on how field-based plant phenomics can enable next-generation physiological breeding in cereal crops for traits related to radiation use efficiency, photosynthesis, and crop biomass. These traits have previously been regarded as difficult and laborious to measure but have recently become a focus as cereal breeders find genetic progress from 'Green Revolution' traits such as harvest index become exhausted. Application of LiDAR, thermal imaging, leaf and canopy spectral reflectance, Chl fluorescence, and machine learning are discussed using wheat and sorghum phenotyping as case studies. A vision of how crop genomics and high-throughput phenotyping could enable the next generation of crop research and breeding is presented.
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Affiliation(s)
- Robert T Furbank
- ARC Centre of Excellence for Translational Photosynthesis, Division of Plant Science, Australian National University, Canberra, 2601, ACT, Australia
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Jose A Jimenez-Berni
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Institute for Sustainable Agriculture (IAS), CSIC, Cordoba, 14004, Spain
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture & Food Innovation, Centre for Crop Science, The University of Queensland, Hermitage Research Station, Warwick, 4370, QLD, Australia
- Agri-Science Queensland, Queensland Department of Agriculture & Fisheries, Hermitage Research Facility, Warwick, 4370, QLD, Australia
| | - Andries B Potgieter
- Queensland Alliance for Agriculture & Food Innovation, Centre for Crop Science, The University of Queensland, Tor Street, Toowoomba, 4350, QLD, Australia
| | - David M Deery
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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19
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van Eeuwijk FA, Bustos-Korts D, Millet EJ, Boer MP, Kruijer W, Thompson A, Malosetti M, Iwata H, Quiroz R, Kuppe C, Muller O, Blazakis KN, Yu K, Tardieu F, Chapman SC. Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:23-39. [PMID: 31003609 DOI: 10.1016/j.plantsci.2018.06.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/05/2018] [Accepted: 06/19/2018] [Indexed: 05/18/2023]
Abstract
New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.
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Affiliation(s)
- Fred A van Eeuwijk
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands.
| | - Daniela Bustos-Korts
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands
| | - Emilie J Millet
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands
| | - Martin P Boer
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands
| | - Addie Thompson
- Institute for Plant Sciences, Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Marcos Malosetti
- Biometris, Wageningen University & Research Centre, P.O. Box 16, 6700 AC Wageningen, The Netherlands
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Roberto Quiroz
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
| | - Christian Kuppe
- Institute for Bio-and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Onno Muller
- Institute for Bio-and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Konstantinos N Blazakis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Alsylio Agrokipiou, P.O. Box 85, 73100 Chania-Crete, Greece
| | - Kang Yu
- Crop Science, Institute of Agricultural Sciences, ETH Zurich, Switzerland; Remote Sensing & Terrestrial Ecology, Department of Earth and Environmental Sciences, KU Leuven, Belgium
| | - Francois Tardieu
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, INRA, 34060 Montpellier, France
| | - Scott C Chapman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia; School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia
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20
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Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/06/2017] [Indexed: 05/20/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
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Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
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21
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Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077/full 10.3389/fpls.2017.01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
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Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
- *Correspondence: Marcelo Menossi
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Nunes-Nesi A, Nascimento VDL, de Oliveira Silva FM, Zsögön A, Araújo WL, Sulpice R. Natural genetic variation for morphological and molecular determinants of plant growth and yield. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2989-3001. [PMID: 27012286 DOI: 10.1093/jxb/erw124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes.
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Affiliation(s)
- Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Vitor de Laia Nascimento
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Franklin Magnum de Oliveira Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Ronan Sulpice
- National University of Ireland, Galway, Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
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