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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 PMCID: PMC11237005 DOI: 10.1038/s42003-024-06525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Cai Y, Chen L, Liu X, Yao W, Hou W. GmNF-YC4 delays soybean flowering and maturation by directly repressing GmFT2a and GmFT5a expression. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1370-1384. [PMID: 38695656 DOI: 10.1111/jipb.13668] [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: 12/06/2023] [Accepted: 04/03/2024] [Indexed: 07/12/2024]
Abstract
Flowering time and growth period are key agronomic traits which directly affect soybean (Glycine max (L.) Merr.) adaptation to diverse latitudes and farming systems. The FLOWERING LOCUS T (FT) homologs GmFT2a and GmFT5a integrate multiple flowering regulation pathways and significantly advance flowering and maturity in soybean. Pinpointing the genes responsible for regulating GmFT2a and GmFT5a will improve our understanding of the molecular mechanisms governing growth period in soybean. In this study, we identified the Nuclear Factor Y-C (NFY-C) protein GmNF-YC4 as a novel flowering suppressor in soybean under long-day (LD) conditions. GmNF-YC4 delays flowering and maturation by directly repressing the expression of GmFT2a and GmFT5a. In addition, we found that a strong selective sweep event occurred in the chromosomal region harboring the GmNF-YC4 gene during soybean domestication. The GmNF-YC4Hap3 allele was mainly found in wild soybean (Glycine soja Siebold & Zucc.) and has been eliminated from G. max landraces and improved cultivars, which predominantly contain the GmNF-YC4Hap1 allele. Furthermore, the Gmnf-yc4 mutants displayed notably accelerated flowering and maturation under LD conditions. These alleles may prove to be valuable genetic resources for enhancing soybean adaptability to higher latitudes.
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Affiliation(s)
- Yupeng Cai
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoqian Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Yao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Hou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Jiang A, Liu J, Gao W, Ma R, Zhang J, Zhang X, Du C, Yi Z, Fang X, Zhang J. Transcriptomic and Metabolomic Analyses Reveal the Key Genes Related to Shade Tolerance in Soybean. Int J Mol Sci 2023; 24:14230. [PMID: 37762532 PMCID: PMC10531609 DOI: 10.3390/ijms241814230] [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: 07/28/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Soybean (Glycine max) is an important crop, rich in proteins, vegetable oils and several other phytochemicals, which is often affected by light during growth. However, the specific regulatory mechanisms of leaf development under shade conditions have yet to be understood. In this study, the transcriptome and metabolome sequencing of leaves from the shade-tolerant soybean 'Nanxiadou 25' under natural light (ND1) and 50% shade rate (SHND1) were carried out, respectively. A total of 265 differentially expressed genes (DEGs) were identified, including 144 down-regulated and 121 up-regulated genes. Meanwhile, KEGG enrichment analysis of DEGs was performed and 22 DEGs were significantly enriched in the top five pathways, including histidine metabolism, riboflavin metabolism, vitamin B6 metabolism, glycerolipid metabolism and cutin, suberine and wax biosynthesis. Among all the enrichment pathways, the most DEGs were enriched in plant hormone signaling pathways with 19 DEGs being enriched. Transcription factors were screened out and 34 differentially expressed TFs (DETFs) were identified. Weighted gene co-expression network analysis (WGCNA) was performed and identified 10 core hub genes. Combined analysis of transcriptome and metabolome screened out 36 DEGs, and 12 potential candidate genes were screened out and validated by quantitative real-time polymerase chain reaction (qRT-PCR) assay, which may be related to the mechanism of shade tolerance in soybean, such as ATP phosphoribosyl transferase (ATP-PRT2), phosphocholine phosphatase (PEPC), AUXIN-RESPONSIVE PROTEIN (IAA17), PURPLE ACID PHOSPHATASE (PAP), etc. Our results provide new knowledge for the identification and function of candidate genes regulating soybean shade tolerance and provide valuable resources for the genetic dissection of soybean shade tolerance molecular breeding.
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Affiliation(s)
- Aohua Jiang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiaqi Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Weiran Gao
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ronghan Ma
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jijun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Xiaochun Zhang
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Chengzhang Du
- Institute of Specialty Crop, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
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Wang W, Pu Y, Wen H, Lu D, Yan M, Liu M, Wu M, Bai H, Shen L, Wu C. Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Yao Y, Xiong E, Qu X, Li J, Liu H, Quan L, Lu W, Zhu X, Chen M, Li K, Chen X, Lian Y, Lu W, Zhang D, Zhou X, Chu S, Jiao Y. WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean. BMC Genomics 2023; 24:494. [PMID: 37641045 PMCID: PMC10463976 DOI: 10.1186/s12864-023-09617-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. RESULTS In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as "Photosynthesis", "Carbon metabolism", and "Fatty acid metabolism", were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. CONCLUSIONS Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.
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Affiliation(s)
- Yanjie Yao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
- Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Erhui Xiong
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xuelian Qu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Junfeng Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hongli Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Leipo Quan
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenyan Lu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuling Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Meiling Chen
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ke Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoming Chen
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yun Lian
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Weiguo Lu
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China.
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Rani R, Raza G, Ashfaq H, Rizwan M, Razzaq MK, Waheed MQ, Shimelis H, Babar AD, Arif M. Genome-wide association study of soybean ( Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1229495. [PMID: 37636105 PMCID: PMC10450938 DOI: 10.3389/fpls.2023.1229495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.
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Affiliation(s)
- Reena Rani
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamza Ashfaq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Qandeel Waheed
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Allah Ditta Babar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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Zhang Y, Gong H, Cui X, Gao C, Li N, Pu Y, Zhang X, Zhao J. Integrated lipidomic and transcriptomic analyses reveal the mechanism of lipid biosynthesis and accumulation during seed development in sesame. FRONTIERS IN PLANT SCIENCE 2023; 14:1211040. [PMID: 37426956 PMCID: PMC10325577 DOI: 10.3389/fpls.2023.1211040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
Sesame is one of the most important oilseed crops and attracts significant attention because of its huge nutritional capacity. However, the molecular mechanisms underlying oil accumulation in sesame remains poorly understood. In this study, lipidomic and transcriptomic analyses in different stages of sesame seed (Luzhi No.1, seed oil content 56%) development were performed to gain insight into the regulatory mechanisms that govern differences in lipid composition, content, biosynthesis, and transport. In total, 481 lipids, including fatty acids (FAs, 38 species), triacylglycerol (TAG, 127 species), ceramide (33 species), phosphatidic acid (20 species), and diacylglycerol (17 species), were detected in developing sesame seed using gas and liquid chromatography-mass spectrometry. Most FAs and other lipids accumulated 21-33 days after flowering. RNA-sequence profiling in developing seed highlighted the enhanced expression of genes involved in the biosynthesis and transport of FAs, TAGs, and membrane lipids, which was similar to that seen during lipid accumulation. Through the differential expression analysis of genes involved in lipid biosynthesis and metabolism during seed development, several candidate genes were found to affect the oil content and FA composition of sesame seed, including ACCase, FAD2, DGAT, G3PDH, PEPCase, WRI1 and WRI1-like genes. Our study reveals the patterns of lipid accumulation and biosynthesis-related gene expression and lays an important foundation for the further exploration of sesame seed lipid biosynthesis and accumulation.
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Affiliation(s)
- Yujuan Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huihui Gong
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinxiao Cui
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chunhua Gao
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanyan Pu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiurong Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Junsheng Zhao
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
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Bioengineering of Soybean Oil and Its Impact on Agronomic Traits. Int J Mol Sci 2023; 24:ijms24032256. [PMID: 36768578 PMCID: PMC9916542 DOI: 10.3390/ijms24032256] [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: 12/24/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Soybean is a major oil crop and is also a dominant source of nutritional protein. The 20% seed oil content (SOC) of soybean is much lower than that in most oil crops and the fatty acid composition of its native oil cannot meet the specifications for some applications in the food and industrial sectors. Considerable effort has been expended on soybean bioengineering to tailor fatty acid profiles and improve SOC. Although significant advancements have been made, such as the creation of high-oleic acid soybean oil and high-SOC soybean, those genetic modifications have some negative impacts on soybean production, for instance, impaired germination or low protein content. In this review, we focus on recent advances in the bioengineering of soybean oil and its effects on agronomic traits.
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Guo X, Yan N, Liu L, Yin X, Chen Y, Zhang Y, Wang J, Cao G, Fan C, Hu Z. Transcriptomic comparison of seeds and silique walls from two rapeseed genotypes with contrasting seed oil content. FRONTIERS IN PLANT SCIENCE 2023; 13:1082466. [PMID: 36714692 PMCID: PMC9880416 DOI: 10.3389/fpls.2022.1082466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Silique walls play pivotal roles in contributing photoassimilates and nutrients to fuel seed growth. However, the interaction between seeds and silique walls impacting oil biosynthesis is not clear during silique development. Changes in sugar, fatty acid and gene expression during Brassica napus silique development of L192 with high oil content and A260 with low oil content were investigated to identify key factors affecting difference of their seed oil content. During the silique development, silique walls contained more hexose and less sucrose than seeds, and glucose and fructose contents in seeds and silique walls of L192 were higher than that of A260 at 15 DAF, and sucrose content in the silique walls of L192 were lower than that of A260 at three time points. Genes related to fatty acid biosynthesis were activated over time, and differences on fatty acid content between the two genotypes occurred after 25 DAF. Genes related to photosynthesis expressed more highly in silique walls than in contemporaneous seeds, and were inhibited over time. Gene set enrichment analysis suggested photosynthesis were activated in L192 at 25 and 35 DAF in silique walls and at both 15 and 35 DAF in the seed. Expressions of sugar transporter genes in L192 was higher than that in A260, especially at 35 DAF. Expressions of genes related to fatty acid biosynthesis, such as BCCP2s, bZIP67 and LEC1s were higher in L192 than in A260, especially at 35 DAF. Meanwhile, genes related to oil body proteins were expressed at much lower levels in L192 than in A260. According to the WGCNA results, hub modules, such as ME.turquoise relative to photosynthesis, ME.green relative to embryo development and ME.yellow relative to lipid biosynthesis, were identified and synergistically regulated seed development and oil accumulation. Our results are helpful for understanding the mechanism of oil accumulation of seeds in oilseed rape for seed oil content improvement.
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Affiliation(s)
- Xupeng Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Na Yan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Linpo Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiangzhen Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Jingqiao Wang
- Institute of Economical Crops, Yunnan Agricultural Academy, Kunming, Yunnan, China
| | - Guozhi Cao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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12
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Wang W, Wen H, Jin Q, Yu W, Li G, Wu M, Bai H, Shen L, Wu C. Comparative transcriptome analysis on candidate genes involved in lipid biosynthesis of developing kernels for three walnut cultivars in Xinjiang. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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13
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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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14
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Lin Y, Xu K, Xu Y, Ji D, Chen C, Wang W, Xie C. Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis. Front Genet 2021; 12:680120. [PMID: 34276783 PMCID: PMC8278576 DOI: 10.3389/fgene.2021.680120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to produce RNA-Seq libraries. Then, we identified key molecular pathways and genes involved in conchosporangia maturation by conducting a weighted gene co-expression network analysis. Two specific modules were identified, and included functions such as phosphorus metabolism, lipid metabolism, and the phosphatidylinositol signaling system. The hub genes that responded positively during conchosporangia maturation encoded diacylglycerol kinase (DGK) and phosphatidylinositol-3-phosphate-5-kinase, which are involved in the synthesis of phosphatidic acid, a key component of lipid metabolism. A full-length DGK sequence of P. haitanensis, designated as PhDGK1, was obtained by rapid-amplification of cDNA ends. Conserved motif and phylogenetic tree analyses showed that PhDGK1 belongs to DGK Cluster II. The transcript level of PhDGK1 increased during conchosporangia maturation in both strains, but increased earlier, and to higher levels, in the early-maturing strain than in the late-maturing strain. This pattern of gene expression was consistent with the patterns of maturity and changes in pigment contents. These results indicate that lipid metabolism plays a key role in regulating conchosporangia maturation in Pyropia spp., and that PhDGK1 might be a useful molecular marker for breeding new early-maturing strains.
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Affiliation(s)
- Yinghui Lin
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China.,Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China.,Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
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Ma L, Cheng X, Wang C, Zhang X, Xue F, Li Y, Zhu Q, Sun J, Liu F. Explore the gene network regulating the composition of fatty acids in cottonseed. BMC PLANT BIOLOGY 2021; 21:177. [PMID: 33849439 PMCID: PMC8042725 DOI: 10.1186/s12870-021-02952-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cottonseed is one of the major sources of vegetable oil. Analysis of the dynamic changes of fatty acid components and the genes regulating the composition of fatty acids of cottonseed oil is of great significance for understanding the biological processes underlying biosynthesis of fatty acids and for genetic improving the oil nutritional qualities. RESULTS In this study, we investigated the dynamic relationship of 13 fatty acid components at 12 developmental time points of cottonseed (Gossypium hirsutum L.) and generated cottonseed transcriptome of the 12 time points. At 5-15 day post anthesis (DPA), the contents of polyunsaturated linolenic acid (C18:3n-3) and saturated stearic acid (C18:0) were higher, while linoleic acid (C18:2n-6) was mainly synthesized after 15 DPA. Using 5 DPA as a reference, 15,647 non-redundant differentially expressed genes were identified in 10-60 DPA cottonseed. Co-expression gene network analysis identified six modules containing 3275 genes significantly associated with middle-late seed developmental stages and enriched with genes related to the linoleic acid metabolic pathway and α-linolenic acid metabolism. Genes (Gh_D03G0588 and Gh_A02G1788) encoding stearoyl-ACP desaturase were identified as hub genes and significantly up-regulated at 25 DPA. They seemed to play a decisive role in determining the ratio of saturated fatty acids to unsaturated fatty acids. FAD2 genes (Gh_A13G1850 and Gh_D13G2238) were highly expressed at 25-50 DPA, eventually leading to the high content of C18:2n-6 in cottonseed. The content of C18:3n-3 was significantly decreased from 5 DPA (7.44%) to 25 DPA (0.11%) and correlated with the expression characteristics of Gh_A09G0848 and Gh_D09G0870. CONCLUSIONS These results contribute to our understanding on the relationship between the accumulation pattern of fatty acid components and the expression characteristics of key genes involved in fatty acid biosynthesis during the entire period of cottonseed development.
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Affiliation(s)
- Lihong Ma
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Xinqi Cheng
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Chuan Wang
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Xinyu Zhang
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Fei Xue
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Yanjun Li
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China
| | - Qianhao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, 2601, Australia
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
| | - Feng Liu
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
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16
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Bao W, Ao D, Wang L, Ling Z, Chen M, Bai Y, Wuyun TN, Chen J, Zhang S, Li F. Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall. BMC PLANT BIOLOGY 2021; 21:152. [PMID: 33761884 PMCID: PMC7992973 DOI: 10.1186/s12870-021-02921-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Prunus pedunculata Pall, the deciduous shrub of Amygdalus subgenus in Rosaceae, is a new kind of desert oil-bearing tree. It has a long story of being planted in the West and North of China for sand fixation and desert control. In addition, the seeds of P. pedunculata are rich of oil, especially the monounsaturated fatty acid and polyunsaturated fatty acid. However, little is known about the molecular mechanisms of oil accumulation during the seed development of P. pedunculata. RESULTS The seeds of P. pedunculata from three independent plants at 10, 18, 24, 31, 39, 45, 59 and 73 days after flowering (DAF) were obtained and the oil compositions were evaluated. It showed that oleic acid was the dominant type of oil content in the mature seeds (from 32.724% at 10DAF to 72.06% at 73DAF). Next, transcriptome sequencing for the developing seeds produced 988.795 million high quality reads and TRINITY assembled 326,271 genes for the first transcriptome for P. pedunculata. After the assembled transcriptome was evaluated by BUSCO with 85.9% completeness, we identified 195,342, 109,850 and 121,897 P. pedunculata genes aligned to NR, GO and KEGG pathway databases, respectively. Then, we predicted 23,229 likely proteins from the assembled transcriptome and identified 1917 signal peptides and 5512 transmembrane related proteins. In the developing seeds we detected 91,362 genes (average FPKM > 5) and correlation analysis indicated three possible development stages - early (10 ~ 24DAF), middle (31 ~ 45DAF) and late (59 ~ 73DAF). We next analyzed the differentially expressed genes (DEGs) in the developing seeds. Interestingly, compared to 10DAF the number of DEGs was increased from 4406 in 18DAF to 27,623 in 73DAF. Based on the gene annotation, we identified 753, 33, 8 and 645 DEGs related to the fatty acid biosynthesis, lipid biosynthesis, oil body and transcription factors. Notably, GPAT, DGD1, LACS2, UBC and RINO were highly expressed at the early development stage, ω6-FAD, SAD, ACP, ACCA and AHG1 were highly expressed at the middle development stage, and LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2 and oleosin genes were highly expressed at the late development stage. CONCLUSIONS This is the first time to study the developing seed transcriptome of P. pedunculata and our findings will provide a valuable resource for future studies. More importantly, it will improve our understanding of molecular mechanisms of oil accumulation in P. pedunculata.
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Affiliation(s)
- Wenquan Bao
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dun Ao
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Zhihao Ling
- Chengdu Jiyu Technology, Chengdu, 610213, Sichuan, China
| | - Maoshan Chen
- Australian Center for Blood Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Yue Bai
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Ta-Na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Junxing Chen
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shuning Zhang
- Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fengming Li
- Inner Mongolia Agricultural University, Hohhot, 010018, China
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Tian L, Gao X, Zhang S, Zhang Y, Ma D, Cui J. Dynamic changes of transcriptome of fifth-instar spodoptera litura larvae in response to insecticide. 3 Biotech 2021; 11:98. [PMID: 33520584 DOI: 10.1007/s13205-021-02651-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/09/2021] [Indexed: 10/22/2022] Open
Abstract
Spodoptera litura is a major insect with a cosmopolitan distribution and strong resistance to multiple insecticides. Determining the molecular basis and key candidate genes of the insecticide resistance of S. litura may help in managing this insect. In this study, fifth-instar S. litura larvae were subjected to transcriptome analysis at 6, 12, 24, 48, and 72 h after feeding on an LC20 dose of avermectin. The result showed that genes responding to avermectin changed dynamically with different gene counts and resistance mechanisms at the fifth instar based on a metabolic pathway map. These responses included degrading the insecticide by a series of P450 and glutathione-S-transferase enzymes starting at the 12 h time point, with subsequent increases in the number of genes involved and shifts to TOLL and immune deficiency (IMD) pathways at 48 h after feeding the insecticide. Weighted correlation network analysis (WGCNA) determined a co-expression module related to the avermectin response at 12 and 24 h (r = 0.403, p = 0.0371; r = 0.436, p = 0.023), in which a hub gene (LOC111358940) related to metalloproteinase activity was identified. In addition, Analysis of the genes in the co-expression module further revealed that eight genes encoding UDP-glucuronosyltransferases were directly associated with insecticide response in S. litura. These results provide better understanding of the avermectin response mechanism of S. litura and may be useful in developing improved control strategies for this species. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s13205-021-02651-9) contains supplementary material, which is available to authorized users.
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18
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Karikari B, Wang Z, Zhou Y, Yan W, Feng J, Zhao T. Identification of quantitative trait nucleotides and candidate genes for soybean seed weight by multiple models of genome-wide association study. BMC PLANT BIOLOGY 2020; 20:404. [PMID: 32873245 PMCID: PMC7466808 DOI: 10.1186/s12870-020-02604-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/16/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Seed weight is a complex yield-related trait with a lot of quantitative trait loci (QTL) reported through linkage mapping studies. Integration of QTL from linkage mapping into breeding program is challenging due to numerous limitations, therefore, Genome-wide association study (GWAS) provides more precise location of QTL due to higher resolution and diverse genetic diversity in un-related individuals. RESULTS The present study utilized 573 breeding lines population with 61,166 single nucleotide polymorphisms (SNPs) to identify quantitative trait nucleotides (QTNs) and candidate genes for seed weight in Chinese summer-sowing soybean. GWAS was conducted with two single-locus models (SLMs) and six multi-locus models (MLMs). Thirty-nine SNPs were detected by the two SLMs while 209 SNPs were detected by the six MLMs. In all, two hundred and thirty-one QTNs were found to be associated with seed weight in YHSBLP with various effects. Out of these, seventy SNPs were concurrently detected by both SLMs and MLMs on 8 chromosomes. Ninety-four QTNs co-localized with previously reported QTL/QTN by linkage/association mapping studies. A total of 36 candidate genes were predicted. Out of these candidate genes, four hub genes (Glyma06g44510, Glyma08g06420, Glyma12g33280 and Glyma19g28070) were identified by the integration of co-expression network. Among them, three were relatively expressed higher in the high HSW genotypes at R5 stage compared with low HSW genotypes except Glyma12g33280. Our results show that using more models especially MLMs are effective to find important QTNs, and the identified HSW QTNs/genes could be utilized in molecular breeding work for soybean seed weight and yield. CONCLUSION Application of two single-locus plus six multi-locus models of GWAS identified 231 QTNs. Four hub genes (Glyma06g44510, Glyma08g06420, Glyma12g33280 & Glyma19g28070) detected via integration of co-expression network among the predicted candidate genes.
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Affiliation(s)
- Benjamin Karikari
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Zili Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yilan Zhou
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wenliang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jianying Feng
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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19
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He M, Qin CX, Wang X, Ding NZ. Plant Unsaturated Fatty Acids: Biosynthesis and Regulation. FRONTIERS IN PLANT SCIENCE 2020; 11:390. [PMID: 32425958 PMCID: PMC7212373 DOI: 10.3389/fpls.2020.00390] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 05/11/2023]
Abstract
In most plants, major unsaturated fatty acids (UFAs) are three C18 species, namely, oleic (18:1), linoleic (18:2), and α-linolenic (18:3) acids. These simple compounds play multiple crucial roles in planta and are also important economic traits of oil crops. The enzymatic steps of C18 UFA biosynthesis have been well established. However, the associated FA/lipid trafficking between the plastid and the endoplasmic reticulum remains largely unclear, as does the regulation of the expression and activities of the involved enzymes. In this review, we will revisit the biosynthesis of C18 UFAs with an emphasis on the trafficking, and present an overview of the key enzymes and their regulation. Of particular interest is the emerging regulatory network composed of transcriptional factors and upstream signaling pathways. The review thereby provides the promise of using physical, biochemical and/or genetic means to manipulate FA composition and increase oil yield in crop improvement.
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20
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Jin Y, Liu L, Hao X, Harry DE, Zheng Y, Huang T, Huang J. Unravelling the MicroRNA-Mediated Gene Regulation in Developing Pongamia Seeds by High-Throughput Small RNA Profiling. Int J Mol Sci 2019; 20:ijms20143509. [PMID: 31319494 PMCID: PMC6678122 DOI: 10.3390/ijms20143509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/07/2023] Open
Abstract
Pongamia (Millettia pinnata syn. Pongamia pinnata) is a multipurpose biofuel tree which can withstand a variety of abiotic stresses. Commercial applications of Pongamia trees may substantially benefit from improvements in their oil-seed productivity, which is governed by complex regulatory mechanisms underlying seed development. MicroRNAs (miRNAs) are important molecular regulators of plant development, while relatively little is known about their roles in seed development, especially for woody plants. In this study, we identified 236 conserved miRNAs within 49 families and 143 novel miRNAs via deep sequencing of Pongamia seeds sampled at three developmental phases. For these miRNAs, 1327 target genes were computationally predicted. Furthermore, 115 differentially expressed miRNAs (DEmiRs) between successive developmental phases were sorted out. The DEmiR-targeted genes were preferentially enriched in the functional categories associated with DNA damage repair and photosynthesis. The combined analyses of expression profiles for DEmiRs and functional annotations for their target genes revealed the involvements of both conserved and novel miRNA-target modules in Pongamia seed development. Quantitative Real-Time PCR validated the expression changes of 15 DEmiRs as well as the opposite expression changes of six targets. These results provide valuable miRNA candidates for further functional characterization and breeding practice in Pongamia and other oilseed plants.
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Affiliation(s)
- Ye Jin
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuehong Hao
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | | | - Yizhi Zheng
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Tengbo Huang
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jianzi Huang
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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