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Xu W, John Martin JJ, Li X, Liu X, Zhang R, Hou M, Cao H, Cheng S. Unveiling the Secrets of Oil Palm Genetics: A Look into Omics Research. Int J Mol Sci 2024; 25:8625. [PMID: 39201312 PMCID: PMC11354864 DOI: 10.3390/ijms25168625] [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: 06/23/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 09/02/2024] Open
Abstract
Oil palm is a versatile oil crop with numerous applications. Significant progress has been made in applying histological techniques in oil palm research in recent years. Whole genome sequencing of oil palm has been carried out to explain the function and structure of the order genome, facilitating the development of molecular markers and the construction of genetic maps, which are crucial for studying important traits and genetic resources in oil palm. Transcriptomics provides a powerful tool for studying various aspects of plant biology, including abiotic and biotic stresses, fatty acid composition and accumulation, and sexual reproduction, while proteomics and metabolomics provide opportunities to study lipid synthesis and stress responses, regulate fatty acid composition based on different gene and metabolite levels, elucidate the physiological mechanisms in response to abiotic stresses, and explain intriguing biological processes in oil palm. This paper summarizes the current status of oil palm research from a multi-omics perspective and hopes to provide a reference for further in-depth research on oil palm.
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Affiliation(s)
- Wen Xu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China
| | - Jerome Jeyakumar John Martin
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xinyu Li
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Xiaoyu Liu
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Ruimin Zhang
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Mingming Hou
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Hongxing Cao
- National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (W.X.); (J.J.J.M.); (X.L.); (X.L.); (R.Z.); (M.H.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Shuanghong Cheng
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China
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Navarro-Quiles C, Lup SD, Muñoz-Nortes T, Candela H, Micol JL. The genetic and molecular basis of haploinsufficiency in flowering plants. TRENDS IN PLANT SCIENCE 2024; 29:72-85. [PMID: 37633803 DOI: 10.1016/j.tplants.2023.07.009] [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: 03/04/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
In diploid organisms, haploinsufficiency can be defined as the requirement for more than one fully functional copy of a gene. In contrast to most genes, whose loss-of-function alleles are recessive, loss-of-function alleles of haploinsufficient genes are dominant. However, forward and reverse genetic screens are biased toward obtaining recessive, loss-of-function mutations, and therefore, dominant mutations of all types are underrepresented in mutant collections. Despite this underrepresentation, haploinsufficient loci have intriguing implications for studies of genome evolution, gene dosage, stability of protein complexes, genetic redundancy, and gene expression. Here we review examples of haploinsufficiency in flowering plants and describe the underlying molecular mechanisms and evolutionary forces driving haploinsufficiency. Finally, we discuss the masking of haploinsufficiency by genetic redundancy, a widespread phenomenon among angiosperms.
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Affiliation(s)
- Carla Navarro-Quiles
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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Sousa EC, Raizada MN. Contributions of African Crops to American Culture and Beyond: The Slave Trade and Other Journeys of Resilient Peoples and Crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.586340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a general unawareness of food crops indigenous to the African continent that have contributed to Western culture. This under-appreciation is particularly relevant in the current context of societal movements to end historic racism and value the contributions of peoples of African origin and African skin colors. Lack of awareness of the contributions of Africa's crops has negative practical consequences, including inadequate investments in preserving and maximizing the use of crop diversity to facilitate breeding. This paper provides an overview and analysis of African crops that have made significant contributions to the United States and globally, and/or hold potential in the twenty-first century. The paper specifically discusses watermelon, coffee, kola, rooibos, oil palm, shea, cowpea/black eyed pea, leafy greens, okra, yam, sorghum, pearl millet, finger millet, teff, and fonio. The review focuses on the intersection of these crops with racialized peoples, with a particular focus on African-Americans starting with slavery. The analysis includes the sites of domestication of African crops, their historical migration out of Africa, their sociocultural contributions to cuisines and products around the world, their uses today, and the indigenous knowledge associated with traditional cultivation and landrace selection. The untapped potential of local genetic resources and indigenous agronomic strategies are also described. The review demonstrates that African crops played an important role in the development of American cuisine, beverages and household products. Many of these crops are nutritious, high value and stress tolerant. The paper concludes that African crops hold significant promise in improving the resiliency of global food production systems, to mitigate climate change and alleviate food insecurity and rural poverty, especially in dry regions of the world. It is hoped that this review contributes to teaching the next generation of agriculturalists, food scientists and international development professionals about the valuable contributions of Africa's resilient crops and peoples.
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Singh R, Low ETL, Ooi LCL, Ong-Abdullah M, Ting NC, Nookiah R, Ithnin M, Marjuni M, Mustaffa S, Yaakub Z, Amiruddin MD, Manaf MAA, Chan KL, Halim MAA, Sanusi NSNM, Lakey N, Sachdeva M, Bacher B, Garner PA, MacDonald JD, Smith SW, Wischmeyer C, Budiman MA, Beil M, Stroff C, Reed J, Van Brunt A, Berg H, Ordway JM, Sambanthamurthi R. Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles. THE NEW PHYTOLOGIST 2020; 226:426-440. [PMID: 31863488 DOI: 10.1111/nph.16387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS-box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two-hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele-specific. Our findings reveal allele-specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single-gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.
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Affiliation(s)
- Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Leslie Cheng-Li Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Maizura Ithnin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohamad Arif Abdul Manaf
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | | | | | | | | | | | | | | | | | | | | | - Jerry Reed
- Orion Genomics, St Louis, MO, 63108, USA
| | | | - Howard Berg
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | | | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6, Persiaran Institusi Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
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Teh CK, Lee HL, Abidin H, Ong AL, Mayes S, Chew FT, Appleton D. A practical genome-enabled legitimacy assay for oil palm breeding and seed production. BMC PLANT BIOLOGY 2019; 19:470. [PMID: 31690276 PMCID: PMC6833287 DOI: 10.1186/s12870-019-2062-x] [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: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Legitimacy in breeding and commercial crop production depends on optimised protocols to ensure purity of crosses and correct field planting of material. In oil palm, the presence of three fruit forms permits these assumptions to be tested, although only after field planting. The presence of incorrect fruit forms in a cross is a clear sign of illegitimacy. Given that tenera forms produce 30% more oil for the same weight of fruit as dura, the presence of low levels of dura contamination can have major effect during the economic lifespan of an oil palm, which is around 25 years. We evaluated two methods for legitimacy test 1) The use of SHELL markers to the gene that determines the shell-thickness trait 2) The use of SNP markers, to determine the legitimacy of the cross. RESULTS Our results indicate that the SHELL markers can theoretically reduce the major losses due to dura contamination of tenera planting material. However, these markers cannot distinguish illegitimate tenera, which reduces the value of having bred elite tenera for commercial planting and in the breeding programme, where fruit form is of limited utility, and incorrect identity could lead to significant problems. We propose an optimised approach using SNPs for routine quality control. CONCLUSIONS Both dura and tenera contamination can be identified and removed at or before the nursery stage. An optimised legitimacy assay using SNP markers coupled with a suitable sampling scheme is now ready to be deployed as a standard control for seed production and breeding in oil palm. The same approach will also be an effective solution for other perennial crops, such as coconut and date palm.
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Affiliation(s)
- Chee-Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
- School of Biosciences, University of Nottingham Malaysia, Semenyih, Selangor Malaysia
| | - Heng-Leng Lee
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
| | - Hafiza Abidin
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
- School of Biosciences, University of Nottingham Malaysia, Semenyih, Selangor Malaysia
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Lower Kent Ridge Rd, Singapore, Singapore
| | - David Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
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