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Mai NTP, Nguyen LTT, Tran SG, To HTM. Genome-wide association study reveals useful QTL and genes controlling the fatty acid composition in rice bran oil using Vietnamese rice landraces. Funct Integr Genomics 2023; 23:150. [PMID: 37156920 DOI: 10.1007/s10142-023-01080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
In rice (Oryza sativa L.), rice bran contains valuable nutritional constituents, such as high unsaturated fat content, tocotrienols, inositol, γ-oryzanol, and phytosterols, all of which are of nutritional and pharmaceuticals interest. There is now a rising market demand for rice bran oil, which makes research into their content and fatty acid profile an area of interest. As it is evident that lipid content has a substantial impact on the eating, cooking, and storage quality of rice, an understanding of the genetic mechanisms that determine oil content in rice is of great importance, equal to that of rice quality. Therefore, in this study, we performed a genome-wide association study on the composition and oil concentration of 161 Vietnamese rice varieties. Five categories of fatty acids in rice bran were discovered and the bran oil concentration profile in different rice accessions was identified. We also identified 229 important markers related to the fatty acid composition of bran oil, distributed mainly on chromosomes 1 and 7. Seven quantitative trait loci and five potential genes related to unsaturated fatty acid content were detected, including OsKASI, OsFAD, OsARF, OsGAPDH, and OsMADS29. These results provide insights into the genetic basis of rice bran oil composition, which is pivotal to the metabolic engineering of rice plants with desirable bran oil content through candidate genes selection.
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Affiliation(s)
- Nga T P Mai
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Linh Thi Thuy Nguyen
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Son Giang Tran
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam
| | - Huong Thi Mai To
- University of Sciences and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, 10000, Ha Noi City, Vietnam.
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Yousefi K, Abdullah SNA, Hatta MAM, Ling KL. Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091913. [PMID: 37176970 PMCID: PMC10181077 DOI: 10.3390/plants12091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023]
Abstract
Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome's structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.
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Affiliation(s)
- Kobra Yousefi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kong Lih Ling
- Laboratory of Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
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Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y. Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. FRONTIERS IN PLANT SCIENCE 2022; 13:1042828. [PMID: 36578341 PMCID: PMC9791139 DOI: 10.3389/fpls.2022.1042828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.
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Affiliation(s)
- Faiza Shafique Khan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapeng Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Peng Shi
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Zhiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yin Min Htwe
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yong Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
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Xu X, Li M, Zou JX, Zheng YS, Li DD. EgMYB108 regulates very long-chain fatty acid (VLCFA) anabolism in the mesocarp of oil palm. PLANT CELL REPORTS 2022; 41:1449-1460. [PMID: 35362736 DOI: 10.1007/s00299-022-02868-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
EgMYB108 regulates VLCFA anabolism in oil palm. Very long-chain fatty acids (VLCFAs), which are fatty acids with more than 18 C, can not only be used as a form of triglyceride (TAG) but also provide precursors for the biosynthesis of cuticle wax, and they exist in plant epidermal cells in the form of wax in higher plants. However, which and how transcriptional factors (TFs) regulate this process is largely unknown in oil palm. In this study, a MYB transcription factor (EgMYB108) with high expression in the mesocarp of oil palm fruit was characterized. Overexpression of EgMYB108 promoted not only total lipid content but also VLCFA accumulation in oil palm embryoids. Subsequently, transient transformation in protoplasts and qRT-PCR analysis indicated that the EgKCS5 and EgLACS4 genes were significantly increased with the overexpression of EgMYB108. Furthermore, yeast one‑hybrid assays, dual-luciferase assays and EMSAs demonstrated that EgMYB108 binds to the promoters of EgKCS5 and EgLACS4 and regulates their transcription. Finally, EgMYB108 interacts with the promoters of EgLACS and EgKCS simultaneously and finally improves the VLCFA and total lipid contents; a pathway summarizing this interaction was depicted.. The results provide new insight into the mechanism by which EgMYB108 regulates lipid and VLCFA accumulation in oil palm.
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Affiliation(s)
- Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Menghan Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Ji-Xin Zou
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yu-Sheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China.
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Jiang H, Guo D, Ye J, Gao Y, Liu H, Wang Y, Xue M, Yan Q, Chen J, Duan L, Li G, Li X, Xie L. Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1697-1710. [PMID: 34228847 DOI: 10.1111/tpj.15411] [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: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.
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Affiliation(s)
- Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiali Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfang Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Huiqing Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Yue Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiaxun Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Lepeng Duan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
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