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Guo C, Yuan X, Yan F, Xiang K, Wu Y, Zhang Q, Wang Z, He L, Fan P, Yang Z, Chen Z, Sun Y, Ma J. Nitrogen Application Rate Affects the Accumulation of Carbohydrates in Functional Leaves and Grains to Improve Grain Filling and Reduce the Occurrence of Chalkiness. FRONTIERS IN PLANT SCIENCE 2022; 13:921130. [PMID: 35812970 PMCID: PMC9270005 DOI: 10.3389/fpls.2022.921130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Chalkiness, which is highly affected by nitrogen (N) management during grain filling, is critical in determining rice appearance quality and consumer acceptability. We investigated the effects of N application rates 75 (N1), 150 (N2), and 225 (N3) kg ha-1 on the source-sink carbohydrate accumulation and grain filling characteristics of two indica hybrid rice cultivars with different chalkiness levels in 2019 and 2020. We further explored the relationship between grain filling and formation of chalkiness in superior and inferior grains. In this study, carbohydrates in the functional leaves and grains of the two varieties, and grain filling parameters, could explain 66.2%, 68.0%, 88.7%, and 91.6% of the total variation of total chalky grain rate and whole chalkiness degree, respectively. They were primarily concentrated in the inferior grains. As the N fertilizer application rate increased, the chalky grain rate and chalkiness degree of both the superior and inferior grains decreased significantly. This interfered with the increase in total chalky grain rate and chalkiness. Moreover, the carbohydrate content in the functional leaves increased significantly in N2 and N3 compared with that in N1. The transfer of soluble sugar from the leaves to the grains decreased the soluble sugar and increased total starch contents, accelerated the development of grain length and width, increased grain water content, and effectively alleviated the contradiction between source and sink. These changes promoted the carbohydrate partition in superior and inferior grains, improved their average filling rate in the middle and later stages, optimized the uniformity of inferior grain fillings, and finally led to the overall reduction in rice chalkiness.
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Affiliation(s)
- Changchun Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Xiaojuan Yuan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Fengjun Yan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Kaihong Xiang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Yunxia Wu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Qiao Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhonglin Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Limei He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Ping Fan
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhiyuan Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Zongkui Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Yongjian Sun
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
| | - Jun Ma
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, China
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Wu X, Liu Y, Zhang Y, Gu R. Advances in Research on the Mechanism of Heterosis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:745726. [PMID: 34646291 PMCID: PMC8502865 DOI: 10.3389/fpls.2021.745726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Heterosis is a common biological phenomenon in nature. It substantially contributes to the biomass yield and grain yield of plants. Moreover, this phenomenon results in high economic returns in agricultural production. However, the utilization of heterosis far exceeds the level of theoretical research on this phenomenon. In this review, the recent progress in research on heterosis in plants was reviewed from the aspects of classical genetics, parental genetic distance, quantitative trait loci, transcriptomes, proteomes, epigenetics (DNA methylation, histone modification, and small RNA), and hormone regulation. A regulatory network of various heterosis-related genes under the action of different regulatory factors was summarized. This review lays a foundation for the in-depth study of the molecular and physiological aspects of this phenomenon to promote its effects on increasing the yield of agricultural production.
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Affiliation(s)
- Xilin Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yan Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yaowei Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Ran Gu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Xiao R, Yuan Y, Zhu F, He S, Ge Q, Wang X, Taha R, Chen K. Transcriptomics and proteomics-based analysis of heterosis on main economic traits of silkworm, Bombyx mori. J Proteomics 2020; 229:103941. [PMID: 32805450 DOI: 10.1016/j.jprot.2020.103941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/11/2020] [Accepted: 08/09/2020] [Indexed: 11/15/2022]
Abstract
The application of silkworm hybrids have promoted the innovation and development of agricultural technology, but the mechanism of heterosis in silkworm has not been explained clearly. In this study, the heterosis of silkworm in the aspects of body weight, silk gland and cocoon weight was investigated by means of silkworm hybridization and multi-omics approaches, including transcriptome and proteome. The results showed that heterosis of silkworm body weight, silk gland and cocoon weight was overdominant, but only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Combined analysis obtained six up-regulated genes and four down-regulated genes that were consistent both in transcriptome and proteome. Gene functional enrichment analysis indicated that most up-regulated genes and proteins were mostly related to metabolism, which led to accelerated metabolism and protein synthesis and contributing to improved heterosis. The up-regulation of 6-phosphate glucose dehydrogenase (G6PDH), phosphatidylethanolamine-binding protein (PEBP) and sHSP20.4, which are involved in metabolism, might be related to silk gland heterosis. SIGNIFICANCE: A combination of transcriptomic and proteomic analysis was used to understand the molecular mechanism of silkworm heterosis. We found that the phenotypic traits of silkworm are overdominant, while the analysis of transcriptome and proteome showed that only part of genes and proteins were overdominant, and most of genes and proteins were non-additive. Some of the genes had unique expression in F1, which was speculated that genes under heterozygous condition may result in rearrangement and cause metabolic changes in the hybrids. Those both up-regulated in transcriptomic and proteomic analysis were found to be involved in various metabolic processes, so as to accelerate metabolism and protein synthesis, thus exhibiting heterosis.
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Affiliation(s)
- Rui Xiao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yi Yuan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Feifei Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Suqun He
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Ge
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xueqi Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Rehab Taha
- Plant Protection Research Institute, Agricultural Research Center, Egypt
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China.
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Ning F, Wu X, Zhang H, Wu Z, Niu L, Yang H, Wang W. Accumulation Profiles of Embryonic Salt-Soluble Proteins in Maize Hybrids and Parental Lines Indicate Matroclinous Inheritance: A Proteomic Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:1824. [PMID: 29118775 PMCID: PMC5661082 DOI: 10.3389/fpls.2017.01824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/10/2017] [Indexed: 05/29/2023]
Abstract
Maize is one of the most widely cultivated crops. It accumulates a large quantity of seed storage proteins, which are important for seed development and germination, and contribute to the nutritional quality of seeds. Based on solubility, the storage proteins are divided into albumins (water-soluble), globulins (salt-soluble), prolamins (alcohol-soluble), and glutelins (acid- or alkali-soluble). Maize hybrids are cultivated due to the superior performance of F1 hybrids than that of their parents, a phenomenon known as heterosis. However, the accumulation patterns of seed storage proteins in maize embryos between the hybrids and their parental inbred lines have not been compared. In the present study, two elite inbred lines of China, Zheng 58 and Chang 7-2, and their reciprocal hybrids (Zheng 58 × Chang 7-2 and Chang 7-2 × Zheng 58) were used to explore parental influences on the accumulation patterns of seed storage proteins in maize embryos. For this purpose, we focused on seed salt-soluble proteins (SSPs) in our experiments. The SSPs were selectively extracted from maize mature embryos after extensive removal of water-soluble albumin and separated using two-dimensional gel electrophoresis (2-DE), followed by mass spectrometry analysis. Our results indicated that the 2-DE SSP profiles of hybrids closely resembled those of their maternal parent rather than the paternal parent. In other words, 2-DE SSP profiles of Zheng 58 × Chang 7-2 were more similar those of Zheng 58 whereas such profiles of Chang 7-2 × Zheng 58 were more similar to those of Chang 7-2 although the 2-DE profiles of all four maize types were quite similar. In total, 12 relatively abundant SSPs spots representing five kinds of proteins were identified, of which nine protein spots displayed non-additive accumulation in at least one hybrid. This study provided additional data on dominance and partial dominance effects on maize hybrids embryos. Besides, earlier studies on accumulation profiles of globulin-1 (also known as vicilin), which is one of the most abundant globulins in maize embryos, also support the above results. This study would be helpful in revealing the mechanisms underlying SSPs accumulation patterns in the hybrids.
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Dahal D, Newton KJ, Mooney BP. Quantitative Proteomics of Zea mays Hybrids Exhibiting Different Levels of Heterosis. J Proteome Res 2016; 15:2445-54. [DOI: 10.1021/acs.jproteome.5b01120] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diwakar Dahal
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kathleen J. Newton
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Brian P. Mooney
- Division of Biological Sciences, ‡Department of Biochemistry, and §The Charles W
Gehrke Proteomics Center, University of Missouri, Columbia, Missouri 65211, United States
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Proteomic patterns associated with heterosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:908-15. [PMID: 26721744 DOI: 10.1016/j.bbapap.2015.12.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/29/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Heterosis is characterized by higher seed yields, plant biomass or other traits in heterozygotes or hybrids compared with their genetically divergent parents, which are often homozygous. Despite extensive investigation of heterosis and its wide application in crops such as maize, rice, wheat and sorghum, its molecular basis is still enigmatic. In the past century, some pioneers have proposed multigene models referring to the complementation of allelic and gene expression variation, which is likely to be an important contributor to heterosis. In addition, there are potential interactions of epigenetic variation involved in heterosis via novel mechanisms. At the level of gene expression, many recent studies have revealed that the heterosis phenomenon can be deciphered not only at the transcriptional level but also at the proteomic level. This review presents an update on the information supporting the involvement of proteomic patterns in heterosis and a possible future direction of the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Di G, Luo X, Huang M, Chen J, Kong X, Miao X, Ke C. Proteomic profiling of eggs from a hybrid abalone and its parental lines: Haliotis discus hannai Ino and Haliotis gigantea. Anim Genet 2015; 46:646-54. [PMID: 26447358 DOI: 10.1111/age.12330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 11/29/2022]
Abstract
Proteomic analysis was performed on the eggs of hybrid abalone and their corresponding parental lines. A total of 915 ± 19 stained protein spots were detected from Haliotis discus hannai♀ × H. discus hannai♂ (DD), 935 ± 16 from H. gigantea♀ × H. gigantea♂ (GG) and 923 ± 13 from H. gigantea♀ × H. discus hannai♂ (GD). The spots from DD and GD were clustered together. The distance between DD and GG was maximal by hierarchical cluster analysis. A total of 112 protein gel spots were identified; of these, 59 were abalone proteins. The proteins were involved in major biological processes including energy metabolism, proliferation, apoptosis, signal transduction, immunity, lipid metabolism, electron carrier proteins, protein biosynthesis and decomposition, and cytoskeletal structure. Three of 20 differential expression protein spots involved in energy metabolism exhibited as upregulated in GD, 13 spots exhibited additivity, and four spots exhibited as downregulated in the offspring. Eleven protein spots were expressed at the highest level in DD. The proteins involved in stress responses included superoxide dismutase, peroxiredoxin 6, thioredoxin peroxidase and glutathione-S-transferase. Two of seven differential expression protein spots involved in response to stress exhibited as upregulated in GD, three exhibited additivity, and two exhibited as downregulated. These results might suggest that proteomic approaches are suitable for the analysis of hybrids and the functional prediction of abalone hybridization.
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Affiliation(s)
- Guilan Di
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.,State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jun Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xianghui Kong
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xiulian Miao
- College of Life Sciences, Liaocheng University, Liaocheng, 252059, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Du W, Gardea-Torresdey JL, Ji R, Yin Y, Zhu J, Peralta-Videa JR, Guo H. Physiological and Biochemical Changes Imposed by CeO2 Nanoparticles on Wheat: A Life Cycle Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11884-11893. [PMID: 26368651 DOI: 10.1021/acs.est.5b03055] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Interactions of nCeO2 with plants have been mostly evaluated at seedling stage and under controlled conditions. In this study, the effects of nCeO2 at 0 (control), 100 (low), and 400 (high) mg/kg were monitored for the entire life cycle (about 7 months) of wheat plants grown in a field lysimeter. Results showed that at high concentration nCeO2 decreased the chlorophyll content and increased catalase and superoxide dismutase activities, compared with control. Both concentrations changed root and leaf cell microstructures by agglomerating chromatin in nuclei, delaying flowering by 1 week, and reduced the size of starch grains in endosperm. Exposed to low concentration produced embryos with larger vacuoles, while exposure to high concentration reduced number of vacuoles, compared with control. There were no effects on the final biomass and yield, Ce concentration in shoots, as well as sugar and starch contents in grains, but grain protein increased by 24.8% and 32.6% at 100 and 400 mg/kg, respectively. Results suggest that more field life cycle studies are needed in order to better understand the effects of nCeO2 in crop plants.
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Affiliation(s)
- Wenchao Du
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University , Nanjing 210046, China
| | - Jorge L Gardea-Torresdey
- Department of Chemistry, The University of Texas at El Paso , El Paso, Texas 79968, United States
- Environmental Science and Engineering PhD Program, The University of Texas at El Paso , El Paso, Texas 79968, United States
- University of California Center for Environmental Implications of Nanotechnology (UC CEIN), The University of Texas at El Paso , El Paso, Texas 79968, United States
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University , Nanjing 210046, China
| | - Ying Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University , Nanjing 210046, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science , Nanjing 210008, China
| | - Jose R Peralta-Videa
- Department of Chemistry, The University of Texas at El Paso , El Paso, Texas 79968, United States
- Environmental Science and Engineering PhD Program, The University of Texas at El Paso , El Paso, Texas 79968, United States
- University of California Center for Environmental Implications of Nanotechnology (UC CEIN), The University of Texas at El Paso , El Paso, Texas 79968, United States
| | - Hongyan Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University , Nanjing 210046, China
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Hu J, Chen X, Zhang H, Ding Y. Genome-wide analysis of DNA methylation in photoperiod- and thermo-sensitive male sterile rice Peiai 64S. BMC Genomics 2015; 16:102. [PMID: 25887533 PMCID: PMC4367915 DOI: 10.1186/s12864-015-1317-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 02/03/2015] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetic modifications play important roles in the regulation of plant development. DNA methylation is an important epigenetic modification that dynamically regulates gene expression during developmental processes. However, little studies have been reported about the methylation profiles of photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice during the fertility transition. Results In this study, using methylated DNA immunoprecipitation sequencing (MeDIP-seq), the global DNA methylation patterns were compared in the rice PTGMS line PA64S under two different environments (different temperatures and day lengths). The profiling of the DNA methylation under two different phenotypes (sterility and fertility) revealed that hypermethylation was observed in PA64S (sterility), and 1258 differentially methylated regions (DMRs) were found between PA64S (sterility) and PA64S (fertility). Twenty differentially methylated genes of them were further validated through bisulfite sequencing, and four of these genes were analyzed by qRT-PCR. Especially, a differentially methylated gene (LOC_Os08g38210), which encoded transcription factor BIM2, is a component of brassinosteroid signaling in rice. The hypermethylated BIM2 gene may suppress some downstream genes in brassinosteroid signaling pathway, and thus affect the male fertility in PA64S. Conclusions The results presented here indicated that hypermethylation was observed in PA64S (sterility). Gene Ontology (GO) analysis and KEGG analysis revealed that flavone and flavonol biosynthrsis, circadian rhythm, photosynthesis and oxidative phosphorylation pathways were involved in sterility-fertility transition of PA64S. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1317-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jihong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Xiaojun Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Hongyuan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Yi Ding
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
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Jorrín-Novo JV, Pascual J, Sánchez-Lucas R, Romero-Rodríguez MC, Rodríguez-Ortega MJ, Lenz C, Valledor L. Fourteen years of plant proteomics reflected in Proteomics: moving from model species and 2DE-based approaches to orphan species and gel-free platforms. Proteomics 2015; 15:1089-112. [PMID: 25487722 DOI: 10.1002/pmic.201400349] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/23/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022]
Abstract
In this article, the topic of plant proteomics is reviewed based on related papers published in the journal Proteomics since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in Proteomics between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published . To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques and their integration with other approaches in the "systems biology" direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in Proteomics to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology.
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Affiliation(s)
- Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba-CeiA3, Cordoba, Spain
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Proteomic analysis of muscle between hybrid abalone and parental lines Haliotis gigantea Reeve and Haliotis discus hannai Ino. Heredity (Edinb) 2015; 114:564-74. [PMID: 25669609 DOI: 10.1038/hdy.2014.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 02/06/2023] Open
Abstract
To understand the potential molecular mechanism of heterosis, protein expression patterns were compared from hybrids of Haliotis gigantea (G) and Haliotis discus hannai (D) using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight analyses. Expression differences were observed in muscle samples from the four groups with 673±21.0 stained spots for H. discus hannai ♀ × H. discus hannai ♂ (DD), 692±25.6 for H. gigantea ♀ × H. gigantea ♂ (GG), 679±16.2 for H. discus hannai ♀ × H. gigantea ♂ (DG) (F1 hybrid) and 700±19 for H. gigantea ♀ × H. discus hannai ♂ (GD) (F1 hybrid). Different 2-DE image muscle protein spots had a mirrored relationship between purebreds and the F1 hybrid, suggesting that all stained spots in F1 hybrid muscle were on 2-DEs from parents. DD and DG clustered together first, and then clustered with GD, whereas the distance of DD and GG was maximal according to hierarchical cluster analysis. We identified 136 differentially expressed protein spots involved in major biological processes, including energy metabolism and stress response. Most energy metabolism proteins were additive, and stress-induced proteins displayed additivity or over-dominance. In these 136 identified protein spots, hybrid offspring with additivity or over-dominance accounted for 68.38%. Data show that a proteomic approach can provide functional prediction of abalone interspecific hybridization.
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Thakur A, Bhatla SC. Proteomic analysis of oil body membrane proteins accompanying the onset of desiccation phase during sunflower seed development. PLANT SIGNALING & BEHAVIOR 2015; 10:e1030100. [PMID: 26786011 PMCID: PMC4854339 DOI: 10.1080/15592324.2015.1030100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 05/20/2023]
Abstract
A noteworthy metabolic signature accompanying oil body (OB) biogenesis during oilseed development is associated with the modulation of the oil body membranes proteins. Present work focuses on 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-based analysis of the temporal changes in the OB membrane proteins analyzed by LC-MS/MS accompanying the onset of desiccation (20-30 d after anthesis; DAA) in the developing seeds of sunflower (Helianthus annuus L.). Protein spots unique to 20-30 DAA stages were picked up from 2-D gels for identification and the identified proteins were categorized into 7 functional classes. These include proteins involved in energy metabolism, reactive oxygen scavenging, proteolysis and protein turnover, signaling, oleosin and oil body biogenesis-associated proteins, desiccation and cytoskeleton. At 30 DAA stage, exclusive expressions of enzymes belonging to energy metabolism, desiccation and cytoskeleton were evident which indicated an increase in the metabolic and enzymatic activity in the cells at this stage of seed development (seed filling). Increased expression of cruciferina-like protein and dehydrin at 30 DAA stage marks the onset of desiccation. The data has been analyzed and discussed to highlight desiccation stage-associated metabolic events during oilseed development.
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Affiliation(s)
- Anita Thakur
- Laboratory of Plant Physiology and Biochemistry; Department of Botany; University of Delhi; Delhi, India
| | - Satish C Bhatla
- Laboratory of Plant Physiology and Biochemistry; Department of Botany; University of Delhi; Delhi, India
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Mohayeji M, Capriotti AL, Cavaliere C, Piovesana S, Samperi R, Stampachiacchiere S, Toorchi M, Lagana A. Heterosis profile of sunflower leaves: A label free proteomics approach. J Proteomics 2014; 99:101-10. [DOI: 10.1016/j.jprot.2014.01.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 12/24/2022]
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14
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Nakamura R, Nakamura R, Adachi R, Hachisuka A, Yamada A, Ozeki Y, Teshima R. Differential analysis of protein expression in RNA-binding-protein transgenic and parental rice seeds cultivated under salt stress. J Proteome Res 2014; 13:489-95. [PMID: 24410502 PMCID: PMC3993897 DOI: 10.1021/pr4006487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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Transgenic plants tolerant to various
environmental stresses are
being developed to ensure a consistent food supply. We used a transgenic
rice cultivar with high saline tolerance by introducing an RNA-binding
protein (RBP) from the ice plant (Mesembryanthemum crystallinum); differences in salt-soluble protein expression between nontransgenic
(NT) and RBP rice seeds were analyzed by 2D difference gel electrophoresis
(2D-DIGE), a gel-based proteomic method. To identify RBP-related changes
in protein expression under salt stress, NT and RBP rice were cultured
with or without 200 mM sodium chloride. Only two protein spots differed
between NT and RBP rice seeds cultured under normal conditions, one
of which was identified as a putative abscisic acid-induced protein.
In NT rice seeds, 91 spots significantly differed between normal and
salt-stress conditions. Two allergenic proteins of NT rice seeds,
RAG1 and RAG2, were induced by high salt. In contrast, RBP rice seeds
yielded seven spots and no allergen spots with significant differences
in protein expression between normal and salt-stress conditions. Therefore,
expression of fewer proteins was altered in RBP rice seeds by high
salt than those in NT rice seeds.
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Affiliation(s)
- Rika Nakamura
- Division of Novel Foods and Immunochemistry, National Institute of Health Sciences , 1-18-1 Kamiyoga, Tokyo 158-8501, Japan
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15
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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16
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DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions. Gene 2013; 537:143-8. [PMID: 24365594 DOI: 10.1016/j.gene.2013.12.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 01/03/2023]
Abstract
Epigenetic modification can occur at a high frequency in crop plants and might generate phenotypic variation without changes in DNA sequences. DNA methylation is an important epigenetic modification that may contribute to environmentally-induced phenotypic variations by regulating gene expression. Rice Photoperiod-Thermo-Sensitive Genic Male Sterile (PTGMS) lines can transform from sterility to fertility under lower temperatures and short-day (SD) conditions during anther development. So far, little is known about the DNA methylation variation of PTGMS throughout the genome in rice. In this study, we investigated DNA cytosine methylation alterations in the young panicles of PTGMS line PA64S under two different conditions using methylation sensitive amplified polymorphism (MSAP) method. Compared with the DNA methylation level of PA64S under lower temperatures and SD conditions (fertility), higher methylation was observed in PA64S (sterility). The sequences of 25 differentially amplified fragments were successfully obtained and annotated. Three methylated fragments, which are homologous to D2, NAD7 and psaA, were confirmed by bisulfite sequencing and their expression levels were also evaluated by qPCR. Real time quantitative PCR analysis revealed that five of the six selected methylated genes were downregulated in PA64S (sterility). These results suggested that DNA methylation may be involved in the sterility-fertility transition of PA64S under two different environmental conditions.
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17
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Marcon C, Lamkemeyer T, Malik WA, Ungrue D, Piepho HP, Hochholdinger F. Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS. J Proteomics 2013; 93:295-302. [DOI: 10.1016/j.jprot.2013.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/28/2013] [Accepted: 04/11/2013] [Indexed: 01/10/2023]
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18
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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19
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Chen ZJ. Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet 2013; 14:471-82. [PMID: 23752794 DOI: 10.1038/nrg3503] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Heterosis, also known as hybrid vigour, is widespread in plants and animals, but the molecular bases for this phenomenon remain elusive. Recent studies in hybrids and allopolyploids using transcriptomic, proteomic, metabolomic, epigenomic and systems biology approaches have provided new insights. Emerging genomic and epigenetic perspectives suggest that heterosis arises from allelic interactions between parental genomes, leading to altered programming of genes that promote the growth, stress tolerance and fitness of hybrids. For example, epigenetic modifications of key regulatory genes in hybrids and allopolyploids can alter complex regulatory networks of physiology and metabolism, thus modulating biomass and leading to heterosis. The conceptual advances could help to improve plant and animal productivity through the manipulation of heterosis.
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Affiliation(s)
- Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712, USA.
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20
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Comparative proteomic analysis of embryos between a maize hybrid and its parental lines during early stages of seed germination. PLoS One 2013; 8:e65867. [PMID: 23776561 PMCID: PMC3679168 DOI: 10.1371/journal.pone.0065867] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. It was observed that maize hybrid Zong3/87-1 exhibited an earlier onset or heterosis in radicle emergence. To get insights into the underlying mechanism of heterosis in radicle emergence, differential proteomic analysis between hybrid and its parental lines was performed. In total, the number of differentially expressed protein spots between hybrid and its parental lines in dry and 24 h imbibed seed embryos were 134 and 191, respectively, among which 47.01% (63/134) and 34.55% (66/191) protein spots displayed nonadditively expressed pattern. Remarkably, 54.55% of nonadditively accumulated proteins in 24 h imbibed seed embryos displayed above or equal to the level of the higher parent patterns. Moreover, 155 differentially expressed protein spots were identified, which were grouped into eight functional classes, including transcription & translation, energy & metabolism, signal transduction, disease & defense, storage protein, transposable element, cell growth & division and unclassified proteins. In addition, one of the upregulated proteins in F1 hybrids was ZmACT2, a homolog of Arabidopsis thaliana ACT7 (AtACT7). Expressing ZmACT2 driven by the AtACT7 promoter partially complemented the low germination phenotype in the Atact7 mutant. These results indicated that hybridization between two parental lines can cause changes in the expression of a variety of proteins, and it is concluded that the altered pattern of gene expression at translational level in the hybrid may be responsible for the observed heterosis.
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21
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He Y, Wang S, Ding Y. Identification of novel glutelin subunits and a comparison of glutelin composition between japonica and indica rice (Oryza sativa L.). J Cereal Sci 2013. [DOI: 10.1016/j.jcs.2012.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Deng ZY, Gong CY, Wang T. Use of proteomics to understand seed development in rice. Proteomics 2013; 13:1784-800. [DOI: 10.1002/pmic.201200389] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/24/2012] [Accepted: 01/07/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Zhu Yun Deng
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
| | - Chun Yan Gong
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology; Institute of Botany; Chinese Academy of Sciences; Haidianqu Beijing China
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23
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Di G, You W, Yu J, Wang D, Ke C. Genetic changes in muscle protein following hybridization between Haliotis diversicolor
reeve Japan and Taiwan populations revealed using a proteomic approach. Proteomics 2013; 13:845-59. [DOI: 10.1002/pmic.201200351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/28/2012] [Accepted: 11/14/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Guilan Di
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Jinjin Yu
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Dexiang Wang
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science; Xiamen University; Xiamen P. R. China
- College of Ocean and Earth Sciences; Xiamen University; Xiamen P. R. China
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24
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Schnable PS, Springer NM. Progress toward understanding heterosis in crop plants. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:71-88. [PMID: 23394499 DOI: 10.1146/annurev-arplant-042110-103827] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description of its molecular underpinnings has remained elusive despite extensive investigation. It appears that there is not a single, simple explanation for heterosis. Instead, it is likely that heterosis arises in crosses between genetically distinct individuals as a result of a diversity of mechanisms. Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids. Hence, multigene models are likely to prove most informative for understanding heterosis. Complementation of allelic variation, as well as complementation of variation in gene content and gene expression patterns, is likely to be an important contributor to heterosis. Epigenetic variation has the potential to interact in hybrid genotypes via novel mechanisms. Several other intriguing hypotheses are also under investigation. In crops, heterosis must be considered within the context of the genomic impacts of prior selection for agronomic traits.
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Affiliation(s)
- Patrick S Schnable
- Center for Plant Genomics and Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA.
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25
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Wang D, Xia Y, Li X, Hou L, Yu J. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. Nucleic Acids Res 2012. [PMID: 23193278 PMCID: PMC3531066 DOI: 10.1093/nar/gks1225] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases—sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions–deletions.
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Affiliation(s)
- Dapeng Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, PR China
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26
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Kaeppler S. Heterosis: Many Genes, Many Mechanisms—End the Search for an Undiscovered Unifying Theory. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/682824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Heterosis is the increase in vigor that is observed in progenies of matings of diverse individuals from different species, isolated populations, or selected strains within species or populations. Heterosis has been of immense economic value in agriculture and has important implications regarding the fitness and fecundity of individuals in natural populations. Genetic models based on complementation of deleterious alleles, especially in the context of linkage and epistasis, are consistent with many observed manifestations of heterosis. The search for the genes and alleles that underlie heterosis, as well as for broader allele-independent, genomewide mechanisms, has encompassed many species and systems. Common themes across these studies indicate that sequence diversity is necessary but not sufficient to produce heterotic phenotypes, and that the molecular pathways that produce heterosis involve chromatin modification, transcriptional control, translation and protein processing, and interactions between and within developmental and biochemical pathways. Taken together, there are many and diverse molecular mechanisms that translate DNA into phenotype, and it is the combination of all these mechanisms across many genes that produce heterosis in complex traits.
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Affiliation(s)
- Shawn Kaeppler
- Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
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27
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Dahal D, Mooney BP, Newton KJ. Specific changes in total and mitochondrial proteomes are associated with higher levels of heterosis in maize hybrids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:70-83. [PMID: 22607058 DOI: 10.1111/j.1365-313x.2012.05056.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The phenomenon of hybrid vigor (heterosis) has long been harnessed by plant breeders to improve world food production. However, the changes that are essential for heterotic responses and the mechanisms responsible for heterosis remain undefined. Large increases in biomass and yield in high-heterosis hybrids suggest that alterations in bioenergetic processes may contribute to heterosis. Progeny from crosses between various inbred lines vary in the extent of vigor observed. Field-grown maize F₁ hybrids that consistently exhibited either low or high heterosis across a variety of environments were examined for changes in proteins that may be correlated with increased plant vigor and yield. Unpollinated ears at the time of flowering (ear shoots) were selected for the studies because they are metabolically active, rich in mitochondria, and the sizes of the ears are diagnostic of yield heterosis. Total protein and mitochondrial proteomes were compared among low- and higher-heterosis hybrids. Two-dimensional difference gel electrophoresis was used to identify allelic and/or isoform differences linked to heterosis. Identification of differentially regulated spots by mass spectrometry revealed proteins involved in stress responses as well as primary carbon and protein metabolism. Many of these proteins were identified in multiple spots, but analysis of their abundances by label-free mass spectrometry suggested that most of the expression differences were due to isoform variation rather than overall protein amount. Thus, our proteomics studies suggest that expression of specific alleles and/or post-translational modification of specific proteins correlate with higher levels of heterosis.
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Affiliation(s)
- Diwakar Dahal
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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28
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Chen D, Xu D, Li M, He J, Gong Y, Wu D, Sun M, Yu Z. Proteomic analysis of Bacillus thuringiensis ΔphaC mutant BMB171/PHB(-1) reveals that the PHB synthetic pathway warrants normal carbon metabolism. J Proteomics 2012; 75:5176-88. [PMID: 22705120 DOI: 10.1016/j.jprot.2012.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/28/2012] [Accepted: 06/03/2012] [Indexed: 10/28/2022]
Abstract
A phaC knockout mutant from Bacillus thuringiensis (Bt) strain BMB171, named BMB171/PHB(-1), was constructed. A physiological and metabolic investigation and a proteomic analysis were conducted for both ΔphaC mutant and its parent strain. Grown in peptone medium with 5 gram glucose per liter as sole carbon source, BMB171/PHB(-1) produced various organic acids. Here the excreted pyruvate, citrate, lactate, acetate and glutamate were quantitatively analyzed. Deletion of phaC gene from the BMB171 strain resulted in 1) growth delay; 2) higher consumption of dioxigen but lower cell yield; 3) stagnation of pH movement; 4) overproduction of organic acids; 5) rapid descent of cell density in the stationary phase; and 6) a sporulation-deficient phenotype. Our proteomic study with qPCR reconfirmation reveals that the absence of PhaC led to a metabolic turmoil which showed repressed glycolysis, and over-expressed TCA cycle, various futile pathways and amino acid synthesis during vegetative growth. It is thus thought that B. thuringiensis BMB171 effectively regulated its carbon metabolism upon the presence of the functional PHB synthetic pathway. The presence of this pathway warrants a PHB-producing bacterium better surviving under different environmental conditions.
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Affiliation(s)
- Deju Chen
- State Key Laboratory of Agricultural Microbiology and National Engineering Research Center for Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
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29
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Zhang C, Yin Y, Zhang A, Lu Q, Wen X, Zhu Z, Zhang L, Lu C. Comparative proteomic study reveals dynamic proteome changes between superhybrid rice LYP9 and its parents at different developmental stages. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:387-98. [PMID: 22209166 DOI: 10.1016/j.jplph.2011.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 11/11/2011] [Accepted: 11/12/2011] [Indexed: 05/05/2023]
Abstract
Heterosis is a common phenomenon in which the hybrids exhibit superior agronomic performance than either inbred parental lines. Although hybrid rice is one of the most successful apotheoses in crops utilizing heterosis, the molecular mechanisms underlying rice heterosis remain elusive. To gain a better understanding of the molecular mechanisms of rice heterosis, comparative leaf proteomic analysis between a superhybrid rice LYP9 and its parental cultivars 9311 and PA64s at tillering, flowering and grain-filling stages were carried out. A total of 384 differentially expressed proteins (DP) were detected and 297 DP were identified, corresponding to 222 unique proteins. As DP were divided into those between the parents (DP(PP)) and between the hybrid and its parents (DP(HP)), the comparative results demonstrate that proteins in the categories of photosynthesis, glycolysis, and disease/defense were mainly enriched in DP. Moreover, the number of identified DP(HP) involved in photosynthesis, glycolysis, and disease/defense increased at flowering and grain-filling stages as compared to that at the tillering stage. Most of the up-regulated DP(HP) involved in the three categories showed greater expression in LYP9 at flowering and grain-filling stages than at the tillering stage. In addition, CO(2) assimilation rate and apparent quantum yield of photosynthesis also showed a greater increase in LYP9 at flowering and grain-filling stages than at the tillering stage. These results suggest that the proteins involved in photosynthesis, glycolysis, and disease/defense as well as their dynamic regulation at different developmental stages may be responsible for heterosis in rice.
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Affiliation(s)
- Chunyan Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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30
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Diz AP, Martínez-Fernández M, Rolán-Alvarez E. Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 2012; 21:1060-80. [PMID: 22268916 DOI: 10.1111/j.1365-294x.2011.05426.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
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Affiliation(s)
- Angel P Diz
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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31
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Farinha AP, Irar S, de Oliveira E, Oliveira MM, Pagès M. Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation. Proteomics 2011; 11:2389-405. [DOI: 10.1002/pmic.201000570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 02/08/2011] [Accepted: 03/03/2011] [Indexed: 01/01/2023]
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32
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Agrawal GK, Rakwal R. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011; 11:1630-49. [DOI: 10.1002/pmic.201000696] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/05/2011] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
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33
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Seed proteomics. J Proteomics 2011; 74:389-400. [DOI: 10.1016/j.jprot.2010.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/08/2010] [Accepted: 12/10/2010] [Indexed: 12/29/2022]
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34
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Teshima R, Nakamura R, Satoh R, Nakamura R. 2D-DIGE analysis of rice proteins from different cultivars. Regul Toxicol Pharmacol 2010; 58:S30-5. [DOI: 10.1016/j.yrtph.2010.05.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 05/20/2010] [Indexed: 11/17/2022]
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35
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Marcon C, Schützenmeister A, Schütz W, Madlung J, Piepho HP, Hochholdinger F. Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development. J Proteome Res 2010; 9:6511-22. [PMID: 20973536 DOI: 10.1021/pr100718d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.
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Affiliation(s)
- Caroline Marcon
- Department of General Genetics, University of Tuebingen, ZMBP, Center for Plant Molecular Biology, 72076 Tuebingen, Germany
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36
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Miernyk JA, Preťová A, Olmedilla A, Klubicová K, Obert B, Hajduch M. Using proteomics to study sexual reproduction in angiosperms. ACTA ACUST UNITED AC 2010; 24:9-22. [PMID: 20830489 DOI: 10.1007/s00497-010-0149-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 08/21/2010] [Indexed: 12/18/2022]
Abstract
While a relative latecomer to the postgenomics era of functional biology, the application of mass spectrometry-based proteomic analysis has increased exponentially over the past 10 years. Some of this increase is the result of transition of chemists, physicists, and mathematicians to the study of biology, and some is due to improved methods, increased instrument sensitivity, and better techniques of bioinformatics-based data analysis. Proteomic Biological processes are typically studied in isolation, and seldom are efforts made to coordinate results obtained using structural, biochemical, and molecular-genetic strategies. Mass spectrometry-based proteomic analysis can serve as a platform to bridge these disparate results and to additionally incorporate both temporal and anatomical considerations. Recently, proteomic analyses have transcended their initial purely descriptive applications and are being employed extensively in studies of posttranslational protein modifications, protein interactions, and control of metabolic networks. Herein, we provide a brief introduction to sample preparation, comparison of gel-based versus gel-free methods, and explanation of data analysis emphasizing plant reproductive applications. We critically review the results from the relatively small number of extant proteomics-based analyses of angiosperm reproduction, from flowers to seedlings, and speculate on the utility of this strategy for future developments and directions.
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Affiliation(s)
- Ján A Miernyk
- Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Nitra, Slovak Republic
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37
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Zhang X, Liu F, Wang W, Li S, Wang C, Zhang X, Wang Y, Wang K. Primary analysis of QTG contribution to heterosis in upland cotton. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4020-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Ferrari F, Fumagalli M, Profumo A, Viglio S, Sala A, Dolcini L, Temporini C, Nicolis S, Merli D, Corana F, Casado B, Iadarola P. Deciphering the proteomic profile of rice (Oryza sativa) bran: a pilot study. Electrophoresis 2010; 30:4083-94. [PMID: 19960476 DOI: 10.1002/elps.200900469] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The exact knowledge of the qualitative and quantitative protein components of rice bran is an essential aspect to be considered for a better understanding of the functional properties of this resource. Aim of the present investigation was to extract the largest number of rice bran proteins and to obtain their qualitative characterization. For this purpose, three different extraction protocols have been applied either on full-fat or on defatted rice bran. Likewise, to identify the highest number of proteins, MS data collected from 1-DE, 2-DE and gel-free procedures have been combined. These approaches allowed to unambiguously identify 43 proteins that were classified as signalling/regulation proteins (30%), proteins with enzymatic activity (30%), storage proteins (30%), transfer (5%) and structural (5%) proteins. The fact that all extraction and identification procedures have been performed in triplicate with an excellent reproducibility provides a rationale for considering the platform of proteins shown in this study as the potential proteome profile of rice bran. It also represents a source of information to evaluate better the qualities of rice bran as food resource.
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Affiliation(s)
- Fabio Ferrari
- Department of Biochemistry, University of Pavia, 27100 Pavia, Italy
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39
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Heterosis in plants: Manifestation in early seed development and prediction approaches to assist hybrid breeding. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11434-009-0326-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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40
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Kim ST, Wang Y, Kang SY, Kim SG, Rakwal R, Kim YC, Kang KY. Developing Rice Embryo Proteomics Reveals Essential Role for Embryonic Proteins in Regulation of Seed Germination. J Proteome Res 2009; 8:3598-605. [DOI: 10.1021/pr900358s] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Yiming Wang
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Sun Young Kang
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Sang Gon Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Randeep Rakwal
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Yong Chul Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
| | - Kyu Young Kang
- Department of Plant Bioscience, Pusan National University, Miryang, 627-706, South Korea, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, 660-701, South Korea, Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, 660-701, South Korea, Health Technology Research Center, National Institute of Advanced Industrial Science and Technology West, Tsukuba 305-8569, Ibaraki, Japan, Research Laboratory for Biotechnology and
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Abstract
By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice LYP9 and its parental cultivars 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG(PP)) and between the hybrid and its parents (DG(HP)), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG(HP) rather than in DG(PP). In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.
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