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Lv X, Li Q, Deng X, Ding S, Sun R, Chen S, Yun W, Dai C, Luo B. Fulvic acid application increases rice seedlings performance under low phosphorus stress. BMC PLANT BIOLOGY 2024; 24:703. [PMID: 39054445 PMCID: PMC11271057 DOI: 10.1186/s12870-024-05435-4] [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: 05/09/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Fulvic acid enhances plant growth and interacts synergistically with phosphate fertilizer to alleviate the agricultural production problem of low phosphorus fertilizer utilization efficiency. However, the underlying mechanism of its action remains poorly understood. In this study, we investigated the impact of fulvic acid application with varying concentrations (0, 40, 60, 80 and 120 mg/L) on rice performance in plants grown in a hydroponic system subjected to low phosphorus stress. The rice growth phenotypes, biomass, root morphology, phosphorus uptake, and the impact of fulvic acid on the rhizosphere environment of rice, were assessed. RESULTS The findings showed that adding appropriate concentrations of exogenous fulvic acid could promote the growth performance of rice under low phosphorus stress. Particularly at T1 (40 mg/L) and T2 (60 mg/L) over the control effectively increased rice biomass by 25.42% and 24.56%, respectively. Fulvic acid treatments stimulated root morphogenesis, up-regulated phosphate transporter genes, and facilitated phosphorus absorption and accumulation. Especially T1 (20.52%), T2 (18.10%) and T3 (20.48%) treatments significantly increased phosphorus uptake in rice, thereby alleviating low phosphorus stress. Additionally, fulvic acid elevated organic acids concentration in roots and up-regulated plasma membrane H+-ATPase genes, promoting organic acids secretion. This metabolic alteration can also alleviate low phosphorus stress in rice. CONCLUSIONS The effect of exogenous fulvic acid on physiological indicators is concentration-dependent under low phosphorus stress, enhances rice performance and reduces reliance on phosphorus fertilizer. This provides new insights to shed light on the mechanism of alleviating low phosphorus stress in rice through fulvic acid application, an eco-friendly tool.
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Affiliation(s)
- Xiaomeng Lv
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Qingchao Li
- Bijie Academy of Agricultural Sciences, Bijie, 551700, China
| | - Xuan Deng
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Shitao Ding
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Ruibo Sun
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Shunquan Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Wenjing Yun
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China
| | - Changrong Dai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224007, China.
| | - Bingbing Luo
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, P. R. China.
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Islam MF, Yamatani H, Takami T, Kusaba M, Sakamoto W. Characterization of organelle DNA degradation mediated by DPD1 exonuclease in the rice genome-edited line. PLANT MOLECULAR BIOLOGY 2024; 114:71. [PMID: 38856917 PMCID: PMC11164812 DOI: 10.1007/s11103-024-01452-x] [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: 03/05/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Mitochondria and plastids, originated as ancestral endosymbiotic bacteria, contain their own DNA sequences. These organelle DNAs (orgDNAs) are, despite the limited genetic information they contain, an indispensable part of the genetic systems but exist as multiple copies, making up a substantial amount of total cellular DNA. Given this abundance, orgDNA is known to undergo tissue-specific degradation in plants. Previous studies have shown that the exonuclease DPD1, conserved among seed plants, degrades orgDNAs during pollen maturation and leaf senescence in Arabidopsis. However, tissue-specific orgDNA degradation was shown to differ among species. To extend our knowledge, we characterized DPD1 in rice in this study. We created a genome-edited (GE) mutant in which OsDPD1 and OsDPD1-like were inactivated. Characterization of this GE plant demonstrated that DPD1 was involved in pollen orgDNA degradation, whereas it had no significant effect on orgDNA degradation during leaf senescence. Comparison of transcriptomes from wild-type and GE plants with different phosphate supply levels indicated that orgDNA had little impact on the phosphate starvation response, but instead had a global impact in plant growth. In fact, the GE plant showed lower fitness with reduced grain filling rate and grain weight in natural light conditions. Taken together, the presented data reinforce the important physiological roles of orgDNA degradation mediated by DPD1.
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Affiliation(s)
- Md Faridul Islam
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Hiroshi Yamatani
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233, Watanuki, Takasaki, Gunma, 370-1292, Japan
| | - Tsuneaki Takami
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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3
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Yan M, Feng F, Xu X, Fan P, Lou Q, Chen L, Zhang A, Luo L, Mei H. Genome-wide association study identifies a gene conferring high physiological phosphorus use efficiency in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1153967. [PMID: 36998687 PMCID: PMC10043302 DOI: 10.3389/fpls.2023.1153967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Phosphate (Pi) is indispensable for the growth and development of plant, and low-Pi stress is a major limitation for crop growth and yield worldwide. The tolerance to low-Pi stress varied among rice germplasm resources. However, the mechanisms underlying the tolerance of rice to low-Pi stress, as a complex quantitative trait, are not clear. We performed a genome-wide association study (GWAS) through a diverse worldwide collection of 191 rice accessions in the field under normal-Pi and low-Pi supply in two years. Twenty and three significant association loci were identified for biomass and grain yield per plant under low-Pi supply respectively. The expression level of OsAAD as a candidate gene from a associated locus was significantly up-regulated after low-Pi stress treatment for five days and tended to return to normal levels after Pi re-supply in shoots. Suppression of OsAAD expression could improve the physiological phosphorus use efficiency (PPUE) and grain yields through affecting the expression of several genes associated with GA biosynthesis and metabolism. OsAAD would be a promising gene for increasing PPUE and grain yield in rice under normal- and low-Pi supply via genome editing.
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Affiliation(s)
- Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Fangjun Feng
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiaoyan Xu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Peiqing Fan
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Anning Zhang
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
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4
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Hashida Y, Tezuka A, Nomura Y, Kamitani M, Kashima M, Kurita Y, Nagano AJ. Fillable and unfillable gaps in plant transcriptome under field and controlled environments. PLANT, CELL & ENVIRONMENT 2022; 45:2410-2427. [PMID: 35610174 PMCID: PMC9544781 DOI: 10.1111/pce.14367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments. We analysed massive transcriptome data of rice plants grown under field and SmartGC conditions to clarify the differences in plant responses to field and controlled environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening but those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature affects transcriptome dynamics only in the morning. We found upregulation of genes related to biotic and abiotic stress, and their expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results reveal fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments and can accelerate the understanding of plant responses to field environments for both basic biology and agricultural applications.
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Affiliation(s)
- Yoichi Hashida
- Faculty of AgricultureTakasaki University of Health and WelfareTakasakiGunmaJapan
| | - Ayumi Tezuka
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Yasuyuki Nomura
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
| | - Mari Kamitani
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Makoto Kashima
- Research Institute for Food and AgricultureRyukoku UniversityOtsuShigaJapan
- College of Science and EngineeringAoyama Gakuin UniversitySagamiharaKanagawaJapan
| | - Yuko Kurita
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
| | - Atsushi J. Nagano
- Faculty of AgricultureRyukoku UniversityOtsuShigaJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaYamagataJapan
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5
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Takehisa H, Ando F, Takara Y, Ikehata A, Sato Y. Transcriptome and hyperspectral profiling allows assessment of phosphorus nutrient status in rice under field conditions. PLANT, CELL & ENVIRONMENT 2022; 45:1507-1519. [PMID: 35128701 DOI: 10.1111/pce.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/11/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) is one of the macronutrients indispensable for crop production, and therefore it is important to understand the potential of plants to adapt to low P conditions. We compared growth and leaf genome-wide transcriptome of four rice cultivars during growth between two fields with different amount of available phosphate and further analysed the acceptable range of P levels for normal growth from the view of both appearance traits and internal P nutrient status, which was measured by profiling the expression of the P indicator gene. This demonstrated that rice plants have a robustness to moderate P-deficient conditions expressing a system for P acquisition and usage without any effects on yield potential and that P indicator gene expression could be a useful index for early diagnosis of P status in plants. To develop a simple method for assessment of P status, we tried to predict the expression level using reflectance spectroscopy and hyperspectral imaging, thereby providing models with good performance. Our findings suggest that rice plants have the potential to adapt to moderate low P conditions in the field and showed that the hyperspectral technique is one of the useful tools for simple measurement of molecular-level dynamics reflecting internal nutrient conditions.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | | | | | - Akifumi Ikehata
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Mandal VK, Jangam AP, Chakraborty N, Raghuram N. Nitrate-responsive transcriptome analysis reveals additional genes/processes and associated traits viz. height, tillering, heading date, stomatal density and yield in japonica rice. PLANTA 2022; 255:42. [PMID: 35038039 DOI: 10.1007/s00425-021-03816-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/27/2021] [Indexed: 05/22/2023]
Abstract
Our transcriptomic analysis expanded the repertoire of nitrate-responsive genes/processes in rice and revealed their phenotypic association with root/shoot, stomata, tiller, panicle/flowering and yield, with agronomic implications for nitrogen use efficiency. Nitrogen use efficiency (NUE) is a multigenic quantitative trait, involving many N-responsive genes/processes that are yet to be fully characterized. Microarray analysis of early nitrate response in excised leaves of japonica rice revealed 6688 differentially expressed genes (DEGs), including 2640 hitherto unreported across multiple functional categories. They include transporters, enzymes involved in primary/secondary metabolism, transcription factors (TFs), EF-hand containing calcium binding proteins, hormone metabolism/signaling and methytransferases. Some DEGs belonged to hitherto unreported processes viz. alcohol, lipid and trehalose metabolism, mitochondrial membrane organization, protein targeting and stomatal opening. 1158 DEGs were associated with growth physiology and grain yield or phenotypic traits for NUE. We identified seven DEGs for shoot apical meristem, 66 for leaf/culm/root, 31 for tiller, 70 for heading date/inflorescence/spikelet/panicle, 144 for seed and 78 for yield. RT-qPCR validated nitrate regulation of 31 DEGs belonging to various important functional categories/traits. Physiological validation of N-dose responsive changes in plant development revealed that relative to 1.5 mM, 15 mM nitrate significantly increased stomatal density, stomatal conductance and transpiration rate. Further, root/shoot growth, number of tillers and grain yield declined and panicle emergence/heading date delayed, despite increased photosynthetic rate. We report the binding sites of diverse classes of TFs such as WRKY, MYB, HMG etc., in the 1 kb up-stream regions of 6676 nitrate-responsive DEGs indicating their role in regulating nitrate response/NUE. Together, these findings expand the repertoire of genes and processes involved in genomewide nitrate response in rice and reveal their physiological, phenotypic and agronomic implications for NUE.
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Affiliation(s)
- Vikas Kumar Mandal
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Annie Prasanna Jangam
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Navjyoti Chakraborty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India
| | - Nandula Raghuram
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi, India.
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7
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Yue L, Li G, Dai Y, Sun X, Li F, Zhang S, Zhang H, Sun R, Zhang S. Gene co-expression network analysis of the heat-responsive core transcriptome identifies hub genes in Brassica rapa. PLANTA 2021; 253:111. [PMID: 33905008 DOI: 10.1007/s00425-021-03630-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Gene co-expression network analysis of the heat-responsive core transcriptome in two contrasting Brassica rapa accessions reveals the main metabolic pathways, key modules and hub genes, are involved in long-term heat stress. Brassica rapa is a widely cultivated and economically important vegetable in Asia. High temperature is a common stress that severely impacts leaf head formation in B. rapa, resulting in reduced quality and production. The purpose of this study was thus to identify candidate heat tolerance genes by comparative transcriptome analysis of two contrasting B. rapa accessions in response to long-term heat stress. Two B. rapa accessions, '268' and '334', which showed significant differences in heat tolerance, were used for RNA sequencing analysis. We identified a total of 11,055 and 8921 differentially expressed genes (DEGs) in '268' and '334', respectively. Functional enrichment analyses of all of the identified DEGs, together with the genes identified from weighted gene co-expression network analyses (WGCNA), revealed that the autophagy pathway, glutathione metabolism, and ribosome biogenesis in eukaryotes were significantly up-regulated, whereas photosynthesis was down-regulated, in the heat resistance of B. rapa '268'. Furthermore, when B. rapa '334' was subjected to long-term high-temperature stress, heat stress caused significant changes in the expression of certain functional genes linked to protein processing in the endoplasmic reticulum and plant hormone signal transduction pathways. Autophagy-related genes might have been induced by persistent heat stress and remained high during recovery. Several hub genes like HSP17.6, HSP17.6B, HSP70-8, CLPB1, PAP1, PYR1, ADC2, and GSTF11 were discussed in this study, which may be potential candidates for further analyses of the response to long-term heat stress. These results should help elucidate the molecular mechanisms of heat stress adaptation in B. rapa.
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Affiliation(s)
- Lixin Yue
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Yun Dai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Xiao Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing, 100081, People's Republic of China.
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Gu M, Hu X, Wang T, Xu G. Modulation of plant root traits by nitrogen and phosphate: transporters, long-distance signaling proteins and peptides, and potential artificial traps. BREEDING SCIENCE 2021; 71:62-75. [PMID: 33762877 PMCID: PMC7973493 DOI: 10.1270/jsbbs.20102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/11/2020] [Indexed: 05/11/2023]
Abstract
As sessile organisms, plants rely on their roots for anchorage and uptake of water and nutrients. Plant root is an organ showing extensive morphological and metabolic plasticity in response to diverse environmental stimuli including nitrogen (N) and phosphorus (P) nutrition/stresses. N and P are two essential macronutrients serving as not only cell structural components but also local and systemic signals triggering root acclimatory responses. Here, we mainly focused on the current advances on root responses to N and P nutrition/stresses regarding transporters as well as long-distance mobile proteins and peptides, which largely represent local and systemic regulators, respectively. Moreover, we exemplified some of the potential pitfalls in experimental design, which has been routinely adopted for decades. These commonly accepted methods may help researchers gain fundamental mechanistic insights into plant intrinsic responses, yet the output might lack strong relevance to the real situation in the context of natural and agricultural ecosystems. On this basis, we further discuss the established-and yet to be validated-improvements in experimental design, aiming at interpreting the data obtained under laboratory conditions in a more practical view.
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Affiliation(s)
- Mian Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
- Corresponding author (e-mail: )
| | - Xu Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
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Takehisa H, Sato Y. Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. BREEDING SCIENCE 2021; 71:76-88. [PMID: 33762878 PMCID: PMC7973498 DOI: 10.1270/jsbbs.20098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.
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Affiliation(s)
- Hinako Takehisa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Kumari S, Sharma N, Raghuram N. Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:627955. [PMID: 34168661 PMCID: PMC8217879 DOI: 10.3389/fpls.2021.627955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 05/04/2021] [Indexed: 05/08/2023]
Abstract
Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein-protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.
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11
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Marzec M, Situmorang A, Brewer PB, Brąszewska A. Diverse Roles of MAX1 Homologues in Rice. Genes (Basel) 2020; 11:E1348. [PMID: 33202900 PMCID: PMC7709044 DOI: 10.3390/genes11111348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious.
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Affiliation(s)
- Marek Marzec
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
| | - Apriadi Situmorang
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Philip B. Brewer
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (A.S.); (P.B.B.)
| | - Agnieszka Brąszewska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland;
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12
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Gong Z, Xiong L, Shi H, Yang S, Herrera-Estrella LR, Xu G, Chao DY, Li J, Wang PY, Qin F, Li J, Ding Y, Shi Y, Wang Y, Yang Y, Guo Y, Zhu JK. Plant abiotic stress response and nutrient use efficiency. SCIENCE CHINA-LIFE SCIENCES 2020; 63:635-674. [PMID: 32246404 DOI: 10.1007/s11427-020-1683-x] [Citation(s) in RCA: 518] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/17/2020] [Indexed: 12/15/2022]
Abstract
Abiotic stresses and soil nutrient limitations are major environmental conditions that reduce plant growth, productivity and quality. Plants have evolved mechanisms to perceive these environmental challenges, transmit the stress signals within cells as well as between cells and tissues, and make appropriate adjustments in their growth and development in order to survive and reproduce. In recent years, significant progress has been made on many fronts of the stress signaling research, particularly in understanding the downstream signaling events that culminate at the activation of stress- and nutrient limitation-responsive genes, cellular ion homeostasis, and growth adjustment. However, the revelation of the early events of stress signaling, particularly the identification of primary stress sensors, still lags behind. In this review, we summarize recent work on the genetic and molecular mechanisms of plant abiotic stress and nutrient limitation sensing and signaling and discuss new directions for future studies.
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Affiliation(s)
- Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Luis R Herrera-Estrella
- Plant and Soil Science Department (IGCAST), Texas Tech University, Lubbock, TX, 79409, USA.,Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, Irapuato, 36610, México.,College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guohua Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dai-Yin Chao
- National Key laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jingrui Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Peng-Yun Wang
- School of Life Science, Henan University, Kaifeng, 457000, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jijang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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13
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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14
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Luo Y, Pang D, Jin M, Chen J, Kong X, Li W, Chang Y, Li Y, Wang Z. Identification of plant hormones and candidate hub genes regulating flag leaf senescence in wheat response to water deficit stress at the grain-filling stage. PLANT DIRECT 2019; 3:e00152. [PMID: 31709381 PMCID: PMC6834085 DOI: 10.1002/pld3.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/26/2019] [Accepted: 06/29/2019] [Indexed: 05/16/2023]
Abstract
In order to clarify the transcriptional regulatory network and physiological mechanisms governing leaf senescence response to drought stress in wheat, experiments were performed using two wheat varieties with contrasting drought tolerance: Fu287 (F287, a drought-sensitive genotype) and Shannong20 (SN20, a drought-resistant genotype). The latter has higher SPAD values, salicylic acid (SA), jasmonic acid (JA), zeatin (Z), zeatin riboside (ZR), and gibberellin (GA 3) content as well as higher expression levels of Cu/Zn-SOD, Mn-SOD, Fe-SOD,POD,CAT, and APX under various water deficit conditions. Conjoint analysis of physiological and biochemical indicators and transcriptome data by weighted gene co-expression network analysis (WGCNA) in the present study provides a useful genomic and molecular resource for studying drought adaptation in wheat. The flag leaf senescence process was changed by altering the concentration of phytohormones. SA, JA, abscisic acid (ABA), Z, ZR, and GA 3 coordinate with each other to control leaf senescence and plant adaptation under drought stress. Further, the leaf senescence process was divided into two phases: the persistence phase and the rapid loss phase. Shorter Chltotal (duration of the flag leaf being photosynthetically active), shorter Chlper (persistence phase), reduced M (inflection point cumulative temperature when senescence rate is the maximum), decreased r max (the maximum senescence rate), larger r 0 (the initial senescence rate), and increased r aver (the average senescence rate) were slightly associated with low grain mass. We speculated that extending the period of the persistence phase by cultivation or chemical control measures could further increase the drought survivability and productivity of wheat.
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Affiliation(s)
- Yongli Luo
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Dangwei Pang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Min Jin
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Jin Chen
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Xiang Kong
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Wenqian Li
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Yonglan Chang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Yong Li
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Zhenlin Wang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
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