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Zhang Y, Wang N, He C, Gao Z, Chen G. Comparative transcriptome analysis reveals major genes, transcription factors and biosynthetic pathways associated with leaf senescence in rice under different nitrogen application. BMC PLANT BIOLOGY 2024; 24:419. [PMID: 38760728 PMCID: PMC11102181 DOI: 10.1186/s12870-024-05129-x] [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: 09/26/2023] [Accepted: 05/10/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important food crops in the world and the application of nitrogen fertilizer is an effective means of ensuring stable and high rice yields. However, excessive application of nitrogen fertilizer not only causes a decline in the quality of rice, but also leads to a series of environmental costs. Nitrogen reutilization is closely related to leaf senescence, and nitrogen deficiency will lead to early functional leaf senescence, whereas moderate nitrogen application will help to delay leaf senescence and promote the production of photosynthetic assimilation products in leaves to achieve yield increase. Therefore, it is important to explore the mechanism by which nitrogen affects rice senescence, to search for genes that are tolerant to low nitrogen, and to delay the premature senescence of rice functional leaves. RESULTS The present study was investigated the transcriptional changes in flag leaves between full heading and mature grain stages of rice (O. sativa) sp. japonica 'NanGeng 5718' under varying nitrogen (N) application: 0 kg/ha (no nitrogen; 0N), 240 kg/ha (moderate nitrogen; MN), and 300 kg/ha (high nitrogen; HN). Compared to MN condition, a total of 10427 and 8177 differentially expressed genes (DEGs) were detected in 0N and HN, respectively. We selected DEGs with opposite expression trends under 0N and HN conditions for GO and KEGG analyses to reveal the molecular mechanisms of nitrogen response involving DEGs. We confirmed that different N applications caused reprogramming of plant hormone signal transduction, glycolysis/gluconeogenesis, ascorbate and aldarate metabolism and photosynthesis pathways in regulating leaf senescence. Most DEGs of the jasmonic acid, ethylene, abscisic acid and salicylic acid metabolic pathways were up-regulated under 0N condition, whereas DEGs related to cytokinin and ascorbate metabolic pathways were induced in HN. Major transcription factors include ERF, WRKY, NAC and bZIP TF families have similar expression patterns which were induced under N starvation condition. CONCLUSION Our results revealed that different nitrogen levels regulate rice leaf senescence mainly by affecting hormone levels and ascorbic acid biosynthesis. Jasmonic acid, ethylene, abscisic acid and salicylic acid promote early leaf senescence under low nitrogen condition, ethylene and ascorbate delay senescence under high nitrogen condition. In addition, ERF, WRKY, NAC and bZIP TF families promote early leaf senescence. The relevant genes can be used as candidate genes for the regulation of senescence. The results will provide gene reference for further genomic studies and new insights into the gene functions, pathways and transcription factors of N level regulates leaf senescence in rice, thereby improving NUE and reducing the adverse effects of over-application of N.
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Affiliation(s)
- Yafang Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ning Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chenggong He
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhiping Gao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guoxiang Chen
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Li D, Wang J, Chen R, Chen J, Zong J, Li L, Hao D, Guo H. Review: Nitrogen acquisition, assimilation, and seasonal cycling in perennial grasses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112054. [PMID: 38423392 DOI: 10.1016/j.plantsci.2024.112054] [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: 12/06/2023] [Revised: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Perennial grasses seasonal nitrogen (N) cycle extends the residence and reuse time of N within the plant system, thereby enhancing N use efficiency. Currently, the mechanism of N metabolism has been extensively examined in model plants and annual grasses, and although perennial grasses exhibit similarities, they also possess distinct characteristics. Apart from assimilating and utilizing N throughout the growing season, perennial grasses also translocate N from aerial parts to perennial tissues, such as rhizomes, after autumn senescence. Subsequently, they remobilize the N from these perennial tissues to support new growth in the subsequent year, thereby ensuring their persistence. Previous studies indicate that the seasonal storage and remobilization of N in perennial grasses are not significantly associated with winter survival despite some amino acids and proteins associated with low temperature tolerance accumulating, but primarily with regrowth during the subsequent spring green-up stage. Further investigation can be conducted in perennial grasses to explore the correlation between stored N and dormant bud outgrowth in perennial tissues, such as rhizomes, during the spring green-up stage, building upon previous research on the relationship between N and axillary bud outgrowth in annual grasses. This exploration on seasonal N cycling in perennial grasses can offer valuable theoretical insights for new perennial grasses varieties with high N use efficiency through the application of gene editing and other advanced technologies.
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Affiliation(s)
- Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Rongrong Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Dongli Hao
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem, Sun Yat-Sen), Nanjing, Jiangsu 210014, China.
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3
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Zhou M, Yang J. Delaying or promoting? Manipulation of leaf senescence to improve crop yield and quality. PLANTA 2023; 258:48. [PMID: 37477756 DOI: 10.1007/s00425-023-04204-1] [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: 03/21/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
MAIN CONCLUSION Senescence influences leaf productivity through two aspects: photosynthesis and nutrient remobilization. Through distinctively manipulating progress of leaf senescence, it is promising to improve crop yield and quality simultaneously. Crop yield and quality are two chief goals pursued in agricultural and horticultural production. The basis of crop yield is leaf photosynthesis. Senescence is the last stage of leaf development, which usually causes decreasing of leaf photosynthetic activity. Delaying leaf senescence through physiological or molecular strategies may result in higher photosynthetic activity with a longer duration, thus producing more photoassimilates for biomass accumulation. On the other side, leaf senescence always induces degradation of macromolecular nutrients (including chlorophylls and proteins), and nutritional elements in leaves are then resorbed for development of other organs. For those crops with non-leaf organs as harvested biomass, translocating nutritional elements from leaves to harvested biomass is an indispensable physiological process to increase crop yield and quality. This review summarized successful studies about effects of delaying or promoting senescence on crop yield or quality improvement. Considering the distinctiveness of various crops, manipulation of leaf senescence should be specialized during agricultural and horticultural practices. Rational regulation of leaf senescence, such as inhibiting senescence to maintain leaf photosynthesis and then promoting senescence (with appropriate onset and efficiency) to remobilize more nutrients from leaves to target organs, may ultimately improve both crop yield and quality.
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Affiliation(s)
- Min Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiading Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Willick IR, Lowry DB. Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod. PHYSIOLOGIA PLANTARUM 2022; 174:e13812. [PMID: 36326192 PMCID: PMC9828680 DOI: 10.1111/ppl.13812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
Plants can cold acclimate to enhance their freezing tolerance by sensing declining temperature and photoperiod cues. However, the factors influencing genotypic variation in the induction of cold acclimation are poorly understood among perennial grasses. We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod. Next, we identified the temperature required to induce cold acclimation by exposing the 16 genotypes for 7 days at 20-6°C constant temperatures under a 10 or 16 h photoperiod. Cold acclimation initiated at temperatures 5 and 7°C higher in upland than in coastal and lowland genotypes. Among upland genotypes the shorter photoperiod induced cold acclimation at a 1°C higher temperature. Genotypes originating from a more northern latitude initiate cold acclimation at higher temperatures and develop higher maximum freezing tolerances. An earlier response to declining temperatures may provide the upland ecotype with additional time to prepare for winter and provide an advantage when plants are subjected to the rapid changes in fall temperature associated with injurious frosts.
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Affiliation(s)
- Ian R. Willick
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
- Kentville Research and Development CentreAgriculture and Agri‐Food CanadaKentvilleNSCanada
| | - David B. Lowry
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
- Department of Ecology, Evolutionary Biology, and BehaviorMichigan State UniversityEast LansingMichiganUSA
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Shrestha V, Chhetri HB, Kainer D, Xu Y, Hamilton L, Piasecki C, Wolfe B, Wang X, Saha M, Jacobson D, Millwood RJ, Mazarei M, Stewart CN. The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass ( Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:893610. [PMID: 35586220 PMCID: PMC9108870 DOI: 10.3389/fpls.2022.893610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Switchgrass (Panicum virgatum L.) has immense potential as a bioenergy crop with the aim of producing biofuel as an end goal. Nitrogen (N)-related sustainability traits, such as nitrogen use efficiency (NUE) and nitrogen remobilization efficiency (NRE), are important factors affecting switchgrass quality and productivity. Hence, it is imperative to develop nitrogen use-efficient switchgrass accessions by exploring the genetic basis of NUE in switchgrass. For that, we used 331 diverse field-grown switchgrass accessions planted under low and moderate N fertility treatments. We performed a genome wide association study (GWAS) in a holistic manner where we not only considered NUE as a single trait but also used its related phenotypic traits, such as total dry biomass at low N and moderate N, and nitrogen use index, such as NRE. We have evaluated the phenotypic characterization of the NUE and the related traits, highlighted their relationship using correlation analysis, and identified the top ten nitrogen use-efficient switchgrass accessions. Our GWAS analysis identified 19 unique single nucleotide polymorphisms (SNPs) and 32 candidate genes. Two promising GWAS candidate genes, caffeoyl-CoA O-methyltransferase (CCoAOMT) and alfin-like 6 (AL6), were further supported by linkage disequilibrium (LD) analysis. Finally, we discussed the potential role of nitrogen in modulating the expression of these two genes. Our findings have opened avenues for the development of improved nitrogen use-efficient switchgrass lines.
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Affiliation(s)
- Vivek Shrestha
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hari B. Chhetri
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David Kainer
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Yaping Xu
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Lance Hamilton
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ben Wolfe
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xueyan Wang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Malay Saha
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Daniel Jacobson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Reginald J. Millwood
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Mitra Mazarei
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - C. Neal Stewart
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Effah Z, Li L, Xie J, Karikari B, Liu C, Xu A, Zeng M. Transcriptome profiling reveals major structural genes, transcription factors and biosynthetic pathways involved in leaf senescence and nitrogen remobilization in rainfed spring wheat under different nitrogen fertilization rates. Genomics 2022; 114:110271. [DOI: 10.1016/j.ygeno.2022.110271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/01/2021] [Accepted: 01/16/2022] [Indexed: 11/24/2022]
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7
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Zhu L, Liu L, Sun H, Zhang Y, Zhu J, Zhang K, Li A, Bai Z, Wang G, Li C. Physiological and Comparative Transcriptomic Analysis Provide Insight Into Cotton ( Gossypium hirsutum L.) Root Senescence in Response. FRONTIERS IN PLANT SCIENCE 2021; 12:748715. [PMID: 34733305 PMCID: PMC8558499 DOI: 10.3389/fpls.2021.748715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) deficiency is one of the pivotal environmental factors that induce leaf senescence. However, little is known regarding the impact of low N on root senescence in cotton. Thus, the objective of this study was to investigate the effect of low nitrogen on root senescence. In this study, the molecular mechanism of cotton root senescence in response to nitrogen deficiency was investigated by combing physiological and transcriptomic analysis when no nitrogen and normal nitrogen (138mg N·kg-1 soil). The results showed that: (1) nitrogen starvation induced the premature senescence of leaf, while delaying root senescence. (2) The increase in catalase (CAT) activity at 60, 80, and 100days after emergence (DAE), combined with decrease of malonaldehyde content at 60, 80, and 100 DAE, and the content of abscisic acid (ABA), all of these contributed to the delay of root senescence by low nitrogen treatment. (3) To study the molecular mechanisms underlying root senescence, the gene expression profiling between low nitrogen and normal nitrogen treatments were compared pairwise at 20, 40, 60, 80, and 100 DAE. A total of 14,607 genes were identified to be differentially expressed at these five points. (5) Most genes involved in glutathione (GSH) and ascorbate peroxidase (APX) synthesis were upregulated, while ABA, apoptosis, caspase, and cell cycle-related differentially expressed genes (DEGs) were downregulated. Coupled with the physiology data, these results provide new insights into the effect of nitrogen starvation on root senescence.
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Affiliation(s)
- Lingxiao Zhu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Liantao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hongchun Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yongjiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jijie Zhu
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Science, Shijiazhuang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Anchang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Zhiying Bai
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Guiyan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Cundong Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
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Ding N, Huertas R, Torres‐Jerez I, Liu W, Watson B, Scheible W, Udvardi M. Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation. PLANT, CELL & ENVIRONMENT 2021; 44:186-202. [PMID: 32822068 PMCID: PMC7821211 DOI: 10.1111/pce.13872] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 05/10/2023]
Abstract
Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.
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Affiliation(s)
- Na Ding
- Noble Research Institute LLCArdmoreOklahomaUSA
| | | | | | - Wei Liu
- Noble Research Institute LLCArdmoreOklahomaUSA
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9
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M Razar R, Missaoui A. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. BMC PLANT BIOLOGY 2020; 20:537. [PMID: 33256587 PMCID: PMC7708163 DOI: 10.1186/s12870-020-02714-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. RESULTS We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21-23.27% for FRH, 4.47-24.06% for NDVI, 4.35-32.77% for SE, and 4.61-29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55-0.64 H2) and NDVI (0.30-0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. CONCLUSION Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
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Affiliation(s)
- Rasyidah M Razar
- Institute of Plant Breeding Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, 30602, Athens, GA, USA
| | - Ali Missaoui
- Institute of Plant Breeding Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, 30602, Athens, GA, USA.
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10
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Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z. LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020; 48:D1069-D1075. [PMID: 31599330 PMCID: PMC6943054 DOI: 10.1093/nar/gkz898] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 12/02/2022] Open
Abstract
The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.
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Affiliation(s)
- Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhao
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Jingchu Luo
- College of Life Sciences, Peking University, Beijing 100871, China.,Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Zhang NN, Zou H, Lin XY, Pan Q, Zhang WQ, Zhang JH, Wei GH, Shangguan ZP, Chen J. Hydrogen sulfide and rhizobia synergistically regulate nitrogen (N) assimilation and remobilization during N deficiency-induced senescence in soybean. PLANT, CELL & ENVIRONMENT 2020; 43:1130-1147. [PMID: 32012309 DOI: 10.1111/pce.13736] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 05/09/2023]
Abstract
Hydrogen sulfide (H2 S) is emerging as an important signalling molecule that regulates plant growth and abiotic stress responses. However, the roles of H2 S in symbiotic nitrogen (N) assimilation and remobilization have not been characterized. Therefore, we examined how H2 S influences the soybean (Glycine max)/rhizobia interaction in terms of symbiotic N fixation and mobilization during N deficiency-induced senescence. H2 S enhanced biomass accumulation and delayed leaf senescence through effects on nodule numbers, leaf chlorophyll contents, leaf N resorption efficiency, and the N contents in different tissues. Moreover, grain numbers and yield were regulated by H2 S and rhizobia, together with N accumulation in the organs, and N use efficiency. The synergistic effects of H2 S and rhizobia were also demonstrated by effects on the enzyme activities, protein abundances, and gene expressions associated with N metabolism, and senescence-associated genes (SAGs) expression in soybeans grown under conditions of N deficiency. Taken together, these results show that H2 S and rhizobia accelerate N assimilation and remobilization by regulation of the expression of SAGs during N deficiency-induced senescence. Thus, H2 S enhances the vegetative and reproductive growth of soybean, presumably through interactions with rhizobia under conditions of N deficiency.
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Affiliation(s)
- Ni-Na Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, P.R. China
| | - Hang Zou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of life sciences, Northwest A&F University, Yangling, P.R. China
| | - Xue-Yuan Lin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, P.R. China
| | - Qing Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of life sciences, Northwest A&F University, Yangling, P.R. China
| | - Wei-Qin Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, P.R. China
| | - Jian-Hua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ge-Hong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of life sciences, Northwest A&F University, Yangling, P.R. China
| | - Zhou-Ping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, P.R. China
| | - Juan Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, P.R. China
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12
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Xie J, Ma A, Fennell A, Ma Q, Zhao J. It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Brief Bioinform 2020; 20:1449-1464. [PMID: 29490019 DOI: 10.1093/bib/bby014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes. However, there is still a considerable gap between biclustering methodology development and comprehensive data interpretation, mainly because of the lack of knowledge for the selection of appropriate biclustering tools and further supporting computational techniques in specific studies. Here, we first deliver a brief introduction to the existing biclustering algorithms and tools in public domain, and then systematically summarize the basic applications of biclustering for biological data and more advanced applications of biclustering for biomedical data. This review will assist researchers to effectively analyze their big data and generate valuable biological knowledge and novel insights with higher efficiency.
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13
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Life History Variation as a Model for Understanding Trade-Offs in Plant-Environment Interactions. Curr Biol 2020; 30:R180-R189. [PMID: 32097648 DOI: 10.1016/j.cub.2020.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
All plants must allocate limited resources to survival, growth, and reproduction. In natural species, allocation strategies reflect trade-offs between survivorship risk and subsequent fitness benefits and are therefore central to a species' ecology. Artificial selection on allocation has generated high-yielding crops that often invest the bare minimum in defense or longevity. Ecological, genetic, and evolutionary analyses of plant life history - particularly with respect to longevity and resource allocation along an axis from annual to perennial species - provides a framework to evaluate trade-offs in plant-environment interactions in natural and managed systems. Recent efforts to develop new model plant systems for research and to increase agricultural resilience and efficiency by developing herbaceous perennial crops motivates our critical assessment of traditional assumptions regarding differences between annual and perennial plant species. Here, we review our present understanding of the genetic basis of physiological, developmental, and anatomical differences in wild and crop species and reach two broad conclusions. First, that perenniality and annuality should be considered syndromes comprised of many interacting traits, and that elucidating the genetic basis of these traits is required to assess models of evolution and to develop successful breeding strategies. Modern phenomic and biotechnology tools will facilitate these enquiries. Second, many classic assumptions about the difference between the two syndromes are supported by limited evidence. Throughout this Review, we highlight key knowledge gaps in the proximate and ultimate mechanisms driving life history variation, and suggest empirical approaches to parameterize trade-offs and to make progress in this critical area of direct relevance to ecology and plant performance in a changing world.
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14
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Yang F, Schäufele R, Liu HT, Ostler U, Schnyder H, Gong XY. Gross and net nitrogen export from leaves of a vegetative C 4 grass. JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153093. [PMID: 31841951 DOI: 10.1016/j.jplph.2019.153093] [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: 06/27/2019] [Revised: 08/31/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) mobilization from mature leaves plays a key role in supplying amino acids to vegetative and reproductive sinks. However, it is unknown if the mobilized N is predominantly sourced by net N-export (a senescence-related process) or other source of N-export from leaves. We used a new approach to partition gross and net N-export from leaf blades at different developmental stages in Cleistogenes squarrosa (a perennial C4 grass). Net N-export was determined as net loss of leaf N with age, while gross N-export was quantified from isotopic mass balances obtained following 24 h-long 15N-labeling with nitrate on 10-12 developmentally distinct (mature and senescing) leaves of individual major tillers. Net N-export was apparent only in older leaves (leaf no. > 7, with leaves numbered basipetally from the tip of the tiller and leaf no. 2 the youngest fully-expanded leaf), while gross N-export was largely independent of leaf age category and was ∼8.4 times greater than the net N-export of a tiller. At whole-tiller level, N import compensated 88 ± 14 (SE) % of gross N-export of all mature blades leading to a net N-export of 0.51 ± 0.07 (SE) μg h-1 tiller-1. N-import was equivalent to 0.09 ± 0.01 (SE) d-1 of total leaf N, similar to reported rates of leaf protein turnover. Gross N-export from all mature blades of a tiller was ∼1.9-times the total demand of the immature tissues of the same (vegetative) tiller. Significant N-export is evident in all mature blades, and is not limited to senescence conditions, implying a much shorter mean residence time of leaf N than that calculated from net N-export. Gross N-export contributes not only to the N demand of the immature tissues of the same tiller but also to N supply of other sinks, such as newly formed tillers. N dynamics at tiller level is integrated with that of the remainder of the shoot, thus highlights the importance of integration of leaf-, tiller-, and plant-scale N dynamics.
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Affiliation(s)
- Fang Yang
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany
| | - Rudi Schäufele
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany
| | - Hai Tao Liu
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany
| | - Ulrike Ostler
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany
| | - Hans Schnyder
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany
| | - Xiao Ying Gong
- Technische Universität München, Lehrstuhl für Grünlandlehre, Alte Akademie 12, D-85354, Freising, Germany.
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15
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Palmer NA, Chowda-Reddy RV, Muhle AA, Tatineni S, Yuen G, Edmé SJ, Mitchell RB, Sarath G. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. PLoS One 2019; 14:e0222080. [PMID: 31513611 PMCID: PMC6742388 DOI: 10.1371/journal.pone.0222080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023] Open
Abstract
The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar 'Kanlow' and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown 'Kanlow', and 'Summer' plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - R. V. Chowda-Reddy
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Anthony A. Muhle
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
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16
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Gallardo K, Besson A, Klein A, Le Signor C, Aubert G, Henriet C, Térézol M, Pateyron S, Sanchez M, Trouverie J, Avice JC, Larmure A, Salon C, Balzergue S, Burstin J. Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages. FRONTIERS IN PLANT SCIENCE 2019; 10:1014. [PMID: 31440268 PMCID: PMC6693388 DOI: 10.3389/fpls.2019.01014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Pea (Pisum sativum L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume. The aim of this study was to unveil the transcriptional regulations occurring in pea leaves before the sharp decrease in chlorophyll breakdown. As a prelude to this study, a time-series analysis of 15N translocation at the whole plant level was performed, which indicated that nitrogen recycling among organs was highly dynamic during this period and varied depending on nitrate availability. Leaves collected on vegetative and reproductive nodes were further analyzed by transcriptomics. The data revealed extensive transcriptome changes in leaves of reproductive nodes during early seed development (from flowering to 14 days after flowering), including an up-regulation of genes encoding transporters, and particularly of sulfate that might sustain sulfur metabolism in leaves of the reproductive part. This developmental period was also characterized by a down-regulation of cell wall-associated genes in leaves of both reproductive and vegetative nodes, reflecting a shift in cell wall structure. Later on, 27 days after flowering, genes potentially switching the metabolism of leaves toward senescence were pinpointed, some of which are related to ribosomal RNA processing, autophagy, or transport systems. Transcription factors differentially regulated in leaves between stages were identified and a gene co-expression network pointed out some of them as potential regulators of the above-mentioned biological processes. The same approach was conducted in Medicago truncatula to identify shared regulations with this wild legume species. Altogether the results give a global view of transcriptional events in leaves of legumes at early reproductive stages and provide a valuable resource of candidate genes that could be targeted by reverse genetics to improve nutrient remobilization and/or delay catabolic processes leading to senescence.
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Affiliation(s)
- Karine Gallardo
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Alicia Besson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Charlotte Henriet
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Morgane Térézol
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Stéphanie Pateyron
- IPS2, Institute of Plant Sciences Paris-Saclay (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay), POPS-Transcriptomic Platform, Saclay Plant Sciences (SPS), Orsay, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Jacques Trouverie
- Normandie Université, Institut National de la Recherche Agronomique, Université de Caen Normandie, UMR INRA–UCBN 950 Ecophysiologie Végétale et Agronomie, SFR Normandie Végétal FED 4277, Caen, France
| | - Jean-Christophe Avice
- Normandie Université, Institut National de la Recherche Agronomique, Université de Caen Normandie, UMR INRA–UCBN 950 Ecophysiologie Végétale et Agronomie, SFR Normandie Végétal FED 4277, Caen, France
| | - Annabelle Larmure
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Sandrine Balzergue
- IPS2, Institute of Plant Sciences Paris-Saclay (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay), POPS-Transcriptomic Platform, Saclay Plant Sciences (SPS), Orsay, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
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17
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Yang J, Udvardi M. Senescence and nitrogen use efficiency in perennial grasses for forage and biofuel production. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:855-865. [PMID: 29444307 DOI: 10.1093/jxb/erx241] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Organ senescence is an important developmental process in plants that enables recycling of nutrients, such as nitrogen, to maximize reproductive success. Nitrogen is the mineral nutrient required in greatest amount by plants, although soil-N limits plant productivity in many natural and agricultural systems, especially systems that receive little or no fertilizer-N. Use of industrial N-fertilizers in agriculture increased crop yields several fold over the past century, although at substantial cost to fossil energy reserves and the environment. Therefore, it is important to optimize nitrogen use efficiency (NUE) in agricultural systems. Organ senescence contributes to NUE in plants and manipulation of senescence in plant breeding programs is a promising approach to improve NUE in agriculture. Much of what we know about plant senescence comes from research on annual plants, which provide most of the food for humans. Relatively little work has been done on senescence in perennial plants, especially perennial grasses, which provide much of the forage for grazing animals and promise to supply much of the biomass required by the future biofuel industry. Here, we review briefly what is known about senescence from studies of annual plants, before presenting current knowledge about senescence in perennial grasses and its relationship to yield, quality, and NUE. While higher yield is a common target, desired N-content diverges between forage and biofuel crops. We discuss how senescence programs might be altered to produce high-yielding, stress-tolerant perennial grasses with high-N (protein) for forage or low-N for biofuels in systems optimized for NUE.
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Affiliation(s)
- Jiading Yang
- Noble Research Institute, Ardmore, OK, USA
- Bioenergy Sciences Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Udvardi
- Noble Research Institute, Ardmore, OK, USA
- Bioenergy Sciences Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, USA
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18
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Palmer NA, Saathoff AJ, Scully ED, Tobias CM, Twigg P, Madhavan S, Schmer M, Cahoon R, Sattler SE, Edmé SJ, Mitchell RB, Sarath G. Seasonal below-ground metabolism in switchgrass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1059-1075. [PMID: 29030891 DOI: 10.1111/tpj.13742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 05/25/2023]
Abstract
Switchgrass (Panicum virgatum), a perennial, polyploid, C4 warm-season grass is among the foremost herbaceous species being advanced as a source of biomass for biofuel end uses. At the end of every growing season, the aerial tissues senesce, and the below-ground rhizomes become dormant. Future growth is dependent on the successful over-wintering of the rhizomes. Although the importance of rhizome health to overall year-upon-year plant productivity has been long recognized, there is limited information on seasonal changes occurring during dormancy at both the transcriptome and metabolite levels. Here, global changes in transcriptomes and metabolites were investigated over two growing seasons in rhizomes harvested from field-grown plants. The objectives were: (a) synthesize information on cellular processes that lead to dormancy; and (b) provide models that could account for major metabolic pathways present in dormant switchgrass rhizomes. Overall, metabolism during dormancy appeared to involve discrete but interrelated events. One was a response to abscisic acid that resulted in dehydration, increases in osmolytes and upregulation of autophagic processes, likely through the target of rapamycin complex and sucrose non-fermentative-related kinase-based signaling cascades. Another was a recalibration of energy transduction through apparent reductions in mitochondrial oxidative phosphorylation, increases in substrate level generation of ATP and reducing equivalents, and recycling of N and possibly CO2 through refixation. Lastly, transcript abundances indicated that cold-related signaling was also occurring. Altogether, these data provide a detailed overview of rhizome metabolism, especially during dormancy, which can be exploited in the future to improve winter survival in switchgrass.
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Affiliation(s)
- Nathan A Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Aaron J Saathoff
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-Agricultural Research Service Center for Grain and Animal Health, Manhattan, KS, 66502, USA
| | - Christian M Tobias
- Crop Improvement and Genetics Research, USDA-ARS, Albany, CA, 94710, USA
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE, 68849, USA
| | | | - Marty Schmer
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Rebecca Cahoon
- Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE, 68588, USA
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Serge J Edmé
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Robert B Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
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19
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Havé M, Marmagne A, Chardon F, Masclaux-Daubresse C. Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2513-2529. [PMID: 27707774 DOI: 10.1093/jxb/erw365] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.
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Affiliation(s)
- Marien Havé
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Anne Marmagne
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Fabien Chardon
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Céline Masclaux-Daubresse
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
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20
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Thomas H, Ougham H. Introduction to a Virtual Issue on plant senescence. THE NEW PHYTOLOGIST 2016; 212:531-536. [PMID: 27735076 DOI: 10.1111/nph.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Howard Thomas
- IBERS, Aberystwyth University, Edward Llwyd Building, Aberystwyth, Ceredigion, SY23 3DA, UK.
| | - Helen Ougham
- IBERS, Aberystwyth University, Edward Llwyd Building, Aberystwyth, Ceredigion, SY23 3DA, UK
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21
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Han M, Wong J, Su T, Beatty PH, Good AG. Identification of Nitrogen Use Efficiency Genes in Barley: Searching for QTLs Controlling Complex Physiological Traits. FRONTIERS IN PLANT SCIENCE 2016; 7:1587. [PMID: 27818673 PMCID: PMC5073129 DOI: 10.3389/fpls.2016.01587] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/07/2016] [Indexed: 05/20/2023]
Abstract
Over the past half century, the use of nitrogen (N) fertilizers has markedly increased crop yields, but with considerable negative effects on the environment and human health. Consequently, there has been a strong push to reduce the amount of N fertilizer used by maximizing the nitrogen use efficiency (NUE) of crops. One approach would be to use classical genetics to improve the NUE of a crop plant. This involves both conventional breeding and quantitative trait loci (QTL) mapping in combination with marker-assisted selection (MAS) to track key regions of the chromosome that segregate for NUE. To achieve this goal, one of initial steps is to characterize the NUE-associated genes, then use the profiles of specific genes to combine plant physiology and genetics to improve plant performance. In this study, on the basis of genetic homology and expression analysis, barley candidate genes from a variety of families that exhibited potential roles in enhancing NUE were identified and mapped. We then performed an analysis of QTLs associated with NUE in field trials and further analyzed their map-location data to narrow the search for these candidate genes. These results provide a novel insight on the identification of NUE genes and for the future prospects, will lead to a more thorough understanding of physiological significances of the diverse gene families that may be associated with NUE in barley.
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Affiliation(s)
- Mei Han
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
| | - Julia Wong
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
| | - Tao Su
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
- *Correspondence: Tao Su
| | - Perrin H. Beatty
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
| | - Allen G. Good
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
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