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Wang L, Lin G, Li Y, Qu W, Wang Y, Lin Y, Huang Y, Li J, Qian C, Yang G, Zuo Q. Phenotype, Biomass, Carbon and Nitrogen Assimilation, and Antioxidant Response of Rapeseed under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1488. [PMID: 38891297 PMCID: PMC11175084 DOI: 10.3390/plants13111488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Salt stress is one of the major adverse factors affecting plant growth and crop production. Rapeseed is an important oil crop, providing high-quality edible oil for human consumption. This experiment was conducted to investigate the effects of salt stress on the phenotypic traits and physiological processes of rapeseed. The soil salinity was manipulated by setting three different levels: 0 g NaCl kg-1 soil (referred to as S0), 1.5 g NaCl kg-1 soil (referred to as S1), and 3.0 g NaCl kg-1 soil (referred to as S2). In general, the results indicated that the plant height, leaf area, and root neck diameter decreased with an increase in soil salinity. In addition, the biomass of various organs at all growth stages decreased as soil salinity increased from S0 to S2. The increasing soil salinity improved the distribution of biomass in the root and leaf at the seedling and flowering stages, indicating that rapeseed plants subjected to salt stress during the vegetative stage are capable of adapting their growth pattern to sustain their capacity for nutrient and water uptake, as well as leaf photosynthesis. However, as the soil salinity increased, there was a decrease in the distribution of biomass in the pod and seed at the maturity stage, while an increase was observed in the root and stem, suggesting that salt stress inhibited carbohydrate transport into reproductive organs. Moreover, the C and N accumulation at the flowering and maturity stages exhibited a reduction in direct correlation with the increase in soil salinity. High soil salinity resulted in a reduction in the C/N, indicating that salt stress exerted a greater adverse effect on C assimilation compared to N assimilation, leading to an increase in seed protein content and a decrease in oil content. Furthermore, as soil salinity increased from S0 to S2, the activity of superoxide dismutase (SOD) and catalase (CAT) and the content of soluble protein and sugar increased by 58.39%, 33.38%, 15.57%, and 13.88% at the seedling stage, and 38.69%, 22.85%, 12.04%, and 8.26% at the flowering stage, respectively. In summary, this study revealed that salt stress inhibited C and N assimilation, leading to a suppressed phenotype and biomass accumulation. The imbalanced C and N assimilation under salt stress contributed to the alterations in the seed oil and protein content. Rapeseed had a certain degree of salt tolerance by improving antioxidants and osmolytes.
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Affiliation(s)
- Long Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Guobing Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yiyang Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenting Qu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yaowei Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yihang Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jing Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chen Qian
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Guang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qingsong Zuo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China; (L.W.); (G.L.); (Y.L.); (W.Q.); (Y.W.); (Y.L.); (Y.H.); (J.L.); (C.Q.); (G.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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Mi C, Zhang Y, Zhao Y, Lin L. Mechanisms of low nighttime temperature promote oil accumulation in Brassica napus L. based on in-depth transcriptome analysis. PHYSIOLOGIA PLANTARUM 2024; 176:e14372. [PMID: 38812077 DOI: 10.1111/ppl.14372] [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: 10/20/2023] [Accepted: 04/08/2024] [Indexed: 05/31/2024]
Abstract
Rape (Brassica napus L.; AACC) is an important oil-bearing crop worldwide. Temperature significantly affects the production of oil crops; however, the mechanisms underlying temperature-promoted oil biosynthesis remain largely unknown. In this study, we found that a temperature-sensitive cultivar (O) could accumulate higher seed oil content under low nighttime temperatures (LNT,13°C) compared with a temperature-insensitive cultivar (S). We performed an in-depth transcriptome analysis of seeds from both cultivars grown under different nighttime temperatures. We found that low nighttime temperatures induced significant changes in the transcription patterns in the seeds of both cultivars. In contrast, the expression of genes associated with fatty acid and lipid pathways was higher in the O cultivar than in the S cultivar under low nighttime temperatures. Among these genes, we identified 14 genes associated with oil production, especially BnLPP and ACAA1, which were remarkably upregulated in the O cultivar in response to low nighttime temperatures compared to S. Further, a WGCNA analysis and qRT-PCR verification revealed that these genes were mainly regulated by five transcription factors, WRKY20, MYB86, bHLH144, bHLH95, and NAC12, whose expression was also increased in O compared to S under LNT. These results allowed the elucidation of the probable molecular mechanism of oil accumulation under LNT conditions in the O cultivar. Subsequent biochemical assays verified that BnMYB86 transcriptionally activated BnLPP expression, contributing to oil accumulation. Meanwhile, at LNT, the expression levels of these genes in the O plants were higher than at high nighttime temperatures, DEGs (SUT, PGK, PK, GPDH, ACCase, SAD, KAS II, LACS, FAD2, FAD3, KCS, KAR, ECR, GPAT, LPAAT, PAP, DGAT, STERO) related to lipid biosynthesis were also upregulated, most of which are used in oil accumulation.
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Affiliation(s)
- Chao Mi
- Agricultural Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Yusong Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yanning Zhao
- Vegetable Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Liangbin Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [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: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Samynathan R, Venkidasamy B, Shanmugam A, Ramalingam S, Thiruvengadam M. Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants. Front Genet 2023; 14:1272446. [PMID: 37886688 PMCID: PMC10597799 DOI: 10.3389/fgene.2023.1272446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.
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Affiliation(s)
- Ramkumar Samynathan
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Ashokraj Shanmugam
- Plant Physiology and Biotechnology Division, UPASI Tea Research Foundation, Coimbatore, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Lab, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, Republic of Korea
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Yu L, Liu D, Yin F, Yu P, Lu S, Zhang Y, Zhao H, Lu C, Yao X, Dai C, Yang QY, Guo L. Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes. BMC Biol 2023; 21:202. [PMID: 37775748 PMCID: PMC10543336 DOI: 10.1186/s12915-023-01705-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Brassica napus is an important oilseed crop providing high-quality vegetable oils for human consumption and non-food applications. However, the regulation between embryo and seed coat for the synthesis of oil and phenylpropanoid compounds remains largely unclear. RESULTS Here, we analyzed the transcriptomes in developing seeds at 2-day intervals from 14 days after flowering (DAF) to 64 DAF. The 26 high-resolution time-course transcriptomes are clearly clustered into five distinct groups from stage I to stage V. A total of 2217 genes including 136 transcription factors, are specifically expressed in the seed and show high temporal specificity by being expressed only at certain stages of seed development. Furthermore, we analyzed the co-expression networks during seed development, which mainly included master regulatory transcription factors, lipid, and phenylpropane metabolism genes. The results show that the phenylpropane pathway is prominent during seed development, and the key enzymes in the phenylpropane metabolic pathway, including TT5, BAN, and the transporter TT19, were directly or indirectly related to many key enzymes and transcription factors involved in oil accumulation. We identified candidate genes that may regulate seed oil content based on the co-expression network analysis combined with correlation analysis of the gene expression with seed oil content and seed coat content. CONCLUSIONS Overall, these results reveal the transcriptional regulation between lipid and phenylpropane accumulation during B. napus seed development. The established co-expression networks and predicted key factors provide important resources for future studies to reveal the genetic control of oil accumulation in B. napus seeds.
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Affiliation(s)
- Liangqian Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feifan Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, 59717, USA
| | - Xuan Yao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
- Yazhouwan National Laboratory, Sanya, 572025, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Yazhouwan National Laboratory, Sanya, 572025, China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- Yazhouwan National Laboratory, Sanya, 572025, China.
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Yang L, Yang L, Ding Y, Chen Y, Liu N, Zhou X, Huang L, Luo H, Xie M, Liao B, Jiang H. Global Transcriptome and Co-Expression Network Analyses Revealed Hub Genes Controlling Seed Size/Weight and/or Oil Content in Peanut. PLANTS (BASEL, SWITZERLAND) 2023; 12:3144. [PMID: 37687391 PMCID: PMC10490140 DOI: 10.3390/plants12173144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/21/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important economic and oilseed crop worldwide, providing high-quality edible oil and high protein content. Seed size/weight and oil content are two important determinants of yield and quality in peanut breeding. To identify key regulators controlling these two traits, two peanut cultivars with contrasting phenotypes were compared to each other, one having a larger seed size and higher oil content (Zhonghua16, ZH16 for short), while the second cultivar had smaller-sized seeds and lower oil content (Zhonghua6, ZH6). Whole transcriptome analyses were performed on these two cultivars at four stages of seed development. The results showed that ~40% of the expressed genes were stage-specific in each cultivar during seed development, especially at the early stage of development. In addition, we identified a total of 5356 differentially expressed genes (DEGs) between ZH16 and ZH6 across four development stages. Weighted gene co-expression network analysis (WGCNA) based on DEGs revealed multiple hub genes with potential roles in seed size/weight and/or oil content. These hub genes were mainly involved in transcription factors (TFs), phytohormones, the ubiquitin-proteasome pathway, and fatty acid synthesis. Overall, the candidate genes and co-expression networks detected in this study could be a valuable resource for genetic breeding to improve seed yield and quality traits in peanut.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430000, China; (L.Y.); (L.Y.); (Y.D.); (Y.C.); (N.L.); (X.Z.); (L.H.); (H.L.); (M.X.); (B.L.)
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Liu S, Liu Z, Hou X, Li X. Genetic mapping and functional genomics of soybean seed protein. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:29. [PMID: 37313523 PMCID: PMC10248706 DOI: 10.1007/s11032-023-01373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01373-5.
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Affiliation(s)
- Shu Liu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhaojun Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 China
| | - Xingliang Hou
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
| | - Xiaoming Li
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025 China
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Fu X, Li G, Hu F, Huang J, Lou Y, Li Y, Li Y, He H, Lv Y, Cheng J. Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes. BMC Genom Data 2023; 24:12. [PMID: 36849914 PMCID: PMC9969625 DOI: 10.1186/s12863-022-01098-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits. Despite high economic importance, the regulatory aspects of bean quality are yet largely unknown in peaberry. A transcriptome analysis was performed by using peaberry and regular coffee beans in this study. RESULTS The result of phenotypic analysis stated a difference in the physical attributes of both coffee beans. In addition, transcriptome analysis revealed low genetic differences. Only 139 differentially expressed genes were detected in which 54 genes exhibited up-regulation and 85 showed down-regulations in peaberry beans compared to regular beans. The majority of differentially expressed genes had functional annotation with cell wall modification, lipid binding, protein binding, oxidoreductase activity, and transmembrane transportation. Many fold lower expression of Ca25840-PMEs1, Ca30827-PMEs2, Ca30828-PMEs3, Ca25839-PMEs4, Ca36469-PGs. and Ca03656-Csl genes annotated with cell wall modification might play a critical role to develop different bean shape patterns in Arabica. The ERECTA family genes Ca15802-ERL1, Ca99619-ERL2, Ca07439-ERL3, Ca97226-ERL4, Ca89747-ERL5, Ca07056-ERL6, Ca01141-ERL7, and Ca32419-ERL8 along lipid metabolic pathway genes Ca06708-ACOX1, Ca29177-ACOX2, Ca01563-ACOX3, Ca34321-CPFA1, and Ca36201-CPFA2 are predicted to regulate different shaped bean development. In addition, flavonoid biosynthesis correlated genes Ca03809-F3H, Ca95013-CYP75A1, and Ca42029-CYP75A2 probably help to generate rarely formed peaberry beans. CONCLUSION Our results provide molecular insights into the formation of peaberry. The data resources will be important to identify candidate genes correlated with the different bean shape patterns in Arabica.
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Affiliation(s)
- Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Guiping Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Jiaxiong Huang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yuqiang Lou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Hongyan He
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - YuLan Lv
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China
| | - Jinhuan Cheng
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Yunnan, Baoshan, 678000, China.
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Wu Y, Sun Z, Qi F, Tian M, Wang J, Zhao R, Wang X, Wu X, Shi X, Liu H, Dong W, Huang B, Zheng Z, Zhang X. Comparative transcriptomics analysis of developing peanut ( Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size. FRONTIERS IN PLANT SCIENCE 2022; 13:958808. [PMID: 36172561 PMCID: PMC9511224 DOI: 10.3389/fpls.2022.958808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.
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Affiliation(s)
- Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Mengdi Tian
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Juan Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruifang Zhao
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiao Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaohui Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinlong Shi
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Hongfei Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Zheng Zheng
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
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11
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Xiong H, Wang R, Jia X, Sun H, Duan R. Transcriptomic analysis of rapeseed ( Brassica napus. L.) seed development in Xiangride, Qinghai Plateau, reveals how its special eco-environment results in high yield in high-altitude areas. FRONTIERS IN PLANT SCIENCE 2022; 13:927418. [PMID: 35982704 PMCID: PMC9379305 DOI: 10.3389/fpls.2022.927418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/01/2022] [Indexed: 06/12/2023]
Abstract
As one of the most important oil crops, rapeseed (Brassica napus) is cultivated worldwide to produce vegetable oil, animal feed, and biodiesel. As the population grows and the need for renewable energy increases, the breeding and cultivation of high-yield rapeseed varieties have become top priorities. The formation of a high rapeseed yield is so complex because it is influenced not only by genetic mechanisms but also by many environmental conditions, such as climatic conditions and different farming practices. Interestingly, many high-yield areas are located in special eco-environments, for example, in the high-altitude Xiangride area of the Qinghai Plateau. However, the molecular mechanisms underlying the formation of high yields in such a special eco-environment area remain largely unknown. Here, we conducted field yield analysis and transcriptome analysis in the Xiangride area. Compared with the yield and environmental factors in the Xinning area (a low-yielding area), we found that the relatively longer daylight length is the key to high rapeseed yield in the Xiangride area, which leads up to a 52.1% increase in rapeseed yield, especially the increase in thousand seed weight and silique number (SN). Combined with transcriptome H-cluster analysis and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses, we can assume that the grain development of rapeseed in the Xiangride area is ahead of schedule and lasts for a long time, leading to the high-yield results in the Xiangride area, confirmed by the expression analysis by quantitative real-time polymerase chain reaction (qRT-PCR) of yield-related genes. Our results provide valuable information for further exploring the molecular mechanism underlying high yield in special ecological environments and provide a helpful reference for studying seed development characteristics in special-producing regions for Brassica napus.
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Affiliation(s)
- Huiyan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruisheng Wang
- Academy of Agricultural and Forestry Sciences of Qinghai University, Key Laboratory of Spring Rape Genetic Improvement of Qinghai Province, Rapeseed Research and Development Center of Qinghai Province, Xining, China
| | - Xianqing Jia
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hezhe Sun
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ruijun Duan
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
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12
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Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
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Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
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13
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Transcriptome and miRNA sequencing analyses reveal the regulatory mechanism of α-linolenic acid biosynthesis in Paeonia rockii. Food Res Int 2022; 155:111094. [DOI: 10.1016/j.foodres.2022.111094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 01/05/2023]
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14
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Turquetti-Moraes DK, Moharana KC, Almeida-Silva F, Pedrosa-Silva F, Venancio TM. Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean. Gene 2022; 808:145976. [PMID: 34592351 DOI: 10.1016/j.gene.2021.145976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022]
Abstract
Soybean is a major source of edible protein and oil. Oil content is a quantitative trait that is significantly determined by genetic and environmental factors. Over the past 30 years, a large volume of soybean genetic, genomic, and transcriptomic data have been accumulated. Nevertheless, integrative analyses of such data remain scarce, in spite of their importance for crop improvement. We hypothesized that the co-occurrence of genomic regions for oil-related traits in different studies may reveal more stable regions encompassing important genetic determinants of oil content and quality in soybean. We integrated publicly available data, obtained with distinct techniques, to discover and prioritize candidate genes involved in oil biosynthesis and regulation in soybean. We detected key fatty acid biosynthesis genes (e.g., BCCP2 and ACCase, FADs, KAS family proteins) and several transcription factors, which are likely regulators of oil biosynthesis. In addition, we identified new candidates for seed oil accumulation and quality, such as Glyma.03G213300 and Glyma.19G160700, which encode a translocator protein homolog and a histone acetyltransferase, respectively. Further, oil and protein genomic hotspots are strongly associated with breeding and not with domestication, suggesting that soybean domestication prioritized other traits. The genes identified here are promising targets for breeding programs and for the development of soybean lines with increased oil content and quality.
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Affiliation(s)
- Dayana K Turquetti-Moraes
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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15
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Wu B, Ruan C, Shah AH, Li D, Li H, Ding J, Li J, Du W. Identification of miRNA-mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree ( Camellia oleifera). Cells 2021; 11:cells11010071. [PMID: 35011633 PMCID: PMC8750442 DOI: 10.3390/cells11010071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/29/2022] Open
Abstract
Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal value that is widely planted in southern China. However, there is no report on the identification of the miRNAs involved in lipid metabolism and seed development in the high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the key periods of oil formation and accumulation in the seeds of tea oil camellia and identified miRNA–mRNA regulatory modules involved in lipid metabolism and seed development. Sixteen small RNA libraries for four development stages of seed oil biosynthesis in high- and low-oil cultivars were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families, and 40 novel miRNAs were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 upregulated miRNAs, and 21 downregulated miRNAs. An integrated analysis of the miRNA and mRNA transcriptome sequence data revealed that 10 miRNA–mRNA regulatory modules were related to lipid metabolism; for example, the regulatory modules of ath-miR858b–MYB82/MYB3/MYB44 repressed seed oil biosynthesis, and a regulation module of csi-miR166e-5p–S-ACP-DES6 was involved in the formation and accumulation of oleic acid. A total of 23 miRNA–mRNA regulatory modules were involved in the regulation of the seed size, such as the regulatory module of hpe-miR162a_L-2–ARF19, involved in early seed development. A total of 12 miRNA–mRNA regulatory modules regulating growth and development were identified, such as the regulatory modules of han-miR156a_L+1–SPL4/SBP2, promoting early seed development. The expression changes of six miRNAs and their target genes were validated using quantitative real-time PCR, and the targeting relationship of the cpa-miR393_R-1–AFB2 regulatory module was verified by luciferase assays. These data provide important theoretical values and a scientific basis for the genetic improvement of new cultivars of tea oil camellia in the future.
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Affiliation(s)
- Bo Wu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
- Correspondence: ; Tel.: +86-411-87652536
| | - Asad Hussain Shah
- Department of Biotechnology, Faculty of Sciences, University of Kotli Azad Jammu and Kashmir, Azad Jammu and Kashmir, Kotli 11100, Pakistan;
| | - Denghui Li
- Guizhou Wulingshan Youcha Technology Innovation Research Institute Co., Ltd., Tongren 554300, China;
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Wei Du
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
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Ahmad M, Waraich EA, Skalicky M, Hussain S, Zulfiqar U, Anjum MZ, Habib ur Rahman M, Brestic M, Ratnasekera D, Lamilla-Tamayo L, Al-Ashkar I, EL Sabagh A. Adaptation Strategies to Improve the Resistance of Oilseed Crops to Heat Stress Under a Changing Climate: An Overview. FRONTIERS IN PLANT SCIENCE 2021; 12:767150. [PMID: 34975951 PMCID: PMC8714756 DOI: 10.3389/fpls.2021.767150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/11/2021] [Indexed: 05/16/2023]
Abstract
Temperature is one of the decisive environmental factors that is projected to increase by 1. 5°C over the next two decades due to climate change that may affect various agronomic characteristics, such as biomass production, phenology and physiology, and yield-contributing traits in oilseed crops. Oilseed crops such as soybean, sunflower, canola, peanut, cottonseed, coconut, palm oil, sesame, safflower, olive etc., are widely grown. Specific importance is the vulnerability of oil synthesis in these crops against the rise in climatic temperature, threatening the stability of yield and quality. The natural defense system in these crops cannot withstand the harmful impacts of heat stress, thus causing a considerable loss in seed and oil yield. Therefore, a proper understanding of underlying mechanisms of genotype-environment interactions that could affect oil synthesis pathways is a prime requirement in developing stable cultivars. Heat stress tolerance is a complex quantitative trait controlled by many genes and is challenging to study and characterize. However, heat tolerance studies to date have pointed to several sophisticated mechanisms to deal with the stress of high temperatures, including hormonal signaling pathways for sensing heat stimuli and acquiring tolerance to heat stress, maintaining membrane integrity, production of heat shock proteins (HSPs), removal of reactive oxygen species (ROS), assembly of antioxidants, accumulation of compatible solutes, modified gene expression to enable changes, intelligent agricultural technologies, and several other agronomic techniques for thriving and surviving. Manipulation of multiple genes responsible for thermo-tolerance and exploring their high expressions greatly impacts their potential application using CRISPR/Cas genome editing and OMICS technology. This review highlights the latest outcomes on the response and tolerance to heat stress at the cellular, organelle, and whole plant levels describing numerous approaches applied to enhance thermos-tolerance in oilseed crops. We are attempting to critically analyze the scattered existing approaches to temperature tolerance used in oilseeds as a whole, work toward extending studies into the field, and provide researchers and related parties with useful information to streamline their breeding programs so that they can seek new avenues and develop guidelines that will greatly enhance ongoing efforts to establish heat stress tolerance in oilseeds.
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Affiliation(s)
- Muhammad Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
- Horticultural Sciences Department, Tropical Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Homestead, FL, United States
| | | | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zohaib Anjum
- Department of Forestry and Range Management, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Habib ur Rahman
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University Bonn, Bonn, Germany
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of Agriculture, University of Ruhuna, Kamburupitiya, Sri Lanka
| | - Laura Lamilla-Tamayo
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh, Saudi Arabia
- Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Shaikh, Egypt
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17
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Yan G, Yu P, Tian X, Guo L, Tu J, Shen J, Yi B, Fu T, Wen J, Liu K, Ma C, Dai C. DELLA proteins BnaA6.RGA and BnaC7.RGA negatively regulate fatty acid biosynthesis by interacting with BnaLEC1s in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2011-2026. [PMID: 33982357 PMCID: PMC8486242 DOI: 10.1111/pbi.13628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 05/25/2023]
Abstract
Seed oil content (SOC) and fatty acid (FA) composition determine the quality and economic value of rapeseed (Brassica napus). Little is known about the role of gibberellic acid (GA) in regulating FA biosynthesis in B. napus. Here, we discovered that four BnaRGAs (B. napus REPRESSOR OF GA), encoding negative regulators of GA signalling, were suppressed during seed development. Compared to the wild type, SOC was reduced in gain-of-function mutants bnaa6.rga-D and ds-3, which also showed reduced oleic acid and increased linoleic acid contents. By contrast, the loss-of-function quadruple mutant bnarga displayed higher SOC during early seed development than the wild type, with increased oleic acid and reduced linoleic acid contents. Notably, only BnaA6.RGA and BnaC7.RGA physically interacted with two BnaLEC1s, which function as essential transcription factors in FA biosynthesis. The FA composition did not significantly differ between bnarga bnalec1 sextuple mutants and bnalec1, suggesting that BnaLEC1s are epistatic to BnaRGAs in the regulation of FA composition. Furthermore, BnaLEC1-induced activation of BnaABI3 expression was repressed by BnaA6.RGA, indicating that GA triggers the degradation of BnaRGAs to relieve their repression of BnaLEC1s, thus promoting the transcription of downstream genes to facilitate oil biosynthesis. Therefore, we uncovered a developmental stage-specific role of GA in regulating oil biosynthesis via the GA-BnaRGA-BnaLEC1 signalling cascade, providing a novel mechanistic understanding of how phytohormones regulate FA biosynthesis in seeds. BnaRGAs represent promising targets for oil crop improvement.
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Affiliation(s)
- Guanbo Yan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Pugang Yu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xia Tian
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Liang Guo
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Bin Yi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Jing Wen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Kede Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Cheng Dai
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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18
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Zeng R, Chen T, Wang X, Cao J, Li X, Xu X, Chen L, Xia Q, Dong Y, Huang L, Wang L, Zhang J, Zhang L. Physiological and Expressional Regulation on Photosynthesis, Starch and Sucrose Metabolism Response to Waterlogging Stress in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:601771. [PMID: 34276712 PMCID: PMC8283264 DOI: 10.3389/fpls.2021.601771] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/07/2021] [Indexed: 05/28/2023]
Abstract
Waterlogging has negative effects on crop yield. Physiological and transcriptome data of two peanut cultivars [Zhongkaihua 1 (ZKH 1) and Huayu 39 (HY 39)] were studied under normal water supply and waterlogging stress for 5 or 10 days at the flowering stage. The results showed that the main stem height, the number of lateral branches, lateral branch length, and the stem diameter increased under waterlogging stress, followed by an increase in dry matter accumulation, which was correlated with the increase in the soil and plant analysis development (SPAD) and net photosynthetic rate (Pn) and the upregulation of genes related to porphyrin and chlorophyll metabolism and photosynthesis. However, the imbalance of the source-sink relationship under waterlogging was the main cause of yield loss, and waterlogging caused an increase in the sucrose and soluble sugar contents and a decrease in the starch content; it also decreased the activities of sucrose synthetase (SS) and sucrose phosphate synthetase (SPS), which may be due to the changes in the expression of genes related to starch and sucrose metabolism. However, the imbalance of the source-sink relationship led to the accumulation of photosynthate in the stems and leaves, which resulted in the decrease of the ratio of pod dry weight to total dry weight (PDW/TDW) and yield. Compared with ZKH 1, the PDW of HY 39 decreased more probably because more photosynthate accumulated in the stem and leaves of HY 39 and could not be effectively transported to the pod.
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Affiliation(s)
- Ruier Zeng
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tingting Chen
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xinyue Wang
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jing Cao
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xi Li
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xueyu Xu
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lei Chen
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Qing Xia
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yonglong Dong
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Luping Huang
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Leidi Wang
- College of Agriculture, South China Agricultural University, Guangzhou, China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science, Jinan, China
| | - Jialei Zhang
- Bio-Tech Research Center, Shandong Academy of Agricultural Science, Jinan, China
| | - Lei Zhang
- College of Agriculture, South China Agricultural University, Guangzhou, China
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19
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Peng L, Qian L, Wang M, Liu W, Song X, Cheng H, Yuan F, Zhao M. Comparative transcriptome analysis during seeds development between two soybean cultivars. PeerJ 2021; 9:e10772. [PMID: 33717671 PMCID: PMC7931715 DOI: 10.7717/peerj.10772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.
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Affiliation(s)
- Li Peng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Linlin Qian
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Meinan Wang
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Wei Liu
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Xiangting Song
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Hao Cheng
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
| | - Fengjie Yuan
- Institute of Crop Science, Zhejiang Academy of Agricultural Sciences, Hang Zhou, China
| | - Man Zhao
- College of Bioengineering and Biotechnology, Zhejiang University of Technology, Hang Zhou, China
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20
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Klees S, Lange TM, Bertram H, Rajavel A, Schlüter JS, Lu K, Schmitt AO, Gültas M. In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data. Int J Mol Sci 2021; 22:E789. [PMID: 33466789 PMCID: PMC7830561 DOI: 10.3390/ijms22020789] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 01/07/2023] Open
Abstract
Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation.
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Affiliation(s)
- Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Thomas Martin Lange
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Hendrik Bertram
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Johanna-Sophie Schlüter
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China;
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (S.K.); (T.M.L.); (H.B.); (A.R.); (J.-S.S.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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21
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Cao L, Jin X, Zhang Y, Zhang M, Wang Y. Transcriptomic and metabolomic profiling of melatonin treated soybean (Glycine max L.) under drought stress during grain filling period through regulation of secondary metabolite biosynthesis pathways. PLoS One 2020; 15:e0239701. [PMID: 33125378 PMCID: PMC7598510 DOI: 10.1371/journal.pone.0239701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/12/2020] [Indexed: 11/18/2022] Open
Abstract
There is a growing need to enhance the productivity of soybean (Glycine max L.) under severe drought conditions in order to improve global food security status. Melatonin, a ubiquitous hormone, could alleviate drought stress in various plants. Earlier, we demonstrated that exogenous melatonin treatment could enhance the tolerance of drought-treated soybean. However, the underlying mechanisms by which this hormone exerts drought resistance is still unclear. The present study used transcriptomic and metabolomic techniques to determine some critical genes and pathways regulating melatonin response to drought conditions. Results showed that exogenous melatonin treatment could increase relative water content and decrease electrolyte leakage in the leaves and increase seed yield under drought stress. Transcriptomic analysis showed that there were 852 core differentially expressed genes (DEGs) that were regulated by drought stress and melatonin in soybean leaves. The most enriched drought-responsive genes are mainly involved in the 'biosynthesis of secondary metabolites'. Metabolomic profiling under drought stress showed higher accumulation levels of secondary metabolites related to drought tolerance after exogenous melatonin treatment. Also, we highlighted the vital role of the pathways including phenylpropanoid, flavonoid, isoflavonoid, and steroid biosynthesis pathways for improvement of drought tolerance in soybean by exogenous melatonin treatment. In all, findings from this study give detailed molecular basis for the application of melatonin as a drought-resistant agent in soybean cultivation.
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Affiliation(s)
- Liang Cao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Xijun Jin
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yuxian Zhang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Mingcong Zhang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Yanhong Wang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
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22
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Nam JW, Yeon J, Jeong J, Cho E, Kim HB, Hur Y, Lee KR, Yi H. Overexpression of Acyl-ACP Thioesterases, CpFatB4 and CpFatB5, Induce Distinct Gene Expression Reprogramming in Developing Seeds of Brassica napus. Int J Mol Sci 2019; 20:E3334. [PMID: 31284614 PMCID: PMC6651428 DOI: 10.3390/ijms20133334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 12/03/2022] Open
Abstract
We examined the substrate preference of Cuphea paucipetala acyl-ACP thioesterases, CpFatB4 and CpFatB5, and gene expression changes associated with the modification of lipid composition in the seed, using Brassica napus transgenic plants overexpressing CpFatB4 or CpFatB5 under the control of a seed-specific promoter. CpFatB4 seeds contained a higher level of total saturated fatty acid (FA) content, with 4.3 times increase in 16:0 palmitic acid, whereas CpFatB5 seeds showed approximately 3% accumulation of 10:0 and 12:0 medium-chain FAs, and a small increase in other saturated FAs, resulting in higher levels of total saturated FAs. RNA-Seq analysis using entire developing pods at 8, 25, and 45 days after flowering (DAF) showed up-regulation of genes for β-ketoacyl-acyl carrier protein synthase I/II, stearoyl-ACP desaturase, oleate desaturase, and linoleate desaturase, which could increase unsaturated FAs and possibly compensate for the increase in 16:0 palmitic acid at 45 DAF in CpFatB4 transgenic plants. In CpFatB5 transgenic plants, many putative chloroplast- or mitochondria-encoded genes were identified as differentially expressed. Our results report comprehensive gene expression changes induced by alterations of seed FA composition and reveal potential targets for further genetic modifications.
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Affiliation(s)
- Jeong-Won Nam
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jinouk Yeon
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jiseong Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Eunyoung Cho
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ho Bang Kim
- Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon 14548, Korea
| | - Yoonkang Hur
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea.
| | - Kyeong-Ryeol Lee
- Department of Agricultural Biotechnology, National Agricultural Science, RDA, Jeonju 55365, Korea.
| | - Hankuil Yi
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea.
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23
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Comparative transcriptome analysis of cultivated and wild seeds of Salvia hispanica (chia). Sci Rep 2019; 9:9761. [PMID: 31278279 PMCID: PMC6611817 DOI: 10.1038/s41598-019-45895-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/17/2019] [Indexed: 12/13/2022] Open
Abstract
Salvia hispanica (chia) constituted an important crop for pre-Columbian civilizations and is considered a superfood for its rich content of essential fatty acids and proteins. In this study, we performed the first comprehensive comparative transcriptome analysis between seeds from cultivated varieties and from accessions collected from native wild populations in Mexico. From the 69,873 annotated transcripts assembled de novo, enriched functional categories and pathways revealed that the lipid metabolism was one of the most activated processes. Expression changes were detected among wild and cultivated groups and among growth conditions in transcripts responsible for triacylglycerol and fatty acid synthesis and degradation. We also quantified storage protein fractions that revealed variation concerning nutraceutical proteins such as albumin and glutelin. Genetic diversity estimated with 23,641 single nucleotide polymorphisms (SNPs) revealed that most of the variation remains in the wild populations, and that a wild-type cultivated variety is genetically related to wild accessions. Additionally, we reported 202 simple sequence repeat (SSRs) markers useful for population genetic studies. Overall, we provided transcript variation that can be used for breeding programs to further develop chia varieties with enhanced nutraceutical traits and tools to explore the genetic diversity and history of this rediscovered plant.
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24
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Wu B, Ruan C, Han P, Ruan D, Xiong C, Ding J, Liu S. Comparative transcriptomic analysis of high- and low-oil Camellia oleifera reveals a coordinated mechanism for the regulation of upstream and downstream multigenes for high oleic acid accumulation. 3 Biotech 2019; 9:257. [PMID: 31192082 DOI: 10.1007/s13205-019-1792-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 06/03/2019] [Indexed: 01/08/2023] Open
Abstract
Tea oil camellia (Camellia oleifera) is an important woody oil tree in southern China. However, little is known regarding the molecular mechanisms that contribute to high oleic acid accumulation in tea oil camellia. Herein, we measured the oil content and fatty acid compositions of high- and low-oil tea oil camellia seeds and investigated the global gene expression profiles by RNA-seq. The results showed that at the early, second and third seed developmental stages, a total of 64, 253, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil cultivars. Gene ontology (GO) enrichment analysis of the identified differentially expressed transcription factors (TFs; ABI3, FUS3, LEC1, WRI1, TTG2 and DOF4.6) revealed some critical GO terms associated with oil biosynthesis and fatty acid accumulation, including glycolysis, zinc ion binding, positive regulation of fatty acid biosynthetic process, triglyceride biosynthetic process, seed coat development, abscisic acid-mediated signaling pathway and embryo development. Comprehensive comparisons of transcriptomic profiles and expression analysis of multigenes based on qRT-PCR showed that coordinated high expression of the upstream genes HAD, EAR and KASI directly increased the relative levels of C16:0-ACP, which provided enough precursor resources for oleic acid biosynthesis. Continuous high expression of the SAD gene accelerated oleic acid synthesis and accumulation, and coordinated low expression of the downstream genes FAD2, FAD3, FAD7, FAD8 and FAE1 decreased the consumption of oleic acid for conversion. The coordinated regulation of these multigenes ensures the high accumulation of oleic acid in the seeds of tea oil camellia. Our data represent a comprehensive transcriptomic study of high- and low-oil tea oil camellia, not only increasing the number of sequences associated with lipid biosynthesis and fatty acid accumulation in public resource databases but also providing a scientific basis for genetic improvement of the oleic acid content in woody oil trees.
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Wang R, Yang Z, Fei Y, Feng J, Zhu H, Huang F, Zhang H, Huang J. Construction and analysis of degradome-dependent microRNA regulatory networks in soybean. BMC Genomics 2019; 20:534. [PMID: 31253085 PMCID: PMC6599275 DOI: 10.1186/s12864-019-5879-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miRNAs does not always indicate the higher/lower level of cleavages and such analysis, thus, sometimes ignores the crucial cleavage events. In the present work, the degradome sequencing data were employed to construct the complete miRNA-mediated gene regulatory network in soybean, unlike the traditional approach starting with small RNA sequencing data. RESULTS We constructed the root-, cotyledon-, leaf- and seed-specific miRNA regulatory networks with the degradome sequencing data and the forthcoming verification of miRNA profiling analysis. As a result, we identified 205 conserved miRNA-target interactions (MTIs) involved with 6 conserved gma-miRNA families and 365 tissue-specific MTIs containing 24 root-specific, 45 leaf-specific, 63 cotyledon-specific and 225 seed-specific MTIs. We found a total of 156 miRNAs in tissue-specific MTIs including 18 tissue-specific miRNAs, however, only 3 miRNAs have consistent tissue-specific expression. Our study showed the degradome-dependent miRNA regulatory networks (DDNs) in four soybean tissues and explored their conservations and specificities. CONCLUSIONS The construction of DDNs may provide the complete miRNA-Target interactions in certain plant tissues, leading to the identification of the conserved and tissue-specific MTIs and sub-networks. Our work provides a basis for further investigation of the roles and mechanisms of miRNA-mediated regulation of tissue-specific growth and development in soybean.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhongyi Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuhan Fei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiejie Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hui Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fang Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
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26
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You J, Zhang Y, Liu A, Li D, Wang X, Dossa K, Zhou R, Yu J, Zhang Y, Wang L, Zhang X. Transcriptomic and metabolomic profiling of drought-tolerant and susceptible sesame genotypes in response to drought stress. BMC PLANT BIOLOGY 2019; 19:267. [PMID: 31221078 PMCID: PMC6585049 DOI: 10.1186/s12870-019-1880-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/10/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes. RESULTS Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame. CONCLUSION The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.
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Affiliation(s)
- Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100 China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiao Wang
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430062 China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, 3320 Sénégal
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
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Du W, Xiong CW, Ding J, Nybom H, Ruan CJ, Guo H. Tandem Mass Tag Based Quantitative Proteomics of Developing Sea Buckthorn Berries Reveals Candidate Proteins Related to Lipid Metabolism. J Proteome Res 2019; 18:1958-1969. [PMID: 30990047 DOI: 10.1021/acs.jproteome.8b00764] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sea buckthorn ( Hippophae L.) is an economically important shrub or small tree distributed in Eurasia. Most of its well-recognized medicinal and nutraceutical products are derived from its berry oil, which is rich in monounsaturated omega-7 (C16:1) fatty acid and polyunsaturated omega-6 (C18:2) and omega-3 (C18:3) fatty acids. In this study, tandem mass tags (TMT)-based quantitative analysis was used to investigate protein profiles of lipid metabolism in sea buckthorn berries harvested 30, 50, and 70 days after flowering. In total, 8626 proteins were identified, 6170 of which were quantified. Deep analysis results for the proteins identified and related pathways revealed initial fatty acid accumulation during whole-berry development. The abundance of most key enzymes involved in fatty acid and triacylglycerol (TAG) biosynthesis peaked at 50 days after flowering, but TAG synthesis through the PDAT (phospholipid: diacylglycerol acyltransferase) pathway mostly occurred early in berry development. In addition, the patterns of proteins involved in lipid metabolism were confirmed by combined quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay, and parallel reaction monitoring analyses. Our data on the proteomic spectrum of sea buckthorn berries provide a scientific basic for understanding lipid metabolism and related pathways in the developing berries.
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Affiliation(s)
- Wei Du
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Chao-Wei Xiong
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Jian Ding
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Hilde Nybom
- Department of Plant Breeding-Balsgård , Swedish University of Agricultural Sciences , Fjälkestadsvägen 459 , SE-29194 Kristianstad , Sweden
| | - Cheng-Jiang Ruan
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Hai Guo
- Conseco Sea Buckthorn Co. Ltd. , Beijing 100038 , China.,Inner Mongolia Hijing Environment Protection Science and Technology Co. Ltd , Inner Mongolia 017000 , China
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Yu L, Guo R, Jiang Y, Ye X, Yang Z, Meng Y, Shao C. Genome-wide identification and characterization of novel microRNAs in seed development of soybean. Biosci Biotechnol Biochem 2019; 83:233-242. [PMID: 30355067 DOI: 10.1080/09168451.2018.1536513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in eukaryotes. However, the information about miRNAs population and their regulatory functions involving in soybean seed development remains incomplete. Base on the Dicer-like1-mediated cleavage signals during miRNA processing could be employed for novel miRNA discovery, a genome-wide search for miRNA candidates involved in seed development was carried out. As a result, 17 novel miRNAs, 14 isoforms of miRNA (isomiRs) and 31 previously validated miRNAs were discovered. These novel miRNAs and isomiRs represented tissue-specific expression and the isomiRs showed significantly higher abundance than that of their miRNA counterparts in different tissues. After target prediction and degradome sequencing data-based validation, 13 novel miRNA-target pairs were further identified. Besides, five targets of 22-nt iso-gma-miR393h were found to be triggered to produce secondary trans-acting siRNA (ta-siRNAs). Summarily, our results could expand the repertoire of miRNAs with potentially important functions in soybean.
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Affiliation(s)
- Lan Yu
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Rongkai Guo
- b Shanghai Institute of Plant Physiology and Ecology , Chinese Academy of Sciences , Shanghai China
| | - Yeqin Jiang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Xinghuo Ye
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Zhihong Yang
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
| | - Yijun Meng
- c College of Life and Environmental Sciences , Hangzhou Normal University , Hangzhou P.R. China
| | - Chaogang Shao
- a College of Life Sciences , Huzhou University , Huzhou P.R. China
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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Yin DD, Li SS, Shu QY, Gu ZY, Wu Q, Feng CY, Xu WZ, Wang LS. Identification of microRNAs and long non-coding RNAs involved in fatty acid biosynthesis in tree peony seeds. Gene 2018; 666:72-82. [PMID: 29738839 DOI: 10.1016/j.gene.2018.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/02/2018] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) act as important molecular regulators in a wide range of biological processes during plant development and seed formation, including oil production. Tree peony seeds contain >90% unsaturated fatty acids (UFAs) and high proportions of α-linolenic acid (ALA, > 40%). To dissect the non-coding RNAs (ncRNAs) pathway involved in fatty acids synthesis in tree peony seeds, we construct six small RNA libraries and six transcriptome libraries from developing seeds of two cultivars (J and S) containing different content of fatty acid compositions. After deep sequencing the RNA libraries, the ncRNA expression profiles of tree peony seeds in two cultivars were systematically and comparatively analyzed. A total of 318 known and 153 new miRNAs and 22,430 lncRNAs were identified, among which 106 conserved and 9 novel miRNAs and 2785 lncRNAs were differentially expressed between the two cultivars. In addition, potential target genes of the microRNA and lncRNAs were also predicted and annotated. Among them, 9 miRNAs and 39 lncRNAs were predicted to target lipid related genes. Results showed that all of miR414, miR156b, miR2673b, miR7826, novel-m0027-5p, TR24651|c0_g1, TR24544|c0_g15, and TR27305|c0_g1 were up-regulated and expressed at a higher level in high-ALA cultivar J when compared to low-ALA cultivar S, suggesting that these ncRNAs and target genes are possibly involved in different fatty acid synthesis and lipid metabolism through post-transcriptional regulation. These results provide a better understanding of the roles of ncRNAs during fatty acid biosynthesis and metabolism in tree peony seeds.
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Affiliation(s)
- Dan-Dan Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan-Shan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qing-Yan Shu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhao-Yu Gu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qian Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng-Yong Feng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Zhong Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Liang-Sheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ding J, Ruan C, Guan Y, Krishna P. Identification of microRNAs involved in lipid biosynthesis and seed size in developing sea buckthorn seeds using high-throughput sequencing. Sci Rep 2018; 8:4022. [PMID: 29507325 PMCID: PMC5838164 DOI: 10.1038/s41598-018-22464-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Sea buckthorn is a plant of medicinal and nutritional importance owing in part to the high levels of essential fatty acids, linoleic (up to 42%) and α-linolenic (up to 39%) acids in the seed oil. Sea buckthorn can produce seeds either via the sexual pathway or by apomixis. The seed development and maturation programs are critically dependent on miRNAs. To understand miRNA-mediated regulation of sea buckthorn seed development, eight small RNA libraries were constructed for deep sequencing from developing seeds of a low oil content line ‘SJ1’ and a high oil content line ‘XE3’. High-throughput sequencing identified 137 known miRNA from 27 families and 264 novel miRNAs. The potential targets of the identified miRNAs were predicted based on sequence homology. Nineteen (four known and 15 novel) and 22 (six known and 16 novel) miRNAs were found to be involved in lipid biosynthesis and seed size, respectively. An integrated analysis of mRNA and miRNA transcriptome and qRT-PCR identified some key miRNAs and their targets (miR164d-ARF2, miR168b-Δ9D, novelmiRNA-108-ACC, novelmiRNA-23-GPD1, novelmiRNA-58-DGAT1, and novelmiRNA-191-DGAT2) potentially involved in seed size and lipid biosynthesis of sea buckthorn seed. These results indicate the potential importance of miRNAs in regulating lipid biosynthesis and seed size in sea buckthorn.
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Affiliation(s)
- Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Ying Guan
- Institute of Berries, Heilongjiang Academy of Agricultural Sciences, Suiling, 152200, China
| | - Priti Krishna
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
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Gacek K, Bartkowiak-Broda I, Batley J. Genetic and Molecular Regulation of Seed Storage Proteins (SSPs) to Improve Protein Nutritional Value of Oilseed Rape ( Brassica napus L.) Seeds. FRONTIERS IN PLANT SCIENCE 2018; 9:890. [PMID: 30013586 PMCID: PMC6036235 DOI: 10.3389/fpls.2018.00890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/07/2018] [Indexed: 05/20/2023]
Abstract
The world-wide demand for additional protein sources for human nutrition and animal feed keeps rising due to rapidly growing world population. Oilseed rape is a second important oil producing crop and the by-product of the oil production is a protein rich meal. The protein in rapeseed meal finds its application in animal feed and various industrial purposes, but its improvement is of great interest, especially for non-ruminants and poultry feed. To be able to manipulate the quality and quantity of seed protein in oilseed rape, understanding genetic architecture of seed storage protein (SSPs) synthesis and accumulation in this crop species is of great interest. For this, application of modern molecular breeding tools such as whole genome sequencing, genotyping, association mapping, and genome editing methods implemented in oilseed rape seed protein improvement would be of great interest. This review examines current knowledge and opportunities to manipulate of SSPs in oilseed rape to improve its quality, quantity and digestibility.
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Affiliation(s)
- Katarzyna Gacek
- Oilseed Crops Research Centre, Plant Breeding and Acclimatization Institute-National Research Institute, Poznań, Poland
| | - Iwona Bartkowiak-Broda
- Oilseed Crops Research Centre, Plant Breeding and Acclimatization Institute-National Research Institute, Poznań, Poland
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- *Correspondence: Jacqueline Batley,
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34
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Sreenivasulu N. Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination. PLANT CELL REPORTS 2017; 36:633-635. [PMID: 28421280 DOI: 10.1007/s00299-017-2135-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
Seeds are heterogeneous storage reserves with wide array of storage compounds that include various soluble carbohydrates, starch polymer, storage proteins and lipids. These stored reserves comprise 70% of the world's caloric intake in the form of food and animal feed produced through sustainable agriculture, which contributes to food and nutritional security. Seed systems biology remains an enigmatic subject in understanding seed storage processes, maturation and pre-germinative metabolism. The reviews and research articles covered in this special issue of Plant Cell Reports highlight recent advances made in the area of seed biology that cover various systems biology applications such as gene regulatory networks, metabolomics, epigenetics and the role of micro-RNA in seed development.
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Affiliation(s)
- Nese Sreenivasulu
- Plant Breeding division, Grain Quality and Nutrition Center, International Rice Research Institute, DAPO Box 7777, 1301, Metro Manila, Philippines.
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