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Cui Y, Yan J, Jiang L, Wang J, Huang M, Zhao X, Shi S. Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining in Larix olgensis. Int J Mol Sci 2024; 25:10212. [PMID: 39337698 PMCID: PMC11432355 DOI: 10.3390/ijms251810212] [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: 08/29/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 09/30/2024] Open
Abstract
Needles play key roles in photosynthesis and branch growth in Larix olgensis. However, genetic variation and SNP marker mining associated with needle and branch-related traits have not been reported yet. In this study, we examined 131 samples of unrelated genotypes from L. olgensis provenance trails. We investigated phenotypic data for seven needle and one branch-related traits before whole genome resequencing (WGRS) was employed to perform a genome-wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci that were significantly correlated with the studied traits. We identified a total of 243,090,868 SNP loci, and among them, we discovered a total of 161 SNP loci that were significantly associated with these traits using a general linear model (GLM). Based on the GWAS results, Kompetitive Allele-Specific PCR (KASP), designed based on the DNA of population samples, were used to validate the loci associated with L. olgensis phenotypes. In total, 20 KASP markers were selected from the 161 SNPs loci, and BSBM01000635.1_4693780, BSBM01000114.1_5114757, and BSBM01000114.1_5128586 were successfully amplified, were polymorphic, and were associated with the phenotypic variation. These developed KASP markers could be used for the genetic improvement of needle and branch-related traits in L. olgensis.
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Affiliation(s)
- Ying Cui
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China; (Y.C.)
| | - Jiawei Yan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, the Chinese Academy of Forestry, 1958 Box, Beijing 100091, China
| | - Luping Jiang
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China; (Y.C.)
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, the Chinese Academy of Forestry, 1958 Box, Beijing 100091, China
| | - Manman Huang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, the Chinese Academy of Forestry, 1958 Box, Beijing 100091, China
| | - Xiyang Zhao
- College of Forestry and Grassland, Jilin Agricultural University, Changchun 130118, China; (Y.C.)
| | - Shengqing Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, the Chinese Academy of Forestry, 1958 Box, Beijing 100091, China
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Mohd Zahid NII, Syed Othman SMI, Mustaffa AF, Ismail I, Che-Othman MH. Fine-tuning plant valuable secondary metabolite biosynthesis via small RNA manipulation: strategies and potential. PLANTA 2024; 260:89. [PMID: 39254898 DOI: 10.1007/s00425-024-04521-z] [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: 11/20/2023] [Accepted: 08/30/2024] [Indexed: 09/11/2024]
Abstract
Plants produce secondary metabolites that serve various functions, including defense against biotic and abiotic stimuli. Many of these secondary metabolites possess valuable applications in diverse fields, including medicine, cosmetic, agriculture, and food and beverage industries, exhibiting their importance in both plant biology and various human needs. Small RNAs (sRNA), such as microRNA (miRNA) and small interfering RNA (siRNA), have been shown to play significant roles in regulating the metabolic pathways post-transcriptionally by targeting specific key genes and transcription factors, thus offering a promising tool for enhancing plant secondary metabolite biosynthesis. In this review, we summarize current approaches for manipulating sRNAs to regulate secondary metabolite biosynthesis in plants. We provide an overview of the latest research strategies for sRNA manipulation across diverse plant species, including the identification of potential sRNAs involved in secondary metabolite biosynthesis in non-model plants. We also highlight the potential future research directions, focusing on the manipulation of sRNAs to produce high-value compounds with applications in pharmaceuticals, nutraceuticals, agriculture, cosmetics, and other industries. By exploring these advanced techniques, we aim to unlock new potentials for biotechnological applications, contributing to the production of high-value plant-derived products.
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Affiliation(s)
- Nur Irdina Izzatie Mohd Zahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia
| | - Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia
| | - Muhamad Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor, Malaysia.
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Wang J, Zhang L, Qi L, Zhang S. Integrated transcriptomic and metabolic analyses provide insights into the maintenance of embryogenic potential and the biosynthesis of phenolic acids and flavonoids involving transcription factors in Larix kaempferi (Lamb.) Carr. FRONTIERS IN PLANT SCIENCE 2022; 13:1056930. [PMID: 36466286 PMCID: PMC9714495 DOI: 10.3389/fpls.2022.1056930] [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: 09/29/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Somatic embryogenesis (SE) techniques have been established for micropropagation or basic research related to plant development in many conifer species. The frequent occurrence of non-embryogenic callus (NEC) during SE has impose constraints on the application of somatic embryogenesis SE in Larix kaempferi (Lamb.) Carr, but the potential regulatory mechanisms are poorly understood. In this study, integrated transcriptomic and metabolomic analyses were performed in embryogenic callus (EC) and NEC originating from a single immature zygotic embryo to better decipher the key molecular and metabolic mechanisms required for embryogenic potential maintenance. The results showed that a total of 13,842 differentially expressed genes (DEGs) were found in EC and NEC, among which many were enriched in plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and the biosynthesis of amino acids pathways. Metabolite profiling showed that 441 differentially accumulated metabolites (DAMs) were identified in EC and NEC. Both EC and NEC had vigorous primary metabolic activities, while most secondary metabolites were upregulated in NEC. Many totipotency-related transcription factor (TF) genes such as BBMs, WUSs, and LEC1 showed higher expression levels in EC compared with NEC, which may result in the higher accumulation of indole 3-acetic acid (IAA) in EC. NEC was characterized by upregulation of genes and metabolites associated with stress responses, such as DEGs involved in jasmonic acid (JA) and ethylene (ETH) biosynthesis and signal transduction pathways, and DEGs and DAMs related to phenylpropanoid and flavonoid biosynthesis. We predicted and analyzed TFs that could target several key co-expressed structural DEGs including two C4H genes, two CcoAOMT genes and three HCT genes involved in phenylpropanoid and flavonoid biosynthesis. Based on the targeted relationship and the co-expression network, two ERFs (Lk23436 and Lk458687), one MYB (Lk34626) and one C2C2-dof (Lk37167) may play an important role in regulating phenolic acid and flavonoid biosynthesis by transcriptionally regulating the expression of these structural genes. This study shows an approach involving integrated transcriptomic and metabolic analyses to obtain insights into molecular events underlying embryogenic potential maintenance and the biosynthesis mechanisms of key metabolites involving TF regulation, which provides valuable information for the improvement of SE efficiency in L. kaempferi.
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Affiliation(s)
- Junchen Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lifeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Liwang Qi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Zhang W, Tang Y, Han Y, Huang L, Zhou W, Zhou C, Hu Y, Lu R, Wang F, Shi W, Liu G. Immunotoxicity of pentachlorophenol to a marine bivalve species and potential toxification mechanisms underpinning. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129681. [PMID: 36104908 DOI: 10.1016/j.jhazmat.2022.129681] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/06/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The ubiquitous presence of pentachlorophenol (PCP) in ocean environments threatens marine organisms. However, its effects on immunity of marine invertebrates at environmentally realistic levels are still largely unknown. In this study, the immunotoxicity of PCP to a representative bivalve species was evaluated. In addition, its impacts on metabolism, energy supply, detoxification, and oxidative stress status were also analysed by physiological examination as well as comparative transcriptomic and metabolomic analyses to reveal potential mechanisms underpinning. Results illustrated that the immunity of blood clams was evidently hampered upon PCP exposure. Additionally, significant alterations in energy metabolism were detected in PCP-exposed clams. Meanwhile, the expressions of key detoxification genes and the in vivo contents (or activity) of key detoxification enzymes were markedly altered. Exposure to PCP also triggered significant elevations in intracellular ROS and MDA whereas evident suppression of haemocyte viability. The abovementioned findings were further supported by transcriptomic and metabolomic analyses. Our results suggest that PCP may hamper the immunity of the blood clam by (i) constraining the cellular energy supply through disrupting metabolism; and (ii) damaging haemocytes through inducing oxidative stress. Considering the high similarity of immunity among species, many marine invertebrates may be threatened by PCP, which deserves more attention.
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Affiliation(s)
- Weixia Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Tang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yu Han
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Huang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaosheng Zhou
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Yuan Hu
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Rongmao Lu
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Fang Wang
- Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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Over-Expression of the Cell-Cycle Gene LaCDKB1;2 Promotes Cell Proliferation and the Formation of Normal Cotyledonary Embryos during Larix kaempferi Somatic Embryogenesis. Genes (Basel) 2021; 12:genes12091435. [PMID: 34573419 PMCID: PMC8468589 DOI: 10.3390/genes12091435] [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: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022] Open
Abstract
Somatic embryogenesis is an effective tool for the production of forest tree seedlings with desirable characteristics; however, the low initiation frequency and productivity of high-quality mature somatic embryos are still limiting factors for Larix kaempferi (Japanese larch). Here, we analyzed the expression pattern of L. kaempferi cyclin-dependent kinase B 1;2 (LaCDKB1;2) during somatic embryogenesis in L. kaempferi and its relationship with the cell proliferation rate. We also analyzed the effect of LaCDKB1;2 over-expression on somatic embryo quality. The results revealed a positive correlation between LaCDKB1;2 expression and the cell proliferation rate during the proliferation stage. After LaCDKB1;2 over-expression, the proliferation rate of cultures increased, and the number of somatic embryos in transgenic cultures was 2.69 times that in non-transformed cultures. Notably, the number of normal cotyledonary embryos in transgenic cultures was 3 times that in non-transformed cultures, indicating that LaCDKB1;2 not only increases the proliferation of cultures and the number of somatic embryos but also improves the quality of somatic embryos. These results provide insight into the regulatory mechanisms of somatic embryogenesis as well as new Larix breeding material.
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