Zea mays and Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA843342 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21994164_1.fastq.gz | Fastqsanger.gz | |||
| SRR21994164_2.fastq.gz | Fastqsanger.gz | |||
| SRR21994165_1.fastq.gz | Fastqsanger.gz | |||
| SRR21994165_2.fastq.gz | Fastqsanger.gz | |||
| SRR21994166_1.fastq.gz | Fastqsanger.gz |
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Project description:Photosynthesis supports life on Earth but the regulatory architecture associated with photosynthesis gene expression is poorly understood. Most crops use either C3 or C4 photosynthesis with the latter allowing significantly higher efficiencies as well as improved water and nitrogen use. Here we use DNAse-SEQ to define >1 million transcription factor binding sites in leaves of grasses that either operate C3 or C4 photosynthesis and that are consistent with significant differences in the modes of gene regulation between the kingdoms of life. Leaf samples were collected from seedlings to allow for comparison of regulatory interactions between species from the same (Zea mays and Sorghum bicolor) and different (Setaria italica) C4 lineages, as well as a C3 grass (Brachypodium distachyon) in order to investigate evolution of C4 photosynthetic gene expression. Additionally bundle sheath tissues were mechanically isolated from C4 species and analysed by DNAse-SEQ to identify DNA regulatory elements controlling cell-specific gene expression patterns.
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Project description:The biochemistry of C4 photosynthesis relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy, where there is increased vein density and the proportion of bundle sheath cells surrounding the veins compared to C3 photosynthesizing species. From a suite of putative Kranz anatomy regulators, TML was identified. Loss of function tml mutations lead to the development of large lateral veins in positions normally occupied by smaller intermediate veins in both C3 and C4 species tested. In order to elucidate the role of TML in vein patterning, we set out to profile transcriptional changes that happen in the leaf primordia upon tml knock-out in the C4 species Zea mays.
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Project description:Sustainability of maize cultivation would benefit tremendously from early sowing but is hampered by low temperatures during early development in temperate climate. We show that allelic variation of subunit M of NADH-dehydrogenase-like (NDH) complex (ndhm1), discovered in a European maize landrace affects several quantitative traits relevant during early development in cold climates through NDH mediating cyclic electron transport (CET) around photosystem I, a process crucial for photosynthesis. Starting from a GWAS for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm) we capitalized on large phenotypic effects of a hAT transposon insertion in ndhm1 on quantitative traits early plant height (EPH), Fv/Fm, chlorophyll content and cold tolerance caused by reduced protein levels of NDHM and associated NDH components. Analysis of the native allelic series of ndhm1 revealed a rare allele of ndhm1 which is associated with smaller but significant effects on maximum potential quantum yield of photosystem II in dark- and light adapted leaves (Fv/Fm, ΦPSII) and early plant height compared to common alleles. Our work showcases the extraction of novel, favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing.
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Project description:Lysine malonylation is a kind of post-translational modifications (PTMs) discovered in recent years, which plays an important regulatory role in plants. Maize (Zea mays L.) is a major global cereal crop. We therefore performed a global malonylome analysis of maize. In total, 1722 uniquely malonylated lysine residues were obtained in 810 proteins. The modified proteins were involved in various biological processes such as photosynthesis, ribosome and oxidative phosphorylation. Notably, a large proportion of the modified proteins (45%) were located in chloroplast, suggesting an indispensable regulatory role of malonylation in photosynthesis and carbon fixation.
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Project description:In a natural ecosystem, the plant is in a symbiotic relationship with beneficial endophytes contributing huge impact on its host plant. Therefore, exploring beneficial endophytes and understanding its interaction is a prospective area of research. The present work aims to characterize the fungal endophytic communities associated with healthy maize and rice plants and to study the deterministic factors influencing plant growth and biocontrol properties against phytopathogens, viz, Pythium ultimum, Sclerotium oryzae, Rhizoctonia solani, and Pyricularia oryzae. A total of 123 endophytic fungi was isolated using the culture-dependent approach from different tissue parts of the plant. Most dominating fungal endophyte associated with both the crops belong to genus Fusarium, Sarocladium, Aspergillus, and Penicillium and their occurrence was not tissue specific. The isolates were screened for in vitro plant growth promotion, stress tolerance, disease suppressive mechanisms and based on the results, each culture from both the cereal crops was selected for further study. Acremonium sp. (ENF 31) and Penicillium simplicisssum (ENF22), isolated from maize and rice respectively could potentially inhibit the growth of all the tested pathogens with 46.47 ± 0.16 mm to 60.09 ± 0.04 mm range zone of inhibition for ENF31 and 35.48 ± 0.14 to 62.29 ± 0.15 mm for ENF22. Both significantly produce the defensive enzymes, ENF31 could tolerate a wide range of pH from 2 to 12, very important criteria, for studying plant growth in different soil types, especially acidic as it is widely prevalent here, making more land unsuitable for cultivation. ENF22 grows in pH range 3-12, with 10% salt tolerating ability, another factor of consideration. Study of root colonization during 7th to 30th days of growth phase reveals that ENF31 could colonize pleasantly in rice, though a maize origin, ranging from 1.02 to 1.21 log10 CFU/g root and in maize, it steadily colonizes ranging from 0.95 to 1.18 log10 CFU, while ENF22 could colonize from 0.98 to 1.24 Log10CFU/g root in rice and 1.01 to 1.24Log10CFU/g root in maize, just the reverse observed in Acremonium sp. Therefore, both the organism has the potency of a promising Bio-resource agent, that we must definitely explore to fill the gap in the agriculture industry.
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Project description:The insecticidal crystalline proteins (Crys) are a family of insect endotoxin functioning in crop protection. As insects keep evolving into tolerance to the existing Crys, it is necessary to discover new Cry proteins to overcome potential threatens. Crys possess three functional domains at their N-termini, and the most active region throughout evolution was found at the domain-III. We swapped domain-IIIs from various Cry proteins and generated seven chimeric proteins. All recombinants were expressed in Escherichia coli and their toxicity was assessed by dietary exposure assays. Three of the seven Crys exhibited a high toxicity to Asian corn borer over the controls. One of them, Cry1Ab-Gc, a chimeric Cry1Ab being replaced with the domain-III of Cry1Gc, showed the highest toxicity to rice stem borer when it was over-expressed in Oryza sativa. Furthermore, it was also transformed into maize, backcrossed into commercial maize inbred lines and then produced hybrid to evaluate their commercial value. Transgenic maize performed significant resistance to the Asian corn borer without affecting the yield. We further showed that this new protein did not have adverse effects on the environment. Our results indicated that domain III swapped of Crys could be used as an efficient method for developing new engineered insecticidal protein.
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Project description:In this study, the phytotoxicity of seven metal oxide nanoparticles(NPs)-titanium dioxide (nTiO₂), silicon dioxide (nSiO₂), cerium dioxide (nCeO₂), magnetite (nFe₃O₄), aluminum oxide (nAl₂O₃), zinc oxide (nZnO) and copper oxide (nCuO)-was assessed on two agriculturally significant crop plants (maize and rice). The results showed that seed germination was not affected by any of the seven metal oxide NPs. However, at the concentration of 2000 mg·L(-1), the root elongation was significantly inhibited by nCuO (95.73% for maize and 97.28% for rice), nZnO (50.45% for maize and 66.75% for rice). On the contrary, minor phytotoxicity of nAl₂O₃ was only observed in maize, and no obvious toxic effects were found in the other four metal oxide NPs. By further study we found that the phytotoxic effects of nZnO, nAl₂O₃ and nCuO (25 to 2000 mg·L(-)¹) were concentration dependent, and were not caused by the corresponding Cu(2+), Zn(2+) and Al(3+) ions (0.11 mg·L(-)¹, 1.27 mg·L(-)¹ and 0.74 mg·L(-)¹, respectively). Furthermore, ZnO NPs (<50 nm) showed greater toxicity than ZnO microparticles(MPs)(<5 μm) to root elongation of both maize and rice. Overall, this study provided valuable information for the application of engineered NPs in agriculture and the assessment of the potential environmental risks.
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Project description:C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.
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Project description:C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.
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