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Yan L, Fang H, Liang Y, Wang Y, Ren F, Xie X, Wu D. Transcriptome analyses of Acer Truncatum Bunge seeds to delineate the genes involved in fatty acid metabolism. BMC Genomics 2024; 25:605. [PMID: 38886635 PMCID: PMC11181630 DOI: 10.1186/s12864-024-10481-1] [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: 09/20/2023] [Accepted: 05/30/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Acer truncatum Bunge is an economic, ecological, oil, and medicinal tree, and its kernel oil is rich in nervonic acid. It is crucial to explore the transcriptional expression patterns of genes affecting fatty acid synthesis to improve the quality of Acer truncatum oil. RESULTS This study used the seeds from high fatty acid strain YQC and those from low fatty acid strain Y38 as the test materials. Specifically, we performed a comparative transcriptome analysis of Y38 seeds and YQC to identify differentially expressed genes (DEGs) at two time points (seeds 30 days after the blooming period and 90 days after the blooming period). Compared with YQC_1 (YQC seeds at 30 days after the blooming period), a total of 3,618 DEGs were identified, including 2,333 up-regulated and 1,285 downregulated DEGs in Y38_1 (Y38 seeds at 30 days after blooming period). In the Y38_2 (Y38 seeds at 90 days after the blooming period) versus YQC_2 (YQC seeds at 90 days after the blooming period) comparison group, 9,340 genes were differentially expressed, including 5,422 up-regulated and 3,918 down-regulated genes. The number of DEGs in Y38 compared to YQC was significantly higher in the late stages of seed development. Gene functional enrichment analyses showed that the DEGs were mainly involved in the fatty acid biosynthesis pathway. And two fatty acid synthesis-related genes and seven nervonic acid synthesis-related genes were validated by qRT-PCR. CONCLUSIONS This study provides a basis for further research on biosynthesizing fatty acids and nervonic acidnervonic acids in A. truncatum seeds.
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Affiliation(s)
- Liping Yan
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Provincial Academy of Forestry, Jinan, Shandong, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yan Liang
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Provincial Academy of Forestry, Jinan, Shandong, China
| | - Yinhua Wang
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Provincial Academy of Forestry, Jinan, Shandong, China
| | - Fei Ren
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Provincial Academy of Forestry, Jinan, Shandong, China
| | - Xiaoman Xie
- Shandong Provincial Forest and Grass Germplasm Resources Center, Jinan, Shandong, China.
| | - Dejun Wu
- Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Shandong Provincial Academy of Forestry, Jinan, Shandong, China.
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Wei L, Yang C, John Martin JJ, Li R, Zhou L, Cheng S, Cao H, Liu X. Metabonomics and Transcriptomic Analysis of Free Fatty Acid Synthesis in Seedless and Tenera Oil Palm. Int J Mol Sci 2024; 25:1686. [PMID: 38338979 PMCID: PMC10855455 DOI: 10.3390/ijms25031686] [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: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Oil palm, a tropical woody oil crop, is widely used in food, cosmetics, and pharmaceuticals due to its high production efficiency and economic value. Palm oil is rich in free fatty acids, polyphenols, vitamin E, and other nutrients, which are beneficial for human health when consumed appropriately. Therefore, investigating the dynamic changes in free fatty acid content at different stages of development and hypothesizing the influence of regulatory genes on free fatty acid metabolism is crucial for improving palm oil quality and accelerating industry growth. LC-MS/MS is used to analyze the composition and content of free fatty acids in the flesh after 95 days (MS1 and MT1), 125 days (MS2 and MT2), and 185 days (MS3 and MT3) of Seedless (MS) and Tenera (MT) oil palm species fruit pollination. RNA-Seq was used to analyze the expression of genes regulating free fatty acid synthesis and accumulation, with differences in genes and metabolites mapped to the KEGG pathway map using the KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis method. A metabolomics study identified 17 types of saturated and 13 types of unsaturated free fatty acids during the development of MS and MT. Transcriptomic research revealed that 10,804 significantly different expression genes were acquired in the set differential gene threshold between MS and MT. The results showed that FabB was positively correlated with the contents of three main free fatty acids (stearic acid, myristate acid, and palmitic acid) and negatively correlated with the contents of free palmitic acid in the flesh of MS and MT. ACSL and FATB were positively correlated with the contents of three main free fatty acids and negatively correlated with free myristate acid. The study reveals that the expression of key enzyme genes, FabB and FabF, may improve the synthesis of free myristate in oil palm flesh, while FabF, ACSL, and FATB genes may facilitate the production of free palmitoleic acid. These genes may also promote the synthesis of free stearic acid and palmitoleic acid in oil palm flesh. However, the FabB gene may inhibit stearic acid synthesis, while ACSL and FATB genes may hinder myristate acid production. This study provides a theoretical basis for improving palm oil quality.
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Affiliation(s)
- Lu Wei
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
- School of Horticulture, Hainan University, Haikou 570228, China
| | - Cheng Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Rui Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Shuanghong Cheng
- College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China;
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
| | - Xiaoyu Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China; (L.W.); (C.Y.); (J.J.J.M.); (R.L.); (L.Z.)
- National Key Laboratory for Tropical Crop Breeding, Haikou 571101, China
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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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Comparative transcriptome profiling and molecular marker development for oil palm fruit color. Sci Rep 2022; 12:15507. [PMID: 36109663 PMCID: PMC9478095 DOI: 10.1038/s41598-022-19890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
Oil palm harvesting is normally determined by fruit exocarp color. To detect expressed sequence tag (EST)-simple sequence repeat (SSR) markers in oil palm hybrid populations, de novo transcriptomic profiling of Nigeria black and Suratthani 1 (Deli × Calabar) plants was performed. More than 46 million high-quality clean reads with a mean length of 1117 bp were generated. Functional annotation and gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the genes were involved in fruit color development and pigment synthesis. Comparison of immature/mature DEGs indicated that nigrescent fruit color was driven by the anthocyanin biosynthesis pathway (ABP); however, the carotenoid biosynthesis pathway (CBP) was involved in the color development of both fruit types. The transcripts of both unique and different genes involved in the ABP and CBP in higher plants were highlighted for further study, especially 3GT, downstream genes in the ABP, and DEARF27 in the CBP. Additionally, SSR primer motifs, namely, 9949, discovered from the DEGs upregulated in the virescent type that encode vacuolar iron transporter (VIT), could separate the nigrescence and virescence traits of Nigeria hybrids. This novel primer has potential to be used as a molecular for further selection in breeding programs especially involving the specific genetic backgrounds described in this study.
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