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Gu C, Zhang Y, Wang M, Lin Y, Zeng B, Zheng X, Song Y, Zeng R. Metabolomic Profiling Reveals the Anti-Herbivore Mechanisms of Rice ( Oryza sativa). Int J Mol Sci 2024; 25:5946. [PMID: 38892132 PMCID: PMC11172427 DOI: 10.3390/ijms25115946] [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: 04/16/2024] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
The use of secondary metabolites of rice to control pests has become a research hotspot, but little is known about the mechanism of rice self-resistance. In this study, metabolomics analysis was performed on two groups of rice (T1, with insect pests; T2, without pests), indicating that fatty acids, alkaloids, and phenolic acids were significantly up-regulated in T1. The up-regulated metabolites (p-value < 0.1) were enriched in linoleic acid metabolism, terpene, piperidine, and pyridine alkaloid biosynthesis, α-linolenic acid metabolism, and tryptophan metabolism. Six significantly up-regulated differential metabolites in T1 were screened out: N-trans-feruloyl-3-methoxytyramine (1), N-trans-feruloyltyramine (2), N-trans-p-coumaroyltyramine (3), N-cis-feruloyltyramine (4), N-phenylacetyl-L-glutamine (5), and benzamide (6). The insect growth inhibitory activities of these six different metabolites were determined, and the results show that compound 1 had the highest activity, which significantly inhibited the growth of Chilo suppressalis by 59.63%. Compounds 2-4 also showed a good inhibitory effect on the growth of Chilo suppressalis, while the other compounds had no significant effect. RNA-seq analyses showed that larval exposure to compound 1 up-regulated the genes that were significantly enriched in ribosome biogenesis in eukaryotes, the cell cycle, ribosomes, and other pathways. The down-regulated genes were significantly enriched in metabolic pathways, oxidative phosphorylation, the citrate cycle (TCA cycle), and other pathways. Eighteen up-regulated genes and fifteen down-regulated genes from the above significantly enriched pathways were screened out and verified by real-time quantitative PCR. The activities of detoxification enzymes (glutathione S-transferase (GST); UDP-glucuronosyltransferase (UGT); and carboxylesterase (CarE)) under larval exposure to compound 1 were measured, which indicated that the activity of GST was significantly inhibited by compound 1, while the activities of the UGT and CarE enzymes did not significantly change. As determined by UPLC-MS, the contents of compound 1 in the T1 and T2 groups were 8.55 ng/g and 0.53 ng/g, respectively, which indicated that pest insects significantly induced the synthesis of compound 1. Compound 1 may enhance rice insect resistance by inhibiting the detoxification enzyme activity and metabolism of Chilo suppressalis, as well as promoting cell proliferation to affect its normal growth and development process. The chemical-ecological mechanism of the insect resistance of rice is preliminarily clarified in this paper.
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Affiliation(s)
- Chengzhen Gu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Yujia Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Mengmeng Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Yangzheng Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Bixue Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Xinyu Zheng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (C.G.); (Y.Z.); (M.W.); (Y.L.); (B.Z.); (X.Z.)
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Ye Z, Mao D, Wang Y, Deng H, Liu X, Zhang T, Han Z, Zhang X. Comparative Genome-Wide Identification of the Fatty Acid Desaturase Gene Family in Tea and Oil Tea. PLANTS (BASEL, SWITZERLAND) 2024; 13:1444. [PMID: 38891253 PMCID: PMC11174766 DOI: 10.3390/plants13111444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Camellia oil is valuable as an edible oil and serves as a base material for a range of high-value products. Camellia plants of significant economic importance, such as Camellia sinensis and Camellia oleifera, have been classified into sect. Thea and sect. Oleifera, respectively. Fatty acid desaturases play a crucial role in catalyzing the formation of double bonds at specific positions of fatty acid chains, leading to the production of unsaturated fatty acids and contributing to lipid synthesis. Comparative genomics results have revealed that expanded gene families in oil tea are enriched in functions related to lipid, fatty acid, and seed processes. To explore the function of the FAD gene family, a total of 82 FAD genes were identified in tea and oil tea. Transcriptome data showed the differential expression of the FAD gene family in mature seeds of tea tree and oil tea tree. Furthermore, the structural analysis and clustering of FAD proteins provided insights for the further exploration of the function of the FAD gene family and its role in lipid synthesis. Overall, these findings shed light on the role of the FAD gene family in Camellia plants and their involvement in lipid metabolism, as well as provide a reference for understanding their function in oil synthesis.
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Affiliation(s)
- Ziqi Ye
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Dan Mao
- National Forest and Seedling Workstation of Hunan Province, The Forestry Department of Hunan Province, Changsha 410004, China; (D.M.); (Y.W.)
| | - Yujian Wang
- National Forest and Seedling Workstation of Hunan Province, The Forestry Department of Hunan Province, Changsha 410004, China; (D.M.); (Y.W.)
| | - Hongda Deng
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Xing Liu
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Tongyue Zhang
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Zhiqiang Han
- The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha 410004, China; (Z.Y.); (H.D.); (X.L.); (T.Z.)
| | - Xingtan Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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El Faqer A, Rabeh K, Alami M, Filali-Maltouf A, Belkadi B. In Silico Identification and Characterization of Fatty Acid Desaturase ( FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress. Bioinform Biol Insights 2024; 18:11779322241248908. [PMID: 38711943 PMCID: PMC11072076 DOI: 10.1177/11779322241248908] [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: 09/26/2023] [Accepted: 04/04/2024] [Indexed: 05/08/2024] Open
Abstract
Fatty acid desaturase (FAD) is the key enzyme that leads to the formation of unsaturated fatty acids by introducing double bonds into hydrocarbon chains, and it plays a critical role in plant lipid metabolism. However, no data are available on enzyme-associated genes in argan trees. In addition, a candidate gene approach was adopted to identify and characterize the gene sequences of interest that are potentially involved in oil quality and abiotic stress. Based on phylogenetic analyses, 18 putative FAD genes of Argania spinosa L. (AsFAD) were identified and assigned to three subfamilies: stearoyl-ACP desaturase (SAD), Δ-12 desaturase (FAD2/FAD6), and Δ-15 desaturase (FAD3/FAD7). Furthermore, gene structure and motif analyses revealed a conserved exon-intron organization among FAD members belonging to the various oil crops studied, and they exhibited conserved motifs within each subfamily. In addition, the gene structure shows a wide variation in intron numbers, ranging from 0 to 8, with two highly conserved intron phases (0 and 1). The AsFAD and AsSAD subfamilies consist of three (H(X)2-4H, H(X)2-3HH, and H/Q (X)2-3HH) and two (EEN(K)RHG and DEKRHE) conserved histidine boxes, respectively. A set of primer pairs were designed for each FAD gene, and tested on DNA extracted from argan leaves, in which all amplicons of the expected size were produced. These findings of candidate genes in A spinosa L. will provide valuable knowledge that further enhances our understanding of the potential roles of FAD genes in the quality of oil and abiotic stress in the argan tree.
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Affiliation(s)
- Abdelmoiz El Faqer
- Team of Microbiology and Molecular Biology, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Karim Rabeh
- Team of Microbiology and Molecular Biology, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohammed Alami
- Team of Microbiology and Molecular Biology, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Team of Microbiology and Molecular Biology, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Bouchra Belkadi
- Team of Microbiology and Molecular Biology, Plant and Microbial Biotechnology, Biodiversity and Environment Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Cao T, Du Q, Ge R, Li R. Genome-wide identification and characterization of FAD family genes in barley. PeerJ 2024; 12:e16812. [PMID: 38436034 PMCID: PMC10909363 DOI: 10.7717/peerj.16812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/29/2023] [Indexed: 03/05/2024] Open
Abstract
Fatty acid desaturases (FADs) play pivotal roles in determining plant stress tolerance. Barley is the most salt-tolerant cereal crop. In this study, we performed genome-wide identification and characterization analysis of the FAD gene family in barley (Hordeum vulgare). A total of 24 HvFADs were identified and divided into four subfamilies based on their amino acid sequence similarity. HvFADs unevenly distributed on six of seven barley chromosomes, and three clusters of HvFADs mainly occurred on the chromosome 2, 3 and 6. Segmental duplication events were found to be a main cause for the HvFAD gene family expansion. The same HvFAD subfamily showed the relatively consistent exon-intron composition and conserved motifs of HvFADs. Cis-element analysis in HvFAD promoters indicated that the expression of HvFADs may be subject to complex regulation, especially stress-responsive elements that may involve in saline-alkaline stress response. Combined transcriptomic data with quantitative experiments, at least five HvFADs highly expressed in roots under salt or alkali treatment, suggesting they may participate in saline or alkaline tolerance in barley. This study provides novel and valuable insights for underlying salt/alkali-tolerant mechanisms in barley.
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Affiliation(s)
- TingTing Cao
- College of Life Science, Hebei Normal University, Hebei, China
| | - QingWei Du
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - RongChao Ge
- College of Life Science, Hebei Normal University, Hebei, China
| | - RuiFen Li
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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5
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Gong D, Cong H, Liu S, Zhang L, Wei T, Shi X, Wang Z, Wu X, Song J. Transcriptome Identification and Analysis of Fatty Acid Desaturase Gene Expression at Different Temperatures in Tausonia pullulans 6A7. Microorganisms 2023; 11:2916. [PMID: 38138060 PMCID: PMC10745852 DOI: 10.3390/microorganisms11122916] [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: 10/30/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Tausonia pullulans 6A7 is a low-temperature yeast strain that can produce lipases. Yeast, which is made up of chassis cells, is an important part of synthetic biology, and the use of the lipase-producing properties of T. pullulans 6A7 for the production of fatty acids provides a new pathway for targeted synthesis in yeast cell factories. In this study, we performed RNA-seq on lipase-producing T. pullulans 6A7 at different temperatures (15 °C, 20 °C, 20 °C without corn oil, and 25 °C). Therefore, a total of 8455 differentially expressed genes were screened, and 16 of them were FAD candidate genes. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of group A (15 °C) vs. group D (25 °C) showed that the pathways of fatty acid biosynthesis (map00061) and the biosynthesis of unsaturated fatty acids (map01040) were significantly enriched. In the proposed temporal analysis of differentially expressed genes among the four temperature modulations, we found differentially expressed genes in nine clusters that had the same expression trends; these genes may be jointly involved in multiple biological processes in T. pullulans 6A7. In addition, we found 16 FAD candidate genes involved in fatty acid biosynthesis, and the expression of these genes had similar expression in the transcriptome trends with the different temperature treatments. These findings will help in future in-depth studies of the function and molecular mechanisms of these important FAD genes involved in fatty acid metabolism in yeast, and they could also be conducive to the establishment of a cellular factory for targeted fatty acid production by using yeast.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150006, China; (D.G.); (H.C.); (S.L.); (L.Z.); (T.W.); (X.S.); (Z.W.); (X.W.)
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Xi R, Liu H, Chen Y, Zhuang H, Han H, Wang H, Wang Q, Li N. Genome-Wide Characterization of Tomato FAD Gene Family and Expression Analysis under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:3818. [PMID: 38005715 PMCID: PMC10675527 DOI: 10.3390/plants12223818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023]
Abstract
The fatty acid desaturase (FAD) gene family plays a crucial regulatory role in the resistance process of plant biomembranes. To understand the role of FADs in tomato growth and development, this study identified and analyzed the tomato FAD gene family based on bioinformatics analysis methods. In this study, 26 SlFADs were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the SlFAD gene family was divided into six branches, and the exon-intron composition and conserved motifs of SlFADs clustered in the same branch were quite conservative. Several hormone and stress response elements in the SlFAD promoter suggest that the expression of SlFAD members is subject to complex regulation; the construction of a tomato FAD protein interaction network found that SlFAD proteins have apparent synergistic effects with SPA and GPAT proteins. qRT-PCR verification results show that SlFAD participates in the expression of tomato root, stem, and leaf tissues; SlFAD8 is mainly highly expressed in leaves; SlFAD9 plays a vital role in response to salt stress; and SlFAB5 regulates all stages of fruit development under the action of exogenous hormones. In summary, this study provides a basis for a systematic understanding of the SlFAD gene family. It provides a theoretical basis for in-depth research on the functional characteristics of tomato SlFAD genes.
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Affiliation(s)
- Rui Xi
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Huifang Liu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Yijia Chen
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hongmei Zhuang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hongwei Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Hao Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Qiang Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences/Xingjiang Engineering Research Center for Vegetables, Urumqi 830091, China; (R.X.); (H.L.); (Y.C.); (H.Z.); (H.H.); (H.W.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
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Yadav M, Panwar R, Rustagi A, Chakraborty A, Roy A, Singh IK, Singh A. Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense. FRONTIERS IN PLANT SCIENCE 2023; 14:1221526. [PMID: 38023937 PMCID: PMC10654349 DOI: 10.3389/fpls.2023.1221526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.
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Affiliation(s)
- Manisha Yadav
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Anjana Rustagi
- Department of Botany, Gargi College, University of Delhi, Delhi, India
| | - Amrita Chakraborty
- EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Forest Molecular Entomology Lab, EXTEMIT-K, EVA 4.0, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- J C Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Department of Botany, Gargi College, University of Delhi, Delhi, India
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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Dvorianinova EM, Zinovieva OL, Pushkova EN, Zhernova DA, Rozhmina TA, Povkhova LV, Novakovskiy RO, Sigova EA, Turba AA, Borkhert EV, Krasnov GS, Ruan C, Dmitriev AA, Melnikova NV. Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data. Int J Mol Sci 2023; 24:14885. [PMID: 37834335 PMCID: PMC10573214 DOI: 10.3390/ijms241914885] [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: 08/13/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.
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Affiliation(s)
| | - Olga L. Zinovieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia
| | - Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Salaria S, Boatwright JL, Johnson N, Madurapperumage A, Joshi P, Thavarajah P, Vandemark G, Thavarajah D. Fatty acid composition and genome-wide associations of a chickpea (Cicer arietinum L.) diversity panel for biofortification efforts. Sci Rep 2023; 13:14002. [PMID: 37635199 PMCID: PMC10460795 DOI: 10.1038/s41598-023-41274-3] [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: 02/10/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023] Open
Abstract
Chickpea is a nutritionally dense pulse crop with high levels of protein, carbohydrates, micronutrients and low levels of fats. Chickpea fatty acids are associated with a reduced risk of obesity, blood cholesterol, and cardiovascular diseases in humans. We measured four primary chickpea fatty acids; palmitic acid (PA), linoleic acid (LA), alpha-linolenic acid (ALA), and oleic acid (OA), which are crucial for human health and plant stress responses in a chickpea diversity panel with 256 accessions (Kabuli and desi types). A wide concentration range was found for PA (450.7-912.6 mg/100 g), LA (1605.7-3459.9 mg/100 g), ALA (416.4-864.5 mg/100 g), and OA (1035.5-1907.2 mg/100 g). The percent recommended daily allowances also varied for PA (3.3-6.8%), LA (21.4-46.1%), ALA (34.7-72%), and OA (4.3-7.9%). Weak correlations were found among fatty acids. Genome-wide association studies (GWAS) were conducted using genotyping-by-sequencing data. Five significant single nucleotide polymorphisms (SNPs) were identified for PA. Admixture population structure analysis revealed seven subpopulations based on ancestral diversity in this panel. This is the first reported study to characterize fatty acid profiles across a chickpea diversity panel and perform GWAS to detect associations between genetic markers and concentrations of selected fatty acids. These findings demonstrate biofortification of chickpea fatty acids is possible using conventional and genomic breeding techniques, to develop superior cultivars with better fatty acid profiles for improved human health and plant stress responses.
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Affiliation(s)
- Sonia Salaria
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - J Lucas Boatwright
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
- Advanced Plant Technology, Clemson University, Clemson, SC, 29634, USA
| | - Nathan Johnson
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Amod Madurapperumage
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Priyanka Joshi
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Pushparajah Thavarajah
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - George Vandemark
- Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Washington State University, 303 Johnson Hall, Pullman, WA, 99164, USA
| | - Dil Thavarajah
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA.
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Shaheen N, Khan UM, Farooq A, Zafar UB, Khan SH, Ahmad S, Azhar MT, Atif RM, Rana IA, Seo H. Comparative transcriptomic and evolutionary analysis of FAD-like genes of Brassica species revealed their role in fatty acid biosynthesis and stress tolerance. BMC PLANT BIOLOGY 2023; 23:250. [PMID: 37173631 PMCID: PMC10176799 DOI: 10.1186/s12870-023-04232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Fatty acid desaturases (FADs) are involved in regulating plant fatty acid composition by adding double bonds to growing hydrocarbon chain. Apart from regulating fatty acid composition FADs are of great importance, and are involved in stress responsiveness, plant development, and defense mechanisms. FADs have been extensively studied in crop plants, and are broadly classed into soluble and non-soluble fatty acids. However, FADs have not yet been characterized in Brassica carinata and its progenitors. RESULTS Here we have performed comparative genome-wide identification of FADs and have identified 131 soluble and 28 non-soluble FADs in allotetraploid B. carinata and its diploid parents. Most soluble FAD proteins are predicted to be resided in endomembrane system, whereas FAB proteins were found to be localized in chloroplast. Phylogenetic analysis classed the soluble and non-soluble FAD proteins into seven and four clusters, respectively. Positive type of selection seemed to be dominant in both FADs suggesting the impact of evolution on these gene families. Upstream regions of both FADs were enriched in stress related cis-regulatory elements and among them ABRE type of elements were in abundance. Comparative transcriptomic data analysis output highlighted that FADs expression reduced gradually in mature seed and embryonic tissues. Moreover, under heat stress during seed and embryo development seven genes remained up-regulated regardless of external stress. Three FADs were only induced under elevated temperature whereas five genes were upregulated under Xanthomonas campestris stress suggesting their involvement in abiotic and biotic stress response. CONCLUSIONS The current study provides insights into the evolution of FADs and their role in B. carinata under stress conditions. Moreover, the functional characterization of stress-related genes would exploit their utilization in future breeding programs of B. carinata and its progenitors.
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Affiliation(s)
- Nabeel Shaheen
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Uzair Muhammad Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ayesha Farooq
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ummul Buneen Zafar
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sultan Habibullah Khan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Shakeel Ahmad
- Seed Center and Plant Genetic Resources Bank, Ministry of Environment, Water & Agriculture, Riyadh, 14712, Saudi Arabia
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- School of Agriculture Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan
- Precision Agriculture and Analytics Lab, National Center in Big Data and Cloud Computing (NCBC), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Iqrar Ahmad Rana
- Center for Advanced Studies in Agriculture and Food security, University of Agriculture, Faisalabad, 38000, Pakistan.
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan.
| | - Hyojin Seo
- Korea Soybean Research Institute, Jinju, 52840, Korea.
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11
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Saini R, Adhikary A, Juneja S, Kumar R, Singh I, Nayyar H, Kumar S. Drought priming triggers diverse metabolic adjustments and induces chilling tolerance in chickpea (Cicer arietinum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:418-439. [PMID: 36493590 DOI: 10.1016/j.plaphy.2022.11.034] [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: 07/20/2022] [Revised: 11/04/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Chickpea (Cicer arietinum L.) suffers from chilling stress at the reproductive stage (<15 °C) which leads to significant yield loss. This study presents a comprehensive plant response to drought priming and its effect on chilling tolerance during the reproductive stage in two chickpea cultivars PBG1 and PBG5. Lipidome profiling (Fatty acid methyl esters analysis), metabolome profiling (GC-MS based untargeted analysis), fatty acid desaturases and antioxidative gene expression (qRT-PCR) were analyzed to monitor physiological and biochemical events after priming during flowering, podding and seed filling stages. Drought priming alleviated membrane damage and chlorophyll degradation by increasing membrane unsaturated fatty acids (18:3) along with up-regulation of various fatty acid desaturases (CaFADs) genes and antioxidative machinery during flowering and improved seed yield in PBG5. PCA, HCA, and KEGG pathway analysis of 87 identified metabolites showed that metabolites were regulated differently in both cultivars under non-primed and primed conditions. The plant response was more apparent at flowering and podding stages which coincided with chilling temperature (<15 °C). Drought priming stimulated many important genes, especially FADs, antioxidative proteins and accumulation of key metabolites (proline and TCA intermediates) required for defense especially in PBG5. This explains that plant's response to drought priming not only depends on developmental stage, and temperature regime (<15 °C) but also on the genotypic-specificity.
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Affiliation(s)
- Rashmi Saini
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Arindam Adhikary
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Sumandeep Juneja
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Rashpal Kumar
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India
| | - Sanjeev Kumar
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151401, India; Department of Botany, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, India.
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Zhang B, Xia P, Yu H, Li W, Chai W, Liang Z. Based on the whole genome clarified the evolution and expression process of fatty acid desaturase genes in three soybeans. Int J Biol Macromol 2021; 182:1966-1980. [PMID: 34052275 DOI: 10.1016/j.ijbiomac.2021.05.161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022]
Abstract
Soybean is an important oil crop cultivated worldwide. With the increasing global population crossed with growing challenging cultivation conditions, improving soybean breeding by selecting important traits is urgent needed. Genes coding for plant fatty acid desaturases (FADs) genes are major candidates for that, because they are involving in controlling fatty acid composition and holding membrane fluidity under abiotic stress. Here, 75 FADs were found in three soybean genomes, which were further classified into four sub-groups. Phylogenetic tree, gene structure, motif and promoter analysis showed that the FAD gene family was conserved in the three soybeans. In addition, the numbers of omega desaturase from Chinese cultivated varieties were significantly higher than those in Chinese wild soybean and ancient polyploid soybean, respectively. However, it was the opposite for the sphingolipid subfamily. These results indicated that each subfamily was subjected to different selection pressures during cultivation and domestication. As the extra genes of the subfamily were very close to other family members' positions on chromosomes, they should be produced by duplication. The cis-element analysis of FAD promoter sequences revealed that upstream sequences of FAD contained abundant light, hormone and abiotic stress responsive cis-elements, suggesting that the quality of soybean could be improved by regulating these stresses. Expression analysis of Chinese wild soybean under salt stress showed that GsDES1.1, GsDES1.2, GsFAD2.1 and GsSLD1 in leaves and GsSLD2, GsSLD5 and GsSLD6 in roots were not closely related to salt stress response. Therefore, we explored the significant role of conserved, duplicated and neofunctionalized FAD in the domestication of soybean, which contributes to the importance of soybean as a global oil crop.
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Affiliation(s)
- Bingxue Zhang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Pengguo Xia
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Haizheng Yu
- Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenrui Li
- Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Zongsuo Liang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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13
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Li J, Liu A, Najeeb U, Zhou W, Liu H, Yan G, Gill RA, Yun X, Bai Q, Xu L. Genome-wide investigation and expression analysis of membrane-bound fatty acid desaturase genes under different biotic and abiotic stresses in sunflower (Helianthus annuus L.). Int J Biol Macromol 2021; 175:188-198. [PMID: 33549671 DOI: 10.1016/j.ijbiomac.2021.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
Membrane-bound fatty acid desaturase (FAD) gene family plays crucial roles in regulation of fatty acid (FA) compositions in plants. Sunflower (Helianthus annuus L.) is an important oilseed crop in the world; however, no comprehensive study on exploring the role of FAD family in relation to stress tolerance in sunflower has been performed yet. In this study, we identified 40 putative FAD genes in H. annuus (HaFAD), which were unevenly distributed across 13 of the total 17 chromosomes. Phylogenetic analysis indicated that HaFAD genes were divided into four subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that tandem duplication events played a crucial role in the expansion of HaFAD gene family. In addition, tissue-specific expression showed that 32 HaFAD genes were widely expressed in various tissues or organs of sunflower. Furthermore, qRT-PCR results revealed significant expression changes of HaFAD genes in response to abiotic (cadmium, drought) and biotic (Orobanche cumana) stresses, suggesting their important functions in response to different stresses. Therefore, our results provide insights into HaFAD gene family in response to different stresses, and some specific up-regulated genes such as HaFAD3.2, HaADS8, HaFAD2.1, and HaADS9 would be the potential candidate genes for the sunflower tolerance breeding.
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Affiliation(s)
- Juanjuan Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ake Liu
- Faculty of Biology Science and Technology, Changzhi University, Shanxi 046011, China.
| | - Ullah Najeeb
- Queensland Alliance for Agriculture and Food Innovation, Centre for Plant Science, The University of Queensland, Toowoomba, QLD 4350, Australia
| | - Weijun Zhou
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rafaqat Ali Gill
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaopeng Yun
- Institute of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010031, China
| | - Quanjiang Bai
- Institute of Plant Protection, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot 010031, China
| | - Ling Xu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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