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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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Liu J, Ke M, Sun Y, Niu S, Zhang W, Li Y. Epigenetic regulation and epigenetic memory resetting during plant rejuvenation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:733-745. [PMID: 37930766 DOI: 10.1093/jxb/erad435] [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: 06/29/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Meng Ke
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, PR China
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Yu A, Zhou Z, Chen Y, Sun J, Li P, Gu X, Liu A. Functional Genome Analyses Reveal the Molecular Basis of Oil Accumulation in Developing Seeds of Castor Beans. Int J Mol Sci 2023; 25:92. [PMID: 38203263 PMCID: PMC10778879 DOI: 10.3390/ijms25010092] [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: 11/22/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Castor (Ricinus communis L.) seeds produce abundant ricinoleic acid during seed maturation, which is important for plant development and human demands. Ricinoleic acid, as a unique hydroxy fatty acid (HFA), possesses a distinct bond structure that could be used as a substitute for fossil fuels. Here, we identified all homologous genes related to glycolysis, hydroxy fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in castor seeds. Furthermore, we investigated their expression patterns globally during five seed development stages. We characterized a total of 66 genes involved in the glycolysis pathway, with the majority exhibiting higher expression levels during the early stage of castor bean seed development. This metabolic process provided abundant acetyl-CoA for fatty acid (FA) biosynthesis. Subsequently, we identified 82 genes involved in the processes of de novo FA biosynthesis and TAG assembly, with the majority exhibiting high expression levels during the middle or late stages. In addition, we examined the expression patterns of the transcription factors involved in carbohydrate and oil metabolism. For instance, RcMYB73 and RcERF72 exhibited high expression levels during the early stage, whereas RcWRI1, RcABI3, and RcbZIP67 showed relatively higher expression levels during the middle and late stages, indicating their crucial roles in seed development and oil accumulation. Our study suggests that the high HFA production in castor seeds is attributed to the interaction of multiple genes from sugar transportation to lipid droplet packaging. Therefore, this research comprehensively characterizes all the genes related to glycolysis, fatty acid biosynthesis, and triacylglycerol (TAG) accumulation in the castor and provides novel insight into exploring the genetic mechanisms underlying seed oil accumulation in the endosperm of castor beans.
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Affiliation(s)
| | | | | | | | | | | | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China; (A.Y.); (Z.Z.); (Y.C.); (J.S.); (P.L.); (X.G.)
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Han B, Li Y, Wu D, Li DZ, Liu A, Xu W. Dynamics of imprinted genes and their epigenetic mechanisms in castor bean seed with persistent endosperm. THE NEW PHYTOLOGIST 2023; 240:1868-1882. [PMID: 37717216 DOI: 10.1111/nph.19265] [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: 03/28/2023] [Accepted: 08/25/2023] [Indexed: 09/19/2023]
Abstract
Genomic imprinting refers to parent-of-origin-dependent gene expression and primarily occurs in the endosperm of flowering plants, but its functions and epigenetic mechanisms remain to be elucidated in eudicots. Castor bean, a eudicot with large and persistent endosperm, provides an excellent system for studying the imprinting. Here, we identified 131 imprinted genes in developing endosperms and endosperm at seed germination phase of castor bean, involving into the endosperm development, accumulation of storage compounds and specially seed germination. Our results showed that the transcriptional repression of maternal allele of DNA METHYLTRANSFERASE 1 (MET1) may be required for maternal genome demethylation in the endosperm. DNA methylation analysis showed that only a small fraction of imprinted genes was associated with allele-specific DNA methylation, and most of them were closely associated with constitutively unmethylated regions (UMRs), suggesting a limited role for DNA methylation in controlling genomic imprinting. Instead, histone modifications can be asymmetrically deposited in maternal and paternal genomes in a DNA methylation-independent manner to control expression of most imprinted genes. These results expanded our understanding of the occurrence and biological functions of imprinted genes and showed the evolutionary flexibility of the imprinting machinery and mechanisms in plants.
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Affiliation(s)
- Bing Han
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yelan Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Di Wu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Wei Xu
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
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Zhang W, Wang H, Ma Y, Gao B, Guan P, Huang X, Ouyang W, Guo M, Chen G, Li G, Li X. Domains Rearranged Methylase 2 maintains DNA methylation at large DNA hypomethylated shores and long-range chromatin interactions in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2333-2347. [PMID: 37539491 PMCID: PMC10579712 DOI: 10.1111/pbi.14134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/25/2023] [Accepted: 07/08/2023] [Indexed: 08/05/2023]
Abstract
DNA methylation plays an important role in gene regulation and genomic stability. However, large DNA hypomethylated regions known as DNA methylation valleys (DMVs) or canyons have also been suggested to serve unique regulatory functions, largely unknown in rice (Oryza sativa). Here, we describe the DMVs in rice seedlings, which were highly enriched with developmental and transcription regulatory genes. Further detailed analysis indicated that grand DMVs (gDMVs) might be derived from nuclear integrants of organelle DNA (NORGs). Furthermore, Domains Rearranged Methylase 2 (OsDRM2) maintained DNA methylation at short DMV (sDMV) shores. Epigenetic maps indicated that sDMVs were marked with H3K4me3 and/or H3K27me3, although the loss of DNA methylation had a negligible effect on histone modification within these regions. In addition, we constructed H3K27me3-associated interaction maps for homozygous T-DNA insertion mutant of the gene (osdrm2) and wild type (WT). From a global perspective, most (90%) compartments were stable between osdrm2 and WT plants. At a high resolution, we observed a dramatic loss of long-range chromatin loops in osdrm2, which suffered an extensive loss of non-CG (CHG and CHH, H = A, T, or C) methylation. From another viewpoint, the loss of non-CG methylation at sDMV shores in osdrm2 could disrupt H3K27me3-mediated chromatin interaction networks. Overall, our results demonstrated that DMVs are a key genomic feature in rice and are precisely regulated by epigenetic modifications, including DNA methylation and histone modifications. OsDRM2 maintained DNA methylation at sDMV shores, while OsDRM2 deficiency strongly affected three-dimensional (3D) genome architectures.
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Affiliation(s)
- Wei Zhang
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Huanhuan Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yuning Ma
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Baibai Gao
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Pengpeng Guan
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Xingyu Huang
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Minrong Guo
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Guoting Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Guoliang Li
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Hubei Key Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
| | - Xingwang Li
- National Key Laboratory of Crop Genetic ImprovementHubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
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Identification and Functional Characterization of the RcFAH12 Promoter from Castor Bean in Arabidopsis thaliana. SEPARATIONS 2022. [DOI: 10.3390/separations10010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Castor (Ricinus communis L.) seed oil is the commercial source of ricinoleate, a valuable raw material used in many industries. Oleoyl-12-hydroxylase (RcFAH12) is a key enzyme in the biosynthesis of ricinoleate, accumulating nearly 90% of the triacylglycerol in castor seeds. Little is known about the transcriptional regulation of RcFAH12. We used rapid amplification of cDNA 5′ ends (5′RACE) to locate the transcription start site (TSS) of RcFAH12, and the sequence of a 2605 bp region, −2506~+99, surrounding the TSS was cloned. We then investigated these regions to promote β-glucuronidase (GUS) expression in transgenic Arabidopsis by the progressive 5′ and 3′ deletions strategies. The GUS staining showed that the GUS accumulation varied in tissues under the control of different deleted fragments of RcFAH12. In addition, the GUS expression driven by the RcFAH12 promoter markedly accumulated in transgenic seeds, which indicated that RcFAH12 might play an important role in the biosynthesis of ricinoleic acid. This study will lay a potential foundation for developing a tissue-specific promoter in oil-seed crops.
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Abel S, Jule LT, Gudata L, Nagaraj N, Shanmugam R, Dwarampudi LP, Stalin B, Ramaswamy K. Preparation and characterization analysis of biofuel derived through seed extracts of Ricinus communis (castor oil plant). Sci Rep 2022; 12:11021. [PMID: 35773362 PMCID: PMC9246933 DOI: 10.1038/s41598-022-14403-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
The current study assesses the prospect of using R. Communis seed oil as a substitute fuel for diesel engines. Biodiesel is prepared from the R. Communis plant seed oil by a single-step base catalytic transesterification procedure. The investigation deals with the Physico-chemical characteristics of R. Communis biodiesel and has been associated with the base diesel. It has been perceived that the characteristics of biodiesel are well-matched with the base diesel under the ASTM D6751 limits correspondingly. R. Communis biodiesel is blended in different proportions with base diesel such as D10, D20, D30, D40, D50 and D100 and is tested in a Kirloskar TV1 single-cylinder, 4 blows DI engine under altered loading conditions. Outcomes demonstrate that BTE and BSFC for D10 as well as D20 are similar to base diesel. BSFC indicates that the precise BSFC of base diesel, D10, D20, D30, D40 and D50 was 0.87, 1.70, 2.60, 3.0, 3.4, and 3.5 kg/kW-hr, respectively. The extreme BTE at full load condition for base diesel, D10, D20, D30, D40, D50 and D100 are 28.2%, 28.1%, 27.9%, 25.5%, 24.1%, and 23.6% , respectively. In the case of engine emissions, R. Communis biodiesel blends provided an average decrease in hydrocarbon (HC), Carbon-monoxide (CO) and carbon dioxide (CO2) associated with base diesel. Nevertheless, R. Communis biodiesel blends discharged high stages of nitrogen oxide (NOx) compares to base diesel. Base diesel, D10, D20, D30, D40, D50, and D100 had UBHC emissions of 45 ppm, 40 ppm, 44 ppm, 46 ppm, 41 ppm, and 43 ppm, respectively. The reduction in CO emissions for D10, D20, D30, D40, D50 and D100 are 0.13%, 0.14%, 0.17%, 0.18% and 0.21% respectively. The dissimilarity in NOx attentiveness within brake powers for D10, D20, D30, D40, and D50 and base diesel are 50-ppm, 100 ppm, 150 ppm, 250 ppm, 350 ppm, and 500 ppm, respectively. The dissimilarity of CO2 emanation with reverence to break powers for the base-diesel, D10, D20, D30, D40, D50, and D100 are 4.8%, 4.9%, 4.8%, 4.56%, 4.9% and 5.1%, respectively. The present research provides a way for renewable petrol blends to substitute diesel for powering diesel engines in that way dropping the reliance on fossil fuels.
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Affiliation(s)
- Saka Abel
- Department of Physics, College of Natural and Computational Science, Dambi Dollo University, Dembi Dolo, Ethiopia
| | - Leta Tesfaye Jule
- Department of Physics, College of Natural and Computational Science, Dambi Dollo University, Dembi Dolo, Ethiopia.,Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dembi Dolo, Ethiopia
| | - Lamessa Gudata
- Department of Physics, College of Natural and Computational Science, Dambi Dollo University, Dembi Dolo, Ethiopia
| | - Nagaprasad Nagaraj
- Department of Mechanical Engineering, ULTRA College of Engineering and Technology, Madurai, Tamil Nadu, 625 104, India
| | - R Shanmugam
- TIFAC, CORE-HD, Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Nilgiris, Ooty, Tamil Nadu, India
| | - L Priyanka Dwarampudi
- Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Nilgiris, Ooty, Tamil Nadu, India
| | - B Stalin
- Department of Mechanical Engineering, Anna University, Regional Campus Madurai, Madurai, Tamil Nadu, 625 019, India
| | - Krishnaraj Ramaswamy
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dembi Dolo, Ethiopia. .,Department of Mechanical Engineering, Dambi Dollo University, Dembi Dolo, Ethiopia.
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