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Guillotin B, Rahni R, Passalacqua M, Mohammed MA, Xu X, Raju SK, Ramírez CO, Jackson D, Groen SC, Gillis J, Birnbaum KD. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 2023; 617:785-791. [PMID: 37165193 PMCID: PMC10657638 DOI: 10.1038/s41586-023-06053-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits1. Key traits that distinguish these species are mediated by specialized cell types2. Here we compare the transcriptomes of root cells in three grass species-Zea mays, Sorghum bicolor and Setaria viridis. We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others-driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops.
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Affiliation(s)
- Bruno Guillotin
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ramin Rahni
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Mohammed Ateequr Mohammed
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Xiaosa Xu
- Cold Spring Harbor Laboratory, New York, NY, USA
| | - Sunil Kenchanmane Raju
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Carlos Ortiz Ramírez
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- UGA-LANGEBIO Cinvestav, Guanajuato, México
| | | | - Simon C Groen
- Department of Nematology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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2
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Singh D, Singh CK, Taunk J, Gaikwad K, Singh V, Sanwal SK, Karwa S, Singh D, Sharma PC, Yadav RK, Pal M. Linking genome wide RNA sequencing with physio-biochemical and cytological responses to catalogue key genes and metabolic pathways for alkalinity stress tolerance in lentil (Lens culinaris Medikus). BMC Plant Biol 2022; 22:99. [PMID: 35247970 PMCID: PMC8897830 DOI: 10.1186/s12870-022-03489-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/03/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Alkaline soils cause low productivity in crop plants including lentil. Alkalinity adaptation strategies in lentil were revealed when morpho-anatomical and physio-biochemical observations were correlated with transcriptomics analysis in tolerant (PDL-1) and sensitive (L-4076) cultivars at seedling stage. RESULTS PDL-1 had lesser salt injury and performed better as compared to L-4076. Latter showed severe wilting symptoms and higher accumulation of Na+ and lower K+ in roots and shoots. PDL-1 performed better under high alkalinity stress which can be attributed to its higher mitotic index, more accumulation of K+ in roots and shoots and less aberrantly dividing cells. Also, antioxidant enzyme activities, osmolytes' accumulation, relative water content, membrane stability index and abscisic acid were higher in this cultivar. Differentially expressed genes (DEGs) related to these parameters were upregulated in tolerant genotypes compared to the sensitive one. Significantly up-regulated DEGs were found to be involved in abscisic acid (ABA) signalling and secondary metabolites synthesis. ABA responsive genes viz. dehydrin 1, 9-cis-epoxycarotenoid dioxygenase, ABA-responsive protein 18 and BEL1-like homeodomain protein 1 had log2fold change above 4.0. A total of 12,836 simple sequence repeats and 4,438 single nucleotide polymorphisms were identified which can be utilized in molecular studies. CONCLUSIONS Phyto-hormones biosynthesis-predominantly through ABA signalling, and secondary metabolism are the most potent pathways for alkalinity stress tolerance in lentil. Cultivar PDL-1 exhibited high tolerance towards alkalinity stress and can be used in breeding programmes for improving lentil production under alkalinity stress conditions.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute of Plant Biotechnology, 110012, New Delhi, India
| | - Vijayata Singh
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Satish Kumar Sanwal
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Sourabh Karwa
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deepti Singh
- Depatment of Botany, Meerut College, 250001, Meerut, India
| | - Parbodh Chander Sharma
- Division of Crop Improvement, Central Soil Salinity Research Institute, 132001, Karnal, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, 208002, Kanpur, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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3
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Hooper CM, Castleden IR, Aryamanesh N, Black K, Grasso SV, Millar AH. CropPAL for discovering divergence in protein subcellular location in crops to support strategies for molecular crop breeding. Plant J 2020; 104:812-827. [PMID: 32780488 DOI: 10.1111/tpj.14961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Agriculture faces increasing demand for yield, higher plant-derived protein content and diversity while facing pressure to achieve sustainability. Although the genomes of many of the important crops have been sequenced, the subcellular locations of most of the encoded proteins remain unknown or are only predicted. Protein subcellular location is crucial in determining protein function and accumulation patterns in plants, and is critical for targeted improvements in yield and resilience. Integrating location data from over 800 studies for 12 major crop species into the cropPAL2020 data collection showed that while >80% of proteins in most species are not localised by experimental data, combining species data or integrating predictions can help bridge gaps at similar accuracy. The collation and integration of over 61 505 experimental localisations and more than 6 million predictions showed that the relative sizes of the protein catalogues located in different subcellular compartments are comparable between crops and Arabidopsis. A comprehensive cross-species comparison showed that between 50% and 80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the phylogenetic relationship of the species. Protein subcellular locations in major biosynthesis pathways are more often conserved than in metabolic pathways. Underlying this conservation is a clear potential for subcellular diversity in protein location between species by means of gene duplication and alternative splicing. Our cropPAL data set and search platform (https://crop-pal.org) provide a comprehensive subcellular proteomics resource to drive compartmentation-based approaches for improving yield, protein composition and resilience in future crop varieties.
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Affiliation(s)
- Cornelia M Hooper
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ian R Castleden
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Nader Aryamanesh
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
- Robinson Research Institute and Adelaide Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kylie Black
- University Library, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Sally V Grasso
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
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4
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Li Y, Li L, Wang Y, Wang YC, Wang NN, Lu R, Wu YW, Li XB. Pollen-Specific Protein PSP231 Activates Callose Synthesis to Govern Male Gametogenesis and Pollen Germination. Plant Physiol 2020; 184:1024-1041. [PMID: 32663166 PMCID: PMC7536655 DOI: 10.1104/pp.20.00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/25/2020] [Indexed: 05/05/2023]
Abstract
Spatiotemporally regulated callose deposition is an essential, genetically programmed phenomenon that promotes pollen development and functionality. Severe male infertility is associated with deficient callose biosynthesis, highlighting the significance of intact callose deposition in male gametogenesis. The molecular mechanism that regulates the crucial role of callose in production of functional male gametophytes remains completely unexplored. Here, we provide evidence that the gradual upregulation of a previously uncharacterized cotton (Gossypium hirsutum) pollen-specific SKS-like protein (PSP231), specifically at the post pollen-mitosis stage, activates callose biosynthesis to promote pollen maturation. Aberrant PSP231 expression levels caused by either silencing or overexpression resulted in late pollen developmental abnormalities and male infertility phenotypes in a dose-dependent manner, highlighting the importance of fine-tuned PSP231 expression. Mechanistic analyses revealed that PSP231 plays a central role in triggering and fine-tuning the callose synthesis and deposition required for pollen development. Specifically, PSP231 protein sequesters the cellular pool of RNA-binding protein GhRBPL1 to destabilize GhWRKY15 mRNAs, turning off GhWRKY15-mediated transcriptional repression of GhCalS4/GhCalS8 and thus activating callose biosynthesis in pollen. This study showed that PSP231 is a key molecular switch that activates the molecular circuit controlling callose deposition toward pollen maturation and functionality and thereby safeguards agricultural crops against male infertility.
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Affiliation(s)
- Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Li Li
- Department of Genetics and Genome Biology, The Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario M5G 0A4, Canada
| | - Yao Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Ya-Chao Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Na-Na Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Rui Lu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Yu-Wei Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
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5
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Wu H, Gontarek BC, Yi G, Beall BD, Neelakandan AK, Adhikari B, Chen R, McCarty DR, Severin AJ, Becraft PW. The thick aleurone1 Gene Encodes a NOT1 Subunit of the CCR4-NOT Complex and Regulates Cell Patterning in Endosperm. Plant Physiol 2020; 184:960-972. [PMID: 32737073 PMCID: PMC7536710 DOI: 10.1104/pp.20.00703] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/22/2020] [Indexed: 05/18/2023]
Abstract
Maize (Zea mays) thick aleurone1 (thk1-R) mutants form multiple aleurone layers in the endosperm and have arrested embryogenesis. Prior studies suggest that thk1 functions downstream of defective kernel1 (dek1) in a regulatory pathway that controls aleurone cell fate and other endosperm traits. The original thk1-R mutant contained an ∼2-Mb multigene deletion, which precluded identification of the causal gene. Here, ethyl methanesulfonate mutagenesis produced additional alleles, and RNA sequencing from developing endosperm was used to identify a candidate gene based on differential expression compared with the wild-type progenitor. Gene editing confirmed the gene identity by producing mutant alleles that failed to complement existing thk1 mutants and that produced multiple-aleurone homozygous phenotypes. Thk1 encodes a homolog of NEGATIVE ON TATA-LESS1, a protein that acts as a scaffold for the CARBON CATABOLITE REPRESSION4-NEGATIVE ON TATA-LESS complex. This complex is highly conserved and essential in all eukaryotes for regulating a wide array of gene expression and cellular activities. Maize also harbors a duplicate locus, thick aleurone-like1, which likely accounts for the ability of thk1 mutants to form viable cells. Transcriptomic analysis indicated that THK1 regulates activities involving cell division, signaling, differentiation, and metabolism. Identification of thk1 provides an important new component of the DEK1 regulatory system that patterns cell fate in endosperm.
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Affiliation(s)
- Hao Wu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Bryan C Gontarek
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa 50011
| | - Gibum Yi
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa 50011
| | - Brandon D Beall
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
- Agronomy Department, Iowa State University, Ames, Iowa 50011
| | | | - Bibechana Adhikari
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa 50011
| | - Rumei Chen
- Department of Crop Genomics and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Donald R McCarty
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611-0690
| | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | - Philip W Becraft
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa 50011
- Agronomy Department, Iowa State University, Ames, Iowa 50011
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6
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Li YF, Zeng XQ, Li Y, Wang L, Zhuang H, Wang Y, Tang J, Wang HL, Xiong M, Yang FY, Yuan XZ, He GH. MULTI-FLORET SPIKELET 2, a MYB Transcription Factor, Determines Spikelet Meristem Fate and Floral Organ Identity in Rice. Plant Physiol 2020; 184:988-1003. [PMID: 32723808 PMCID: PMC7536674 DOI: 10.1104/pp.20.00743] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/21/2020] [Indexed: 05/09/2023]
Abstract
An understanding of flower and panicle development is crucial for improving yield and quality in majority of grass crops. In this study, we used mapping-based cloning to identify MULTI-FLORET SPIKELET2 (MFS2), which encodes a MYB transcription factor and regulates flower and spikelet development in rice (Oryza sativa). In the mfs2 mutant, specification of palea identity was severely disturbed and showed degradation or transformation into a lemma-like organ, and the number of all floral organs was increased to varying degrees. Due to the increase in the number of floral organs and development of extra transformed palea/marginal region of the palea-like organs, some mfs2 spikelets had a tendency to produce two florets. These defects implied that the mfs2 mutation caused abnormal specification of palea identity and partial loss of spikelet determination. We confirm that MFS2 is a transcriptional repressor that shows strong repression activity by means of two typical ethylene-responsive element binding factor-associated amphiphilic motifs, one of which locates at the C terminus and is capable of interaction with three rice TOPLESS and TOPLESS-related proteins. The results indicate that MFS2 acts as a repressor that regulates floral organ identities and spikelet meristem determinacy in rice by forming a repression complex with rice TOPLESS and TOPLESS-related proteins.
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Affiliation(s)
- Yun-Feng Li
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xiao-Qin Zeng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yun Li
- Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Deyang, Sichuan 618000, China
| | - Ling Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Hui Zhuang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yan Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jun Tang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Hong-Lei Wang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Mao Xiong
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Fa-Yu Yang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Xiao-Zhen Yuan
- Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Deyang, Sichuan 618000, China
| | - Guang-Hua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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7
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Ostrowska-Mazurek A, Kasprzak P, Kubala S, Zaborowska M, Sobieszczuk-Nowicka E. Epigenetic Landmarks of Leaf Senescence and Crop Improvement. Int J Mol Sci 2020; 21:ijms21145125. [PMID: 32698545 PMCID: PMC7404090 DOI: 10.3390/ijms21145125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/04/2023] Open
Abstract
This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding.
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Affiliation(s)
- Agnieszka Ostrowska-Mazurek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Piotr Kasprzak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Magdalena Zaborowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
- Correspondence: ; Tel.: +48-61-829-5892
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8
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Abstract
Autophagy is a major degradation and recycling pathway in plants. It functions to maintain cellular homeostasis and is induced by environmental cues and developmental stimuli. Over the past decade, the study of autophagy has expanded from model plants to crop species. Many features of the core machinery and physiological functions of autophagy are conserved among diverse organisms. However, several novel functions and regulators of autophagy have been characterized in individual plant species. In light of its critical role in development and stress responses, a better understanding of autophagy in crop plants may eventually lead to beneficial agricultural applications. Here, we review recent progress on understanding autophagy in crops and discuss potential future research directions.
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Affiliation(s)
- Jie Tang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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9
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Abstract
Proteome profiling aims to unravel the mystery of biological complexity encoded by the genome. The successful proteome profiling largely depends upon analytical approaches because single-step proteome characterization of eukaryotic cells is difficult due to the large number of proteins expressed and their complex physiochemical properties. Organellar proteomics helps in identifying a refined set of proteins by pinpointing certain activities to specific organelles, thereby increasing our knowledge of cellular processes. The reliability of a plant organelle proteome is intimately dependent on the purity of the organelle preparation. Methodological improvements in sample handling, organelle fractionation, and protein extraction are therefore crucial to plant subcellular proteomics. The nuclear proteins are organized into complex regulatory networks and perform varied cellular functions. Therefore, characterization of the nuclear proteome is an important step toward accumulating knowledge about regulation of gene expression and function. In this chapter, we present methods for the isolation of nuclei, purification of nuclear proteins, and proteome profiling that have been adapted for proteomic characterization of economically important crop species, such as chickpea.
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Affiliation(s)
- Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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10
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Ronceret A, Vielle-Calzada JP. Meiosis, unreduced gametes, and parthenogenesis: implications for engineering clonal seed formation in crops. Plant Reprod 2015; 28:91-102. [PMID: 25796397 DOI: 10.1007/s00497-015-0262-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/09/2015] [Indexed: 05/18/2023]
Abstract
Meiosis and unreduced gametes. Sexual flowering plants produce meiotically derived cells that give rise to the male and female haploid gametophytic phase. In the ovule, usually a single precursor (the megaspore mother cell) undergoes meiosis to form four haploid megaspores; however, numerous mutants result in the formation of unreduced gametes, sometimes showing female specificity, a phenomenon reminiscent of the initiation of gametophytic apomixis. Here, we review the developmental events that occur during female meiosis and megasporogenesis at the light of current possibilities to engineer unreduced gamete formation. We also provide an overview of the current understanding of mechanisms leading to parthenogenesis and discuss some of the conceptual implications for attempting the induction of clonal seed production in cultivated plants.
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Affiliation(s)
- Arnaud Ronceret
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36821, Irapuato, Guanajuato, Mexico
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11
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Lin MT, Occhialini A, Andralojc PJ, Parry MAJ, Hanson MR. A faster Rubisco with potential to increase photosynthesis in crops. Nature 2014; 513:547-50. [PMID: 25231869 PMCID: PMC4176977 DOI: 10.1038/nature13776] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/14/2014] [Indexed: 01/20/2023]
Abstract
In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield. However, the complex nature of Rubisco's assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins.
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Affiliation(s)
- Myat T Lin
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA [2]
| | - Alessandro Occhialini
- 1] Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK [2]
| | - P John Andralojc
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Lu D, Cai X, Yan F, Sun X, Wang X, Lu W. Effects of high temperature after pollination on physicochemical properties of waxy maize flour during grain development. J Sci Food Agric 2014; 94:1416-1421. [PMID: 24122670 DOI: 10.1002/jsfa.6433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 09/05/2013] [Accepted: 10/04/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Waxy maize is grown in South China, where high temperatures frequently prevail. The effect of high-temperature stress on grain development of waxy maize is not known. RESULTS High temperature decreased the grain fresh weight and volume, and lowered the grain dry weight and water content after 22 days after pollination (DAP). Plants exposed to high temperature had low starch content, and high protein and soluble sugar contents at maturity. Starch iodine binding capacity and granule size were increased by heat stress at all grain-filling stages. The former parameter decreased, while the latter parameter increased gradually with grain development. High temperature increased the peak and breakdown viscosity before 30 DAP, but the value decreased at maturity. Pasting and gelatinization temperatures at different stages were increased by heat stress and gradually decreased with grain development under both high-temperature and control conditions. Gelatinization enthalpy increased initially but decreased after peaking at 22 DAP under both control and heat stress conditions. High temperature decreased gelatinization enthalpy after 10 DAP. Retrogradation percentage value increased with high temperature throughout grain development. CONCLUSION High temperature after pollination changes the dynamics of grain filling of waxy maize, which may underlie the observed changes in its pasting and thermal properties.
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Affiliation(s)
- Dalei Lu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, 225009, China
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13
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Abstract
Soil salinity is a major constraint to agriculture. To improve salinity tolerance of crops, various traits can be incorporated, including ion exclusion, osmotic tolerance and tissue tolerance. We review the roles of a range of genes involved in salt tolerance traits. Different tissues and cells are adapted for specific and often diverse function, so it is important to express the genes in specific cell-types and to pyramid a range of traits. Modern biotechnology (marker-assisted selection or genetic engineering) needs to be increasingly used to introduce the correct combination of genes into elite crop cultivars. Importantly, the effects of introduced genes need to be evaluated in the field to determine their effect on salinity tolerance and yield improvement.
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Affiliation(s)
- Stuart J Roy
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA 5064, Australia
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Laboratory (GPlantS Lab), Av. da República, 2780-157 Oeiras, Portugal; Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mark Tester
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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Abstract
Fungal and oomycete plant parasites are among the most devastating pathogens of food crops. These microbes secrete effector proteins inside plant cells to manipulate host processes and facilitate colonization. How these effectors reach the host cytoplasm remains an unclear and debated area of plant research. In this article, we examine recent conflicting findings that have generated discussion in the field. We also highlight promising approaches based on studies of both parasite and host during infection. Ultimately, this knowledge may inform future broad spectrum strategies for protecting crops from such pathogens.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- INRA, Interactions Arbres/Microorganismes, UMR 1136, Champenoux, France
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Acharya S, Ranjan R, Pattanaik S, Maiti IB, Dey N. Efficient chimeric plant promoters derived from plant infecting viral promoter sequences. Planta 2014; 239:381-96. [PMID: 24178585 DOI: 10.1007/s00425-013-1973-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/01/2013] [Indexed: 05/03/2023]
Abstract
In the present study, we developed a set of three chimeric/hybrid promoters namely FSgt-PFlt, PFlt-UAS-2X and MSgt-PFlt incorporating different important domains of Figwort Mosaic Virus sub-genomic transcript promoter (FSgt, -270 to -60), Mirabilis Mosaic Virus sub-genomic transcript promoter (MSgt, -306 to -125) and Peanut Chlorotic Streak Caulimovirus full-length transcript promoter (PFlt-, -353 to +24 and PFlt-UAS, -353 to -49). We demonstrated that these chimeric/hybrid promoters can drive the expression of reporter genes in different plant species including tobacco, Arabidopsis, petunia, tomato and spinach. FSgt-PFlt, PFlt-UAS-2X and MSgt-PFlt promoters showed 4.2, 1.5 and 1.2 times stronger GUS activities compared to the activity of the CaMV35S promoter, respectively, in tobacco protoplasts. Protoplast-derived recombinant promoter driven GFP showed enhanced accumulation compared to that obtained under the CaMV35S promoter. FSgt-PFlt, PFlt-UAS-2X and MSgt-PFlt promoters showed 3.0, 1.3 and 1.0 times stronger activities than the activity of the CaMV35S² (a modified version of the CaMV35S promoter with double enhancer domain) promoter, respectively, in tobacco (Nicotiana tabacum, var. Samsun NN). Alongside, we observed a fair correlation between recombinant promoter-driven GUS accumulation with the corresponding uidA-mRNA level in transgenic tobacco. Histochemical (X-gluc) staining of whole transgenic seedlings and fluorescence images of ImaGene Green™ treated floral parts expressing the GUS under the control of recombinant promoters also support above findings. Furthermore, we confirmed that these chimeric promoters are inducible in the presence of 150 μM salicylic acid (SA) and abscisic acid (ABA). Taken altogether, we propose that SA/ABA inducible chimeric/recombinant promoters could be used for strong expression of gene(s) of interest in crop plants.
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Affiliation(s)
- Sefali Acharya
- Division of Gene Function and Regulation, Department of Biotechnology, Institute of Life Sciences, Government of India, Nalco Square, Chandrasekharpur, Bhubaneswar, 751 023, Odisha, India
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16
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Eeckhaut T, Lakshmanan PS, Deryckere D, Van Bockstaele E, Van Huylenbroeck J. Progress in plant protoplast research. Planta 2013; 238:991-1003. [PMID: 23955146 DOI: 10.1007/s00425-013-1936-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/18/2013] [Indexed: 06/02/2023]
Abstract
In this review we focus on recent progress in protoplast regeneration, symmetric and asymmetric hybridization and novel technology developments. Regeneration of new species and improved culture techniques opened new horizons for practical breeding in a number of crops. The importance of protoplast sources and embedding systems is discussed. The study of reactive oxygen species effects and DNA (de)condensation, along with thorough phytohormone monitoring, are in our opinion the most promising research topics in the further strive for rationalization of protoplast regeneration. Following, fusion and fragmentation progress is summarized. Genomic, transcriptomic and proteomic studies have led to better insights in fundamental processes such as cell wall formation, cell development and chromosome rearrangements in fusion products, whether or not obtained after irradiation. Advanced molecular screening methods of both genome and cytoplasmome facilitate efficient screening of both symmetric and asymmetric fusion products. We expect that emerging technologies as GISH, high resolution melting and next generation sequencing will pay major contributions to our insights of genome creation and stabilization, mainly after asymmetric hybridization. Finally, we demonstrate agricultural valorization of somatic hybridization through enumerating recent introgression of diverse traits in a number of commercial crops.
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Affiliation(s)
- Tom Eeckhaut
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium.
| | - Prabhu Shankar Lakshmanan
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Dieter Deryckere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
| | - Erik Van Bockstaele
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Johan Van Huylenbroeck
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
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17
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Abstract
In this review we focus on recent progress in protoplast regeneration, symmetric and asymmetric hybridization and novel technology developments. Regeneration of new species and improved culture techniques opened new horizons for practical breeding in a number of crops. The importance of protoplast sources and embedding systems is discussed. The study of reactive oxygen species effects and DNA (de)condensation, along with thorough phytohormone monitoring, are in our opinion the most promising research topics in the further strive for rationalization of protoplast regeneration. Following, fusion and fragmentation progress is summarized. Genomic, transcriptomic and proteomic studies have led to better insights in fundamental processes such as cell wall formation, cell development and chromosome rearrangements in fusion products, whether or not obtained after irradiation. Advanced molecular screening methods of both genome and cytoplasmome facilitate efficient screening of both symmetric and asymmetric fusion products. We expect that emerging technologies as GISH, high resolution melting and next generation sequencing will pay major contributions to our insights of genome creation and stabilization, mainly after asymmetric hybridization. Finally, we demonstrate agricultural valorization of somatic hybridization through enumerating recent introgression of diverse traits in a number of commercial crops.
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Affiliation(s)
- Tom Eeckhaut
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium.
| | - Prabhu Shankar Lakshmanan
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Dieter Deryckere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
| | - Erik Van Bockstaele
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
- Department of Plant Production, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Johan Van Huylenbroeck
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 21, 9090, Melle, Belgium
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18
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Duhamel M, Vandenkoornhuyse P. Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication. Trends Plant Sci 2013; 18:597-600. [PMID: 24055138 DOI: 10.1016/j.tplants.2013.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/22/2013] [Accepted: 08/28/2013] [Indexed: 05/25/2023]
Abstract
Food demand will increase concomitantly with human population. Food production therefore needs to be high enough and, at the same time, minimize damage to the environment. This equation cannot be solved with current strategies. Based on recent findings, new trajectories for agriculture and plant breeding which take into account the belowground compartment and evolution of mutualistic strategy, are proposed in this opinion article. In this context, we argue that plant breeders have the opportunity to make use of native arbuscular mycorrhizal (AM) symbiosis in an innovative ecologically intensive agriculture.
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Affiliation(s)
- Marie Duhamel
- Université de Rennes I, CNRS UMR6553 EcoBio, Campus Beaulieu, F-35042 Rennes, France; Institute of Ecological Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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19
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Tanino K. From lab to nature: assessing injury in xylem parenchyma cells. Tree Physiol 2012; 32:815-818. [PMID: 22802428 DOI: 10.1093/treephys/tps061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Karen Tanino
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada S7N 5A8.
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20
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Abstract
Proteomics is a useful analytical approach for investigating crop responses to stress. Recent remarkable advances in proteomic techniques allow for the identification of a wider range of proteins than was previously possible. The application of proteomic techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops. Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate. Waterlogging resulting from flooding causes significant reductions in the growth and yield of several crops. Transient flooding displaces gases in soil pores and often causes hypoxia in plants grown on land with poor drainage. Changes in protein expression and post-translational modification of proteins occur as plants activate their defense system in response to flooding stress. In this review, we discuss the contributions that proteomic studies have made toward increasing our understanding of the well-organized cellular response to flooding in soybean and other crops. The biological relevance of the proteins identified using proteomic techniques in regard to crop stress tolerance will be discussed as well.
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Affiliation(s)
- Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki, 305-8518, Japan.
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21
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Adani F, Papa G, Schievano A, Cardinale G, D'Imporzano G, Tambone F. Nanoscale structure of the cell wall protecting cellulose from enzyme attack. Environ Sci Technol 2011; 45:1107-13. [PMID: 21174466 DOI: 10.1021/es1020263] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The cell wall structure protects cellulose from enzymatic attack and its successive fermentation. The nature of this protection consists in the very complex macroscopic and microscopic structure of cell wall that limits transport. Explaining this kind of protection is critical in future research to improve cell polymer availability for enzymatic attack. This research shows that the complete description of the cell wall topography at a nanoscale level allows a mechanistic understanding of cellulose protection. For this purpose, we used gas adsorption methods (CO(2) at 273 K and N(2) at 77 K) to detect mesoporosity (pore size of 1.5-30 nm diameter; MeS) and microporosity (pore size of 0.3-1.5 nm diameter; MiS) of the cell wall of five energy crops, i.e., giant cane, rivet wheat straw, miscanthus, proso millet, and sorghum. The presence of both hemicelluloses in the spaces between cellulose fibrils and the unhydrolyzable and highly cross-linked lignocarbohydrate complex (LCC) determines a microporous (80% pores having diameters below 0.8 nm) structure of the cell wall that prevents the cellulase enzymes from coming into direct contact with the cellulose, as their sizes exceed the cell wall pore size. On the other hand, the removal of the hemicelluloses and of the LCC complex determines a reduction of the MiS and an increase of the available surface for enzymatic attack, i.e., pores >5 nm diameter. This was confirmed by the good negative (r = -0.87, P < 0.001, n = 11) and positive (r = 0.78, P < 0.005, n = 11) correlations found for microporosity and mesoporosity (pores of diameters >5 nm), respectively, vs the glucose production, by cellulase enzyme attack in specific enzymatic hydrolysis tests performed on biomass samples.
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Affiliation(s)
- Fabrizio Adani
- Gruppo RICICLA, Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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23
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Faoro F, Iriti M. Plant cell death and cellular alterations induced by ozone: key studies in Mediterranean conditions. Environ Pollut 2009; 157:1470-1477. [PMID: 18973970 DOI: 10.1016/j.envpol.2008.09.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 09/12/2008] [Indexed: 05/27/2023]
Abstract
An account of histo-cytological and ultrastructural studies on ozone effect on crop and forest species in Italy is given, with emphasis on induced cell death and the underlying mechanisms. Cell death phenomena possibly due to ambient O(3) were recorded in crop and forest species. In contrast, visible O(3) effects on Mediterranean vegetation are often unclear. Microscopy is thus suggested as an effective tool to validate and evaluate O(3) injury to Mediterranean vegetation. A DAB-Evans blue staining was proposed to validate O(3) symptoms at the microscopic level and for a pre-visual diagnosis of O(3) injury. The method has been positively tested in some of the most important crop species, such as wheat, tomato, bean and onion and, with some restriction, in forest species, and it also allows one to gain some very useful insights into the mechanisms at the base of O(3) sensitivity or tolerance.
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Affiliation(s)
- Franco Faoro
- Istituto di Patologia Vegetale, Università di Milano and CNR, Istituto di Virologia Vegetale, U.O.T di Milano, Via Celoria 2, 20133 Milan, Italy.
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Xu Q, Wen X, Deng X. Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose". Genetics 2008; 178:2081-91. [PMID: 18245857 PMCID: PMC2323798 DOI: 10.1534/genetics.107.086421] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 01/22/2008] [Indexed: 11/18/2022] Open
Abstract
From chestnut rose, a promising fruit crop of the Rosa genus, powdery mildew disease-resistant and susceptible genotypes and their F(1) progeny were used to isolate nucleotide-binding-site (NBS)-encoding genes using 19 degenerate primer pairs and an additional cloning method called overlapping extension amplification. A total of 126 genes were harvested; of these, 38 were from a resistant parent, 37 from a susceptible parent, and 51 from F(1) progeny. A phylogenetic tree was constructed, which revealed that NBS sequences from parents and F(1) progeny tend to form a mixture and are well distributed among the branches of the tree. Mapping of these NBS genes suggested that their organization in the genome is a "tandem duplicated cluster" and, to a lesser extent, a "heterogeneous cluster." Intraspecific polymorphisms and interspecific divergence were detected by Southern blotting with NBS-encoding genes as probes. Sequencing on the nucleotide level revealed even more intraspecific variation: for the R4 gene, 9.81% of the nucleotides are polymorphic. Amino acid sites under positive selection were detected in the NBS region. Some NBS-encoding genes were meiotically unstable, which may due to recombination and deletion events. Moreover, a transposon-like element was isolated in the flanking region of NBS genes, implying a possible role for transposon in the evolutionary history of resistance genes.
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Affiliation(s)
- Qiang Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
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Butorina AK, Do NT. [The rhythms of daily mitotic activity in Vigna radiata (L.) R. Wilczek]. Tsitologiia 2008; 50:729-733. [PMID: 18822794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The daily mitotic activity (MA) in Vigna radiata (L.) R. Wilczek. has been studied using local cultivar for Vietnam No I 176. It has been shown that the curve of mitotic activity has five peaks. Maximum mitotic index (MI) was observed at 04:00 (5.93 %) and the other peaks were at 02:00 (5.58 %), 08:00 (4.70 %), 12:00 (4.60 %) and at 22:00 (4.60 %). If we took into account that duration of the mitotic cycle in Vigna radiata makes up ten hours, we can propose that there are two peaks of MA within each cycle. It may be due to the presence of two meristematic cell subpopulations which enter mitosis at different time and have nearly equal duration of the cell cycle.
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Abstract
Phosphorus (P) is an essential plant nutrient and one of the most limiting in natural habitats as well as in agricultural production world-wide. The control of P acquisition efficiency and its subsequent uptake and translocation in vascular plants is complex. The physiological role of key cellular structures in plant P uptake and underlying molecular mechanisms are discussed in this review, with emphasis on phosphate transport across the cellular membrane at the root and arbuscular-mycorrhizal (AM) interfaces. The tools of molecular genetics have facilitated novel approaches and provided one of the major driving forces in the investigation of the basic transport mechanisms underlying plant P nutrition. Genetic engineering holds the potential to modify the system in a targeted way at the root-soil or AM symbiotic interface. Such approaches should assist in the breeding of crop plants that exhibit improved P acquisition efficiency and thus require lower inputs of P fertilizer for optimal growth. Whether engineering of P transport systems can contribute to enhanced P uptake will be discussed.
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Affiliation(s)
- Marcel Bucher
- ETH Zurich, Institute of Plant Sciences, Experimental Station Eschikon 33, CH-8315 Lindau, Switzerland.
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27
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Abstract
Phosphorus (P) is an essential plant nutrient and one of the most limiting in natural habitats as well as in agricultural production world-wide. The control of P acquisition efficiency and its subsequent uptake and translocation in vascular plants is complex. The physiological role of key cellular structures in plant P uptake and underlying molecular mechanisms are discussed in this review, with emphasis on phosphate transport across the cellular membrane at the root and arbuscular-mycorrhizal (AM) interfaces. The tools of molecular genetics have facilitated novel approaches and provided one of the major driving forces in the investigation of the basic transport mechanisms underlying plant P nutrition. Genetic engineering holds the potential to modify the system in a targeted way at the root-soil or AM symbiotic interface. Such approaches should assist in the breeding of crop plants that exhibit improved P acquisition efficiency and thus require lower inputs of P fertilizer for optimal growth. Whether engineering of P transport systems can contribute to enhanced P uptake will be discussed.
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Affiliation(s)
- Marcel Bucher
- ETH Zurich, Institute of Plant Sciences, Experimental Station Eschikon 33, CH-8315 Lindau, Switzerland.
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Abstract
Eggplant is an economically important vegetable crop in Asia and Africa, and although it is grown in Europe and the United States, it does not account for a significant percentage of agricultural production. It is susceptible to a number of pathogens and insects, with bacterial and fungal wilts being the most devastating. Attempts to improve resistance through introgression of traits from wild relatives have had limited success owing to sexual incompatibilities. Therefore, a crop improvement approach that combines both conventional breeding and biotechnological techniques would be beneficial. This chapter describes an Agrobacterium-mediated transformation protocol for eggplant based on inoculation of seedling explants (cotyledons and hypocotyls) and leaves. We have used this protocol to recover transformants from two different types of eggplant, a Solanum melongena L. breeding line, and S. melongena L. var. Black Eggplant. The selectable marker gene used was neomycin phosphotransferase II (nptII) and the selection agent was kanamycin. In vitro grown transformants acclimated readily to greenhouse conditions.
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Affiliation(s)
- Joyce Van Eck
- The Boyce Thompson Institute for Plant Research, Inc., Ithaca, NY, USA
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Ruhland M, Engelhardt G, Wallnöfer PR. Transformation of the mycotoxin ochratoxin A in plants. 2. Time course and rates of degradation and metabolite production in cell-suspension cultures of different crop plants. Mycopathologia 1996; 134:97-102. [PMID: 9011828 DOI: 10.1007/bf00436871] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Ochratoxin A, one of the most toxic mycotoxins, can be metabolized nearly completely by suspension cultures of various plant cells. The transformation products identified in this study were almost the same in the cell-suspension cultures of maize, carrot, tomato, potato, soybean, wheat and barley, but the quantitative distribution differed strongly depending on incubation time and species of plant-cell culture. The compounds were extracted with ethyl acetate and detected by reversed-phase HPLC with gradient elution. From the result it is supposed that besides ochratoxin A also ochratoxin derivatives may occur in food and feedstuff of plant origin.
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Affiliation(s)
- M Ruhland
- Bayerische Landesantalt für Ernährung, Abteilung Ernährung, München, Germany
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