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Nugroho RAP, Zaag I, Lamade E, Lukman R, Caliman JP, Tcherkez G. Metabolomics-Assisted Breeding in Oil Palm: Potential and Current Perspectives. Int J Mol Sci 2024; 25:9833. [PMID: 39337319 PMCID: PMC11431877 DOI: 10.3390/ijms25189833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 09/07/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Oil palm is presently the most important oil-producing crop worldwide in terms of oil production and consumption. However, oil palm cultivation faces important challenges such as adverse climatic conditions, expensive fertilization requirements, and fungal pathogens, including Ganoderma. Intense efforts in oil palm breeding are devoted to improving both oil production yield and resistance to environmental cues. Metabolomics can be of interest because it provides many quantitative traits and metabolic signatures that can be selected for to optimize oil palm performance. Here, we briefly review how metabolomics can help oil palm breeding, and to do so, we give examples of recent metabolomics analyses and provide a roadmap to use metabolomics-assisted breeding.
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Affiliation(s)
- Rizki Anjal P Nugroho
- Institut de Recherche en Horticulture et Semences, Université d'Angers, 49070 Beaucouzé, France
- Sinar Mas Agro Resources and Technology Research Institute (SMARTRI), Jalan Teuku Umar 19, Pekanbaru 28112, Riau, Indonesia
| | - Ismail Zaag
- Institut de Recherche en Horticulture et Semences, Université d'Angers, 49070 Beaucouzé, France
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ABSYS, 34398 Montpellier, France
- Systèmes de Pérennes, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 34398 Montpellier, France
| | - Emmanuelle Lamade
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ABSYS, 34398 Montpellier, France
- Systèmes de Pérennes, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 34398 Montpellier, France
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Rudy Lukman
- Sinar Mas Agro Resources and Technology Research Institute (SMARTRI), Jalan Teuku Umar 19, Pekanbaru 28112, Riau, Indonesia
| | - Jean-Pierre Caliman
- Sinar Mas Agro Resources and Technology Research Institute (SMARTRI), Jalan Teuku Umar 19, Pekanbaru 28112, Riau, Indonesia
| | - Guillaume Tcherkez
- Institut de Recherche en Horticulture et Semences, Université d'Angers, 49070 Beaucouzé, France
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Karunarathna SC, Patabendige NM, Lu W, Asad S, Hapuarachchi KK. An In-Depth Study of Phytopathogenic Ganoderma: Pathogenicity, Advanced Detection Techniques, Control Strategies, and Sustainable Management. J Fungi (Basel) 2024; 10:414. [PMID: 38921400 PMCID: PMC11204718 DOI: 10.3390/jof10060414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
Phytopathogenic Ganoderma species pose a significant threat to global plant health, resulting in estimated annual economic losses exceeding USD (US Dollars) 68 billion in the agriculture and forestry sectors worldwide. To combat this pervasive menace effectively, a comprehensive understanding of the biology, ecology, and plant infection mechanisms of these pathogens is imperative. This comprehensive review critically examines various aspects of Ganoderma spp., including their intricate life cycle, their disease mechanisms, and the multifaceted environmental factors influencing their spread. Recent studies have quantified the economic impact of Ganoderma infections, revealing staggering yield losses ranging from 20% to 80% across various crops. In particular, oil palm plantations suffer devastating losses, with an estimated annual reduction in yield exceeding 50 million metric tons. Moreover, this review elucidates the dynamic interactions between Ganoderma and host plants, delineating the pathogen's colonization strategies and its elicitation of intricate plant defense responses. This comprehensive analysis underscores the imperative for adopting an integrated approach to Ganoderma disease management. By synergistically harnessing cultural practices, biological control, and chemical treatments and by deploying resistant plant varieties, substantial strides can be made in mitigating Ganoderma infestations. Furthermore, a collaborative effort involving scientists, breeders, and growers is paramount in the development and implementation of sustainable strategies against this pernicious plant pathogen. Through rigorous scientific inquiry and evidence-based practices, we can strive towards safeguarding global plant health and mitigating the dire economic consequences inflicted by Ganoderma infections.
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Affiliation(s)
- Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China;
- National Institute of Fundamental Studies, Hantane Road, Kandy 20000, Sri Lanka
| | | | - Wenhua Lu
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Suhail Asad
- School of Biology and Chemistry, Pu’er University, Pu’er 665000, China;
| | - Kalani K. Hapuarachchi
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
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Garzón-Martínez GA, Osorio-Guarín JA, Moreno LP, Bastidas S, Barrero LS, Lopez-Cruz M, Enciso-Rodríguez FE. Genomic selection for morphological and yield-related traits using genome-wide SNPs in oil palm. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:71. [PMID: 37313322 PMCID: PMC10248711 DOI: 10.1007/s11032-022-01341-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/29/2022] [Indexed: 06/15/2023]
Abstract
Oil palm is the most important oil crop worldwide. Colombia is the fourth largest producer, primarily relying on production from interspecific hybrids, derived from crosses between Elaeis oleifera and Elaeis guineensis (OxG). However, conventional breeding can take up to 20 years to generate a new variety. Therefore, reducing the breeding cycle while improving the genetic gain for complex traits is desirable. Genomic selection (GS) is an approach with the potential to achieve this goal. In this study, we evaluated 431 F1 interspecific hybrids (OxG) and 444 backcrosses (BC1) for morphological and yield-related traits. Genomic predictions were performed with the G-BLUP model using three different population datasets for training the model: the same population (TRN1), the other population (TRN2), and both populations (TRN1+2). Higher multi-family prediction accuracies were obtained for foliar area (0.3 in OxG) and trunk height (0.47 in BC1) when the model was trained with TRN1. Single-family prediction accuracies were lower in the OxG compared to BC1 families for traits such as trunk diameter, trunk height, bunch number, and yield using TRN1. Conversely, lower prediction accuracies were obtained for most traits when the model was trained using TRN2 (< 0.1). Multi-trait models showed a substantial increase of the predictions for traits such as yield (0.22 for OxG and 0.44 for BC1), because of the genetic correlations between traits. The results herein highlighted the potential of GS for parental selection in OxG and BC1 populations, but further studies are required to improve the models to select individuals by their genetic value. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01341-5.
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Affiliation(s)
- Gina A. Garzón-Martínez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Mosquera, Cundinamarca Colombia
| | - Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Mosquera, Cundinamarca Colombia
| | - Leidy P. Moreno
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Palmira, Valle del Cauca Colombia
| | - Silvio Bastidas
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Palmira, Valle del Cauca Colombia
| | - Luz Stella Barrero
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Mosquera, Cundinamarca Colombia
| | - Marco Lopez-Cruz
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI USA
| | - Felix E. Enciso-Rodríguez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Mosquera, Cundinamarca Colombia
- Blueberry Breeding Program, Department of Horticulture Sciences, University of Florida, 2211 Fifield Hall, 2550 Hull Rd, Gainesville, FL 32611 USA
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Seyum EG, Bille NH, Abtew WG, Munyengwa N, Bell JM, Cros D. Genomic selection in tropical perennial crops and plantation trees: a review. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:58. [PMID: 37313015 PMCID: PMC10248687 DOI: 10.1007/s11032-022-01326-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
To overcome the multiple challenges currently faced by agriculture, such as climate change and soil deterioration, more efficient plant breeding strategies are required. Genomic selection (GS) is crucial for the genetic improvement of quantitative traits, as it can increase selection intensity, shorten the generation interval, and improve selection accuracy for traits that are difficult to phenotype. Tropical perennial crops and plantation trees are of major economic importance and have consequently been the subject of many GS articles. In this review, we discuss the factors that affect GS accuracy (statistical models, linkage disequilibrium, information concerning markers, relatedness between training and target populations, the size of the training population, and trait heritability) and the genetic gain expected in these species. The impact of GS will be particularly strong in tropical perennial crops and plantation trees as they have long breeding cycles and constrained selection intensity. Future GS prospects are also discussed. High-throughput phenotyping will allow constructing of large training populations and implementing of phenomic selection. Optimized modeling is needed for longitudinal traits and multi-environment trials. The use of multi-omics, haploblocks, and structural variants will enable going beyond single-locus genotype data. Innovative statistical approaches, like artificial neural networks, are expected to efficiently handle the increasing amounts of heterogeneous multi-scale data. Targeted recombinations on sites identified from profiles of marker effects have the potential to further increase genetic gain. GS can also aid re-domestication and introgression breeding. Finally, GS consortia will play an important role in making the best of these opportunities. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01326-4.
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Affiliation(s)
- Essubalew Getachew Seyum
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Ngalle Hermine Bille
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Wosene Gebreselassie Abtew
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Norman Munyengwa
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
| | - Joseph Martin Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - David Cros
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France
- UMR AGAP Institut, CIRAD, INRAE, Univ. Montpellier, Institut Agro, 34398 Montpellier, France
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Murphy DJ, Goggin K, Paterson RRM. Oil palm in the 2020s and beyond: challenges and solutions. CABI AGRICULTURE AND BIOSCIENCE 2021; 2:39. [PMID: 34661165 PMCID: PMC8504560 DOI: 10.1186/s43170-021-00058-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Oil palm, Elaeis guineensis, is by far the most important global oil crop, supplying about 40% of all traded vegetable oil. Palm oils are key dietary components consumed daily by over three billion people, mostly in Asia, and also have a wide range of important non-food uses including in cleansing and sanitizing products. MAIN BODY Oil palm is a perennial crop with a > 25-year life cycle and an exceptionally low land footprint compared to annual oilseed crops. Oil palm crops globally produce an annual 81 million tonnes (Mt) of oil from about 19 million hectares (Mha). In contrast, the second and third largest vegetable oil crops, soybean and rapeseed, yield a combined 84 Mt oil but occupy over 163 Mha of increasingly scarce arable land. The oil palm crop system faces many challenges in the 2020s. These include increasing incidence of new and existing pests/diseases and a general lack of climatic resilience, especially relating to elevated temperatures and increasingly erratic rainfall patterns, plus downstream issues relating to supply chains and consumer sentiment. This review surveys the oil palm sector in the 2020s and beyond, its major challenges and options for future progress. CONCLUSIONS Oil palm crop production faces many future challenges, including emerging threats from climate change and pests and diseases. The inevitability of climate change requires more effective international collaboration for its reduction. New breeding and management approaches are providing the promise of improvements, such as much higher yielding varieties, improved oil profiles, enhanced disease resistance, and greater climatic resilience.
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Affiliation(s)
- Denis J. Murphy
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 4AT UK
| | - Kirstie Goggin
- School of Applied Sciences, University of South Wales, Pontypridd, CF37 4AT UK
- School of Pharmacy and Pharmaceutical Sciences, University of Cardiff, CF10 3NB Cardiff, UK
| | - R. Russell M. Paterson
- CEB-Centre of Biological Engineering, Gualtar Campus, University of Minho, 4710-057 Braga, Portugal
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor D.E. Malaysia
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