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Yin Z, Hao S, Zhao Y, Li J, Cui Y, Ge Y, Pang Q. Skin proteomic screening and functional analysis of differential proteins associated with coat color in sheep (Ovis aries). Anim Biosci 2024; 37:1503-1516. [PMID: 38754850 PMCID: PMC11366522 DOI: 10.5713/ab.24.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE Coat color is an important characteristic and economic trait in domestic sheep. In this study, we explored the potential mechanisms and the signaling pathways involved in coat color regulation for sheep. METHODS Isobaric tags for relative and absolute quantification (iTRAQ) technology was used to catalog global protein expression profiles in skin of sheep with black versus white coat color. Immunofluorescence was used to observe the expression localization of differential protein. Western blot and quantitative real time polymerase chain reaction (qRT-PCR) were used to evaluate their role in the coat color formation of sheep. RESULTS A total of 136 differential proteins were obtained in different coat colors, including 101 up-regulated and 35 down-regulated. Pigmentation function entries were enriched through gene ontology annotation. Tyrosine metabolism and platelet activation signaling pathway were extracted by Kyoto encyclopedia of genes and genomes analysis. Apolipoprotein A-1 (APOA1) and fibrinogen alpha chain (FGA) were found to be critical differential proteins by the interaction of differential proteins in the direct-interaction network diagram. Strikingly, twenty candidate differential proteins were screened, from which beta-actin (ACTB) protein showed higher expression in white sheep skin, while albumin (ALB), APOA1, MAOA (amine oxidase) and FGA proteins showed higher expression in black sheep skin, which was validated by immunofluorescence, western blot, and qRT-PCR. CONCLUSION This study identified several novel proteins that may be involved in the coat color formation of sheep. The white and black sheep skin proteome profiles obtained provide a valuable resource for future research to understand the network of protein expression controlling skin physiology and melanogenesis in sheep.
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Affiliation(s)
- Zhihong Yin
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003,
China
| | - Shitong Hao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003,
China
| | - Yuanyuan Zhao
- Guizhou Provincial Key Laboratory for Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Guizhou 554300,
China
| | - Jinglong Li
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003,
China
| | - Yunli Cui
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801,
China
| | - Yaming Ge
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003,
China
| | - Quanhai Pang
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801,
China
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Rashid MRA, Hossain MS, Fahim MD, Islam MS, Tahzib-E-Alindo, Prito RH, Sheikh MSA, Ali MS, Hasan M, Islam M. Comprehensive dataset of annotated rice panicle image from Bangladesh. Data Brief 2023; 51:109772. [PMID: 38020434 PMCID: PMC10661701 DOI: 10.1016/j.dib.2023.109772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Bangladesh's economy is primarily driven by the agriculture sector. Rice is one of the staple food of Bangladesh. The count of panicles per unit area serves as a widely used indicator for estimating rice yield, facilitating breeding efforts, and conducting phenotypic analysis. By calculating the number of panicles within a given area, researchers and farmers can assess crop density, plant health, and prospective production. The conventional method of estimating rice yields in Bangladesh is time-consuming, inaccurate, and inefficient. To address the challenge of detecting rice panicles, this article provides a comprehensive dataset of annotated rice panicle images from Bangladesh. Data collection was done by a drone equipped with a 4 K resolution camera, and it took place on April 25, 2023, in Bonkhoria Gazipur, Bangladesh. During the day, the drone captured the rice field from various heights and perspectives. After employing various image processing techniques for curation and annotation, the dataset was generated using images extracted from drone video clips, which were then annotated with information regarding rice panicles. The dataset is the largest publicly accessible collection of rice panicle images from Bangladesh, consisting of 2193 original images and 5701 augmented images.
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Affiliation(s)
| | - Md. Shafayat Hossain
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - MD Fahim
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - Md. Shajibul Islam
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - Tahzib-E-Alindo
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - Rizvee Hassan Prito
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | | | - Md Sawkat Ali
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - Mahamudul Hasan
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
| | - Maheen Islam
- Department of Computer Science and Engineering, East West University, Dhaka, Bangladesh
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Ahn E, Prom LK, Magill C. Multi-Trait Genome-Wide Association Studies of Sorghum bicolor Regarding Resistance to Anthracnose, Downy Mildew, Grain Mold and Head Smut. Pathogens 2023; 12:779. [PMID: 37375469 DOI: 10.3390/pathogens12060779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Multivariate linear mixed models (mvLMMs) are widely applied for genome-wide association studies (GWAS) to detect genetic variants affecting multiple traits with correlations and/or different plant growth stages. Subsets of multiple sorghum populations, including the Sorghum Association Panel (SAP), the Sorghum Mini Core Collection and the Senegalese sorghum population, have been screened against various sorghum diseases such as anthracnose, downy mildew, grain mold and head smut. Still, these studies were generally performed in a univariate framework. In this study, we performed GWAS based on the principal components of defense-related multi-traits against the fungal diseases, identifying new potential SNPs (S04_51771351, S02_66200847, S09_47938177, S08_7370058, S03_72625166, S07_17951013, S04_66666642 and S08_51886715) associated with sorghum's defense against these diseases.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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4
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Li F, Liu Y, Zhang X, Liu L, Yan Y, Ji X, Kong F, Zhao Y, Li J, Peng T, Sun H, Du Y, Zhao Q. Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2022; 15:52. [PMID: 36302917 PMCID: PMC9613846 DOI: 10.1186/s12284-022-00600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. RESULTS In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. CONCLUSIONS Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.
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Affiliation(s)
- Fei Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ye Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xiaohua Zhang
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Lingzhi Liu
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yun Yan
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Xin Ji
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Fanshu Kong
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yafan Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Junzhou Li
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Ting Peng
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Hongzheng Sun
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China
| | - Yanxiu Du
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
| | - Quanzhi Zhao
- Henan Key Laboratory of Rice Biology, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, No. 15, Longzihu University Park, Zhengdong New Area, Zhengzhou, China.
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Wu Y, Fang W, Peng W, Jiang M, Chen G, Xiong F. Sucrose transporter in rice. PLANT SIGNALING & BEHAVIOR 2021; 16:1952373. [PMID: 34269147 PMCID: PMC8525984 DOI: 10.1080/15592324.2021.1952373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
Plant photosynthesis processes play vital roles in crop plant development. Understanding carbohydrate partitioning via sugar transport is one of the potential ways to modify crop biomass, which is tightly linked to plant architecture, such as plant height and panicle size. Based on the literature, we highlight recent findings to summarize phloem loading by sucrose transport in rice. In rice, sucrose transporters, OsSUTs (sucrose transporters) and OsSWEETs (sugars are eventually exported transporters) import sucrose and export cells between phloem parenchyma cells and companion cells. Before sucrose transporters perform their functions, several transcription factors can induce sucrose transporter gene transcription levels, such as Oryza sativa DNA binding with one finger 11 (OsDOF11) and Oryza sativa Nuclear Factor Y B1 (OsNF-YB1). In addition to native regulator genes, environmental factors, such as CO2 concentration, drought stress and increased temperature, also affect sucrose transporter gene transcription levels. However, more research work is needed on formation regulation webs. Elucidation of the phloem loading mechanism could improve our understanding of rice development under multiple conditions and facilitate its manipulation to increase crop productivity.
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Affiliation(s)
- Yunfei Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
| | - wenchun Fang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
| | - Wangmenghan Peng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
| | - Min Jiang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
| | - Gang Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
| | - Fei Xiong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laboratory of Agriculture &agri-product Safety, Yangzhou University, Yangzhou, China
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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7
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Liang Y, Tabien RE, Tarpley L, Mohammed AR, Septiningsih EM. Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage. AOB PLANTS 2021; 13:plab043. [PMID: 34354811 PMCID: PMC8331054 DOI: 10.1093/aobpla/plab043] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.
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Affiliation(s)
- Yuya Liang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | - Lee Tarpley
- Texas A&M Agrilife Research Center, Beaumont, TX 77713, USA
| | | | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
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8
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Gao B, Hu S, Jing L, Niu X, Wang Y, Zhu J, Wang Y, Yang L. Alterations in Source-Sink Relations Affect Rice Yield Response to Elevated CO 2: A Free-Air CO 2 Enrichment Study. FRONTIERS IN PLANT SCIENCE 2021; 12:700159. [PMID: 34276751 PMCID: PMC8283783 DOI: 10.3389/fpls.2021.700159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 05/29/2023]
Abstract
To understand the effects of source-sink relationships on rice yield response to elevated CO2 levels (eCO2), we conducted a field study using a popular japonica cultivar grown in a free-air CO2 enrichment environment in 2017-2018. The source-sink ratio of rice was set artificially via source-sink treatments (SSTs) at the heading stage. Five SSTs were performed in 2017 (EXP1): cutting off the flag leaf (LC1) and the top three functional leaves (LC3), removing one branch in every three branches of a panicle (SR1/3) and one branch in every two branches of a panicle (SR1/2), and the control (CK) without any leaf cutting or spikelet removal. The eCO2 significantly increased grain yield by 15.7% on average over all treatments; it significantly increased grain yield of CK, LC1, LC3, SR1/3, and SR1/2 crops by 13.9, 18.1, 25.3, 12.0, and 10.9%, respectively. The yield response to eCO2 was associated with a significant increase of panicle number and fully-filled grain percentage (FGP), and the response of crops under different SSTs was significantly positively correlated with FGP and the average grain weight of the seeds. Two SSTs (CK and LC3) were performed in 2018 (EXP2), which confirmed that the yield response of LC3 crops (25.1%) to eCO2 was significantly higher than that of CK (15.9%). Among the different grain positions, yield response to eCO2 of grains attached to the lower secondary rachis was greater than that of grains attached to the upper primary rachis. Reducing the source-sink ratio via leaf-cutting enhanced the net photosynthetic rate response of the remaining leaves to eCO2 and increased the grain filling ability. Conversely, spikelet removal increased the non-structural carbohydrate (NSC) content of the stem, causing feedback inhibition and photosynthetic down-regulation. This study suggests that reducing the source-sink ratio by adopting appropriate management measures can increase the response of rice to eCO2.
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Affiliation(s)
- Bo Gao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, China
| | - Shaowu Hu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Liquan Jing
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xichao Niu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yunxia Wang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yulong Wang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Lianxin Yang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, China
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Zhao H, Li Z, Amjad H, Zhong G, Khan MU, Zhang Z, Lin W. Proteomic analysis reveals a role of ADP-glucose pyrophosphorylase in the asynchronous filling of rice superior and inferior spikelets. Protein Expr Purif 2021; 183:105875. [PMID: 33741528 DOI: 10.1016/j.pep.2021.105875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 03/08/2021] [Indexed: 12/28/2022]
Abstract
The poor grain filling of inferior spikelets (IS) situated on the lower secondary rachis branch leads to a remarkable decrease in rice yield and quality. The AGPase small subunit 2 (AGPS2) encodes a small subunit of adenosine diphosphate-glucose pyrophosphorylase (AGPase) enzyme, which plays an important role in sucrose-starch conversion and starch biosynthesis in the grain filling of rice. In the present study, qPCR analysis showed low expression abundance of AGPS2 in IS, compared to the superior spikelets (SS), which was consistent with the lower grain weight of IS. To evaluate the molecular mechanism of AGPS2, we first identified the AGPS2 interaction network through Co-immunoprecipitation (Co-IP). In total, 29 proteins of AGPS2 interaction network were characterized by LC-MS/MS. Bioinformatics analysis revealed that, the characterized proteins in the interaction network are likely to be related to starch synthesis, sugar conversion, energy pathway, and folding/modification, and most of them were involved in the grain filling of rice. The sequent Co-IP analysis showed that AGPS2 can bind to starch branching enzyme (SBE), pullulanase (PUL) and starch debranching enzyme (DBE) and assemble into starch synthesizing protein complex (SSPC). In addition, the 14-3-3 protein GF14e was also found to interact with AGPS2. Further analysis by qPCR showed that the expression of GF14e was much higher on IS than on SS. The qPCR results also showed that the expression of GF14e was relatively stable in SS, but changed significantly in IS under alternate wetting and moderate soil drying (WMD), which is consistent with the AGPS2 expression pattern. Our present work provides direct molecular evidence for the different expression patterns of AGPS2 in SS and IS, which could be greatly helpful for the molecular amelioration of the poor grain filling of IS in rice.
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Affiliation(s)
- Hong Zhao
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhou Li
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Subtropical Agriculture Research Institute, Fujian Academy of Agricultural Sciences, Zhangzhou, Fujian, China
| | - Hira Amjad
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guopei Zhong
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Muhammad Umar Khan
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhixing Zhang
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China; Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Zhang H, Chen J, Shan S, Cao F, Chen G, Zou Y, Huang M, Abou-Elwafa SF. Proteomic profiling reveals differentially expressed proteins associated with amylose accumulation during rice grain filling. BMC Genomics 2020; 21:714. [PMID: 33059592 PMCID: PMC7561244 DOI: 10.1186/s12864-020-07105-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amylose accumulation in rice grains is controlled by genetic and environmental factors. Amylose content is a determinant factor of rice quality in terms of cooking and eating. Great variations in amylose content in indica rice cultivars have been observed. The current study was to identify differentially expressed proteins in starch and sucrose metabolism and glycolysis/gluconeogenesis pathways and their relationships to amylose synthesis using two rice cultivars possess contrasting phenotypes in grain amylose content. RESULTS Synthesis and accumulation of amylose in rice grains significantly affected the variations between rice cultivars in amylose contents. The high amylose content cultivar has three down-regulated differentially expressed proteins, i.e., LOC_Os01g62420.1, LOC_Os02g36600.1, and LOC_Os08g37380.2 in the glycolysis/gluconeogenesis pathway, which limit the glycolytic process and decrease the glucose-1-phosphate consumption. In the starch and sucrose metabolic pathway, an up-regulated protein, i.e., LOC_Os06g04200.1 and two down-regulated proteins, i.e., LOC_Os05g32710.1 and LOC_Os04g43360.1 were identified (Figure 4). Glucose-1-phosphate is one of the first substrates in starch synthesis and glycolysis that are catalyzed to form adenosine diphosphate glucose (ADPG), then the ADPG is catalyzed by granule-bound starch synthase I (GBSS I) to elongate amylose. CONCLUSIONS The results indicate that decreasing the consumption of glucose-1-phosphate in the glycolytic process is essential for the formation of ADPG and UDPG, which are substrates for amylose synthesis. In theory, amylose content in rice can be regulated by controlling the fate of glucose-1-phosphate.
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Affiliation(s)
- Hengdong Zhang
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.,Qianxinan Institute of Karst Regional Development Xingyi, Xingyi, 652400, Guizhou, China
| | - Jiana Chen
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Shuanglü Shan
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Fangbo Cao
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Guanghui Chen
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yingbin Zou
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Min Huang
- Crop and Environment Research Center, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| | - Salah F Abou-Elwafa
- Agronomy Department, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
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11
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Metabolomic analysis reveals metabolites and pathways involved in grain quality traits of high-quality rice cultivars under a dry cultivation system. Food Chem 2020; 326:126845. [DOI: 10.1016/j.foodchem.2020.126845] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/28/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023]
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12
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Kimbembe RER, Li G, Fu G, Feng B, Fu W, Tao L, Chen T. Proteomic analysis of salicylic acid regulation of grain filling of two near-isogenic rice (Oryza sativa L.) varieties under soil drying condition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:659-672. [PMID: 32348929 DOI: 10.1016/j.plaphy.2020.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 05/28/2023]
Abstract
Grain filling is the final determinant of yield, and this process is susceptible to abiotic stresses. Salicylic acid (SA) regulates grain filling in rice plants. A comparative proteomic study was conducted to understand how SA mediates grain filling under soil drying (SD) condition. Zhefu802 and its near-isogenic line (NIL) were planted in pots in an artificial chamber. SA (100 mg L-1) was applied, followed by SD treatment (with a water potential of -30 to -35 kPa) at anthesis. The results showed that the grain yield and grain weight significantly decreased under SD in Zhefu802, but not in its NIL variety. SD also decreased expression of photosynthesis-related proteins in grains of Zhefu802, which resulted in its poorer drought resistance. Furthermore, the decreased grain filling rate rather than the grain size explained the observed decreased grain weight and grain yield under SD. Interestingly, these reductions were reversed by SA. Expression of proteins involved in glycolysis/TCA circle, starch and sucrose metabolism, antioxidation and detoxication, oxidative phosphorylation, transcription, translation, and signal transduction, were significantly down-regulated under SD and were significantly up-regulated in response to SA. The expression of these proteins was examined at transcriptional level and similar results were obtained. Inhibited expression of these proteins and related pathways contributed to the observed decrease in the grain filling rate of Zhefu802, and application of SA up-regulated expression of these proteins to improve grain weight. The findings of this study provide new insights into grain filling regulation by SA, and offer the scientific foundation for cultivation practice.
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Affiliation(s)
- Romesh Eric Romy Kimbembe
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guangyan Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guanfu Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Weimeng Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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13
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Wang G, Li H, Gong Y, Yang J, Yi Y, Zhang J, Ye N. Expression profile of the carbon reserve remobilization from the source to sink in rice in response to soil drying during grain filling. Food Energy Secur 2020. [DOI: 10.1002/fes3.204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Guanqun Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China College of Agriculture Hunan Agricultural University Changsha China
- Department of Biology Hong Kong Baptist University Kowloon Hong Kong
| | - Haoxuan Li
- Department of Biology Hong Kong Baptist University Kowloon Hong Kong
| | - Yulong Gong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology The Chinese University of Hong Kong Shatin Hong Kong
| | - Jianchang Yang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province Yangzhou University Yangzhou China
| | - Yake Yi
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China College of Agriculture Hunan Agricultural University Changsha China
| | - Jianhua Zhang
- Department of Biology Hong Kong Baptist University Kowloon Hong Kong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology The Chinese University of Hong Kong Shatin Hong Kong
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China College of Agriculture Hunan Agricultural University Changsha China
- Department of Biology Hong Kong Baptist University Kowloon Hong Kong
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14
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Zhang Y, Liu G, Cheng Y, Xu J, Wang C, Yang J. The effects of dry cultivation on grain‐filling and chalky grains of upland rice and paddy rice. Food Energy Secur 2020. [DOI: 10.1002/fes3.198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yajie Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
| | - Gaosheng Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
| | - Yadan Cheng
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
| | - Jingnan Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
| | - Chen Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University YangzhouChina
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15
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Chen E, Zhang X, Yang Z, Zhang C, Wang X, Ge X, Li F. BR deficiency causes increased sensitivity to drought and yield penalty in cotton. BMC PLANT BIOLOGY 2019; 19:220. [PMID: 31138186 PMCID: PMC6537406 DOI: 10.1186/s12870-019-1832-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/15/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Brassinosteroids (BRs) play crucial roles in drought tolerance, but the underlying molecular mechanisms remain unclear in the important oilseed and fiber crop, cotton (Gossypium hirsutum L.). RESULTS To elucidate how BRs mediate drought tolerance in cotton, a cotton brassinosteroid (BR)-deficient mutant, pag1 (pagoda1), was employed for analysis. Importantly, the pag1 mutant showed increased sensitivity to drought stress, with shorter primary roots and fewer lateral roots. The number of stomata was significantly increased in the mutant, and the stomata aperture was much wider than that of the control plants. These mutant plants therefore showed an increased water loss rate. Furthermore, the abscisic acid (ABA) content, photosynthetic efficiency and starch content of the mutant were significantly lower than those of the wild type. The overall performance of the mutant plants was worse than that of the wild-type control under both normal and drought conditions. Moreover, Proteomic analysis revealed reduced levels of stress-related proteins in pag1 plants. CONCLUSIONS These results suggest that BRs may modulate the drought tolerance of cotton by regulating much genes that related to drought stress and multiple organ responses to drought, including root growth, stomata development, the stomata aperture and photosynthesis. This study provides an important basis for understanding drought resistance regulated by BRs and cultivating drought-resistant cotton lines.
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Affiliation(s)
- Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Zuoren Yang
- Zhengzhou Research base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Chaojun Zhang
- Zhengzhou Research base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoqian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
| | - Fuguang Li
- Zhengzhou Research base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 China
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16
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Wang GQ, Li HX, Feng L, Chen MX, Meng S, Ye NH, Zhang J. Transcriptomic analysis of grain filling in rice inferior grains under moderate soil drying. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1597-1611. [PMID: 30690492 PMCID: PMC6411378 DOI: 10.1093/jxb/erz010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 01/08/2019] [Indexed: 05/18/2023]
Abstract
Moderate soil drying imposed at the post-anthesis stage significantly increases starch accumulation in inferior grains of rice, but how this process is regulated at the level of gene expression remains unclear. In this study, we applied moderate drying (MD) treatments to the soil at the post-anthesis stage and followed the dynamics of the conversion process of soluble sugars to starch in inferior grains using RNA-seq analysis. An elevated level of ABA induced by MD was consistently associated with down-regulation of ABA8ox2, suggesting that lower expression of this gene may be responsible for the higher ABA content, potentially resulting in better filling in inferior grains. In addition, MD treatments up-regulated genes encoding five key enzymes involved sucrose-to-starch conversion and increased the activities of enzymes responsible for soluble-sugar reduction and starch accumulation in inferior grains. Differentially expressed transcription factors, including NAC, GATA, WRKY, and M-type MADS, were predicted to interact with other proteins in mediating filling of inferior grains as a response to MD. Transient expression analysis showed that NAC activated WAXY expression by binding to its promoter, indicating that NAC played a key role in starch synthesis of inferior grains under MD treatment. Our results provide new insights into the molecular mechanisms that regulate grain filling in inferior grains of rice under moderate soil drying.
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Affiliation(s)
- Guan-Qun Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Hao-Xuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mo-Xian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Shuan Meng
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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17
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Zenda T, Liu S, Wang X, Jin H, Liu G, Duan H. Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms. Int J Mol Sci 2018; 19:E3225. [PMID: 30340410 PMCID: PMC6213998 DOI: 10.3390/ijms19103225] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 01/22/2023] Open
Abstract
Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance.
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Affiliation(s)
- Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
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18
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Wang WQ, Jensen ON, Møller IM, Hebelstrup KH, Rogowska-Wrzesinska A. Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves. PLANT METHODS 2018; 14:72. [PMID: 30159003 PMCID: PMC6109330 DOI: 10.1186/s13007-018-0341-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 08/16/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Sample preparation is a critical process for proteomic studies. Many efficient and reproducible sample preparation methods have been developed for mass spectrometry-based proteomic analysis of human and animal tissues or cells, but no attempt has been made to evaluate these protocols for plants. We here present an LC-MS/MS-based proteomics study of barley leaf aimed at optimization of methods to achieve efficient and unbiased trypsin digestion of proteins prior to LC-MS/MS based sequencing and quantification of peptides. We evaluated two spin filter-aided sample preparation protocols using either sodium dodecyl-sulphate or sodium deoxycholate (SDC), and three in-solution digestion (ISD) protocols using SDC or trichloroacetic acid/acetone precipitation. RESULTS The proteomics workflow identified and quantified up to 1800 barley proteins based on sequencing of up to 6900 peptides per sample. The two spin filter-based protocols provided a 12-38% higher efficiency than the ISD protocols, including more proteins of low abundance. Among the ISD protocols, a simple one-step reduction and S-alkylation method (OP-ISD) was the most efficient for barley leaf sample preparation; it identified and quantified 1500 proteins and displayed higher peptide-to-protein inference ratio and higher average amino acid sequence coverage of proteins. The two spin filter-aided sample preparation protocols are compatible with TMT labelling for quantitative proteomics studies. They exhibited complementary performance as about 30% of the proteins were identified by either one or the other protocol, but also demonstrated a positive bias for membrane proteins when using SDC as detergent. CONCLUSIONS We provide detailed protocols for efficient plant protein sample preparation for LC-MS/MS-based proteomics studies. Spin filter-based protocols are the most efficient for the preparation of leaf samples for MS-based proteomics. However, a simple protocol provides comparable results although with different peptide digestion profile.
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Affiliation(s)
- Wei-Qing Wang
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Ole Nørregaard Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Kim H. Hebelstrup
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, 4200 Slagelse, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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19
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Su H, Zhang H, Wei X, Pan D, Jing L, Zhao D, Zhao Y, Qi B. Comparative Proteomic Analysis of Rana chensinensis Oviduct. Molecules 2018; 23:1384. [PMID: 29890619 PMCID: PMC6099995 DOI: 10.3390/molecules23061384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/31/2018] [Accepted: 06/05/2018] [Indexed: 12/31/2022] Open
Abstract
As one of most important traditional Chinese medicine resources, the oviduct of female Rana chensinensis (Chinese brown frog) was widely used in the treatment of asthenia after sickness or delivery, deficiency in vigor, palpitation, and insomnia. Unlike other vertebrates, the oviduct of Rana chensinensis oviduct significantly expands during prehibernation, in contrast to the breeding period. To explain this phenomenon at the molecular level, the protein expression profiles of Rana chensinensis oviduct during the breeding period and prehibernation were observed using isobaric tags for relative and absolute quantitation (iTRAQ) technique. Then, all identified proteins were used to obtain gene ontology (GO) annotation. Ultimately, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis was performed to predict the pathway on differentially expressed proteins (DEPs). A total of 4479 proteins were identified, and 312 of them presented different expression profiling between prehibernation and breeding period. Compared with prehibernation group, 86 proteins were upregulated, and 226 proteins were downregulated in breeding period. After KEGG enrichment analysis, 163 DEPs were involved in 6 pathways, which were lysosome, RNA transport, glycosaminoglycan degradation, extracellular matrix (ECM)⁻receptor interaction, metabolic pathways and focal adhesion. This is the first report on the protein profiling of Rana chensinensis oviduct during the breeding period and prehibernation. Results show that this distinctive physiological phenomenon of Rana chensinensis oviduct was mainly involved in ECM⁻receptor interaction, metabolic pathways, and focal adhesion.
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Affiliation(s)
- Hang Su
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - He Zhang
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Xinghua Wei
- Jilin Science Service Center, Changchun 130021, China.
| | - Daian Pan
- School of Clinical Medicine, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Li Jing
- Practice Innovations Center, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Yu Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Bin Qi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China.
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20
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iTRAQ-based quantitative proteomic analysis reveals pathways associated with re-establishing desiccation tolerance in germinating seeds of Caragana korshinskii Kom. J Proteomics 2018; 179:1-16. [DOI: 10.1016/j.jprot.2018.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 01/04/2023]
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21
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Zhang N, Zhang L, Zhao L, Ren Y, Cui D, Chen J, Wang Y, Yu P, Chen F. iTRAQ and virus-induced gene silencing revealed three proteins involved in cold response in bread wheat. Sci Rep 2017; 7:7524. [PMID: 28790462 PMCID: PMC5548720 DOI: 10.1038/s41598-017-08069-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/03/2017] [Indexed: 11/09/2022] Open
Abstract
By comparing the differentially accumulated proteins from the derivatives (UC 1110 × PI 610750) in the F10 recombinant inbred line population which differed in cold-tolerance, altogether 223 proteins with significantly altered abundance were identified. The comparison of 10 cold-sensitive descendant lines with 10 cold-tolerant descendant lines identified 140 proteins that showed decreased protein abundance, such as the components of the photosynthesis apparatus and cell-wall metabolism. The identified proteins were classified into the following main groups: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, sulfur metabolism, nitrogen metabolism, RNA metabolism, energy production, cell-wall metabolism, membrane and transportation, and signal transduction. Results of quantitative real-time PCR of 20 differentially accumulated proteins indicated that the transcriptional expression patterns of 10 genes were consistent with their protein expression models. Virus-induced gene silencing of Hsp90, BBI, and REP14 genes indicated that virus-silenced plants subjected to cold stress had more severe drooping and wilting, an increased rate of relative electrolyte leakage, and reduced relative water content compared to viral control plants. Furthermore, ultrastructural changes of virus-silenced plants were destroyed more severely than those of viral control plants. These results indicate that Hsp90, BBI, and REP14 potentially play vital roles in conferring cold tolerance in bread wheat.
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Affiliation(s)
- Ning Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lingran Zhang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lei Zhao
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yan Ren
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dangqun Cui
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jianhui Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongyan Wang
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pengbo Yu
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Feng Chen
- Agronomy College/National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.
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You C, Chen L, He H, Wu L, Wang S, Ding Y, Ma C. iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice. BMC PLANT BIOLOGY 2017; 17:100. [PMID: 28592253 PMCID: PMC5463490 DOI: 10.1186/s12870-017-1050-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage). CONCLUSIONS Reduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.
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Affiliation(s)
- Cuicui You
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Haibing He
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Chen Y, Fu X, Mei X, Zhou Y, Cheng S, Zeng L, Dong F, Yang Z. Proteolysis of chloroplast proteins is responsible for accumulation of free amino acids in dark-treated tea ( Camellia sinensis ) leaves. J Proteomics 2017; 157:10-17. [DOI: 10.1016/j.jprot.2017.01.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/19/2017] [Accepted: 01/27/2017] [Indexed: 01/09/2023]
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Yang X, Zhang Z, Gu T, Dong M, Peng Q, Bai L, Li Y. Quantitative proteomics reveals ecological fitness cost of multi-herbicide resistant barnyardgrass ( Echinochloa crus-galli L.). J Proteomics 2017; 150:160-169. [DOI: 10.1016/j.jprot.2016.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/18/2016] [Accepted: 09/21/2016] [Indexed: 01/10/2023]
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Wu S, Ning F, Zhang Q, Wu X, Wang W. Enhancing Omics Research of Crop Responses to Drought under Field Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:174. [PMID: 28261236 PMCID: PMC5306382 DOI: 10.3389/fpls.2017.00174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 01/27/2017] [Indexed: 05/18/2023]
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Fu G, Feng B, Zhang C, Yang Y, Yang X, Chen T, Zhao X, Zhang X, Jin Q, Tao L. Heat Stress Is More Damaging to Superior Spikelets than Inferiors of Rice ( Oryza sativa L.) due to Their Different Organ Temperatures. FRONTIERS IN PLANT SCIENCE 2016; 7:1637. [PMID: 27877180 PMCID: PMC5099171 DOI: 10.3389/fpls.2016.01637] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/17/2016] [Indexed: 05/05/2023]
Abstract
In general, the fertility and kernel weight of inferior spikelets of rice (Oryza Sativa L.) are obviously lower than those of superior spikelets, especially under abiotic stress. However, different responses to heat stress are seemed to show between the superior and inferior spikelet, and this response is scarcely documented that the intrinsic factors remain elusive. In order to reveal the mechanism underlying, two rice plants with different heat tolerance were subjected to heat stress of 40°C at anthesis. The results indicated that a greater decrease in fertility and kernel weight was observed in superior spikelets compared to inferior spikelets. This decrease was primarily ascribed to their different organ temperatures, in which the temperature of the superior spikelets was significantly higher than that of inferior spikelets. We inferred the differences in canopy temperature, light intensity and panicle types, were the primary reasons for the temperature difference between superior and inferior spikelets. Under heat stress, the fertility and kernel weight of superior and inferior spikelets decreased as the panicle numbers per plant were reduced, which was accompanied by significantly increasing the canopy temperatures. Thus, it was suggested that the rice plant with characteristic features of an upright growth habit and loose panicles might be more susceptible to heat stress resulting from their higher canopy and spikelets temperatures.
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Affiliation(s)
- Guanfu Fu
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Baohua Feng
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | | | | | | | | | | | | | - Qianyu Jin
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
| | - Longxing Tao
- State Key Laboratory of Rice Biology, China National Rice Research InstituteHangzhou, China
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28
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Chen L, Huang Y, Xu M, Cheng Z, Zhang D, Zheng J. iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis. PLoS One 2016; 11:e0159238. [PMID: 27415428 PMCID: PMC4944901 DOI: 10.1371/journal.pone.0159238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/29/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Black rice (Oryza sativa L.), whose pericarp is rich in anthocyanins (ACNs), is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear. RESULTS The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP). Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF). The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR) analysis, these genes had differed in transcriptional and translational expression during grain development. CONCLUSIONS Expression analyses of metabolism-related protein groups belonging to different functional categories and subcategories indicated that significantly upregulated proteins were related to flavonoid and starch synthesis. On the other hand, the downregulated proteins were determined to be related to nitrogen metabolism, as well as other functional categories and subcategories, including photosynthesis, redox homeostasis, tocopherol biosynthetic, and signal transduction. The results provide valuable new insights into the characterization and understanding of ACN pigment production in black rice.
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Affiliation(s)
- Linghua Chen
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- Jinshan College of Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Yining Huang
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- Department of Food and Biology Engineering, Zhangzhou Institute of Technology, Zhangzhou Fujian, China
| | - Ming Xu
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Zuxin Cheng
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
| | - Dasheng Zhang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory for Plant Functional Genomics and Resources, Shanghai, China
| | - Jingui Zheng
- FujianAgriculture and Forestry University, Fuzhou Fujian, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
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Guo B, Luan H, Lin S, Lv C, Zhang X, Xu R. Comparative Proteomic Analysis of Two Barley Cultivars (Hordeum vulgare L.) with Contrasting Grain Protein Content. FRONTIERS IN PLANT SCIENCE 2016; 7:542. [PMID: 27200019 PMCID: PMC4843811 DOI: 10.3389/fpls.2016.00542] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/05/2016] [Indexed: 05/24/2023]
Abstract
Grain protein contents (GPCs) of barley seeds are significantly different between feed and malting barley cultivars. However, there is still no insight into the proteomic analysis of seed proteins between feed and malting barley cultivars. Also, the genetic control of barley GPC is still unclear. GPCs were measured between mature grains of Yangsimai 3 and Naso Nijo. A proteome profiling of differentially expressed protein was established by using a combination of 2-DE and tandem mass spectrometry. In total, 502 reproducible protein spots in barley seed proteome were detected with a pH range of 4-7 and 6-11, among these 41 protein spots (8.17%) were detected differentially expressed between Yangsimai 3 and Naso Nijo. Thirty-four protein spots corresponding to 23 different proteins were identified, which were grouped into eight categories, including stress, protein degradation and post-translational modification, development, cell, signaling, glycolysis, starch metabolism, and other functions. Among the identified proteins, enolase (spot 274) and small subunit of ADP-glucose pyrophosphorylase (spot 271) are exclusively expressed in barley Yangsimai 3, which may be involved in regulating seed protein expression. In addition, malting quality is characterized by an accumulation of serpin protein, Alpha-amylase/trypsin inhibitor CMb and Alpha-amylase inhibitor BDAI-1. Most noticeably, globulin, an important storage protein in barley seed, undergoes post-translational processing in both cultivars, and also displays different expression patterns.
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Affiliation(s)
- Baojian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Haiye Luan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
- JiangSu Coastal Area Institute of Agricultural SciencesYancheng, China
| | - Shen Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Chao Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Xinzhong Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Rugen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou UniversityYangzhou, China
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30
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Pi E, Qu L, Hu J, Huang Y, Qiu L, Lu H, Jiang B, Liu C, Peng T, Zhao Y, Wang H, Tsai SN, Ngai S, Du L. Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars. Mol Cell Proteomics 2016; 15:266-88. [PMID: 26407991 PMCID: PMC4762511 DOI: 10.1074/mcp.m115.051961] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/15/2015] [Indexed: 12/23/2022] Open
Abstract
Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856).
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Affiliation(s)
- Erxu Pi
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China;
| | - Liqun Qu
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Jianwen Hu
- §Shanghai Applied Protein Technology Co. Ltd, Shanghai, 200233, PR China
| | - Yingying Huang
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Lijuan Qiu
- ¶The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Hongfei Lu
- ‖College of Life Science, Zhejiang Sci-Tech University, Hangzhou, 310018, PR China
| | - Bo Jiang
- **College of Biology and Food Engineering, Changshu Institute of Technology, Changshu 215500, PR China
| | - Cong Liu
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Tingting Peng
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Ying Zhao
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Huizhong Wang
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China
| | - Sau-Na Tsai
- ‡‡Centre for Soybean Research of Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Saiming Ngai
- ‡‡Centre for Soybean Research of Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Liqun Du
- From the ‡College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, PR China;
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Chen T, Xu G, Wang Z, Zhang H, Yang J, Zhang J. Expression of proteins in superior and inferior spikelets of rice during grain filling under different irrigation regimes. Proteomics 2015; 16:102-21. [PMID: 26442785 DOI: 10.1002/pmic.201500070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 12/21/2022]
Abstract
Poor grain filling of later-flowering inferior spikelets is a serious problem in modern rice cultivars, but the reason and regulation remain unclear. This study investigated post-anthesis protein expression in relation with grain filling and the possibility to use irrigation methods to enhance grain filling through regulating protein expression. One japonica rice cultivar was field-grown under three irrigation treatments imposed during the grain filling period: alternate wetting and moderate soil-drying (WMD), alternate wetting and severe soil-drying (WSD), and conventional irrigation. High resolution 2DE, combined with MALDI/TOF, was used to compare differential protein expression between superior and inferior spikelets. Results showed that the expression of proteins that function in photosynthesis, carbohydrate and energy metabolism, amino acids metabolism and defense responses were largely down-regulated in inferior spikelets compared to those in superior spikelets. The WMD treatment enhanced grain filling rate and the expression of these proteins, whereas the WSD treatment decreased them. Similar results were observed for transcript levels of the genes encoding these proteins. These results suggest that down-regulated expression of the proteins associated with grain filling contribute to the poor grain filling of inferior spikelets, and post-anthesis WMD could improve grain filling through regulating protein expression in the spikelets.
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Affiliation(s)
- Tingting Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China.,State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, P. R. China
| | - Genwen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Zhiqin Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Hao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianchang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, P. R. China
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32
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Sun H, Peng T, Zhao Y, Du Y, Zhang J, Li J, Xin Z, Zhao Q. Dynamic Analysis of Gene Expression in Rice Superior and Inferior Grains by RNA-Seq. PLoS One 2015; 10:e0137168. [PMID: 26355995 PMCID: PMC4565701 DOI: 10.1371/journal.pone.0137168] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/13/2015] [Indexed: 01/10/2023] Open
Abstract
Poor grain filling of inferior grains located on lower secondary panicle branch causes great drop in rice yield and quality. Dynamic gene expression patterns between superior and inferior grains were examined from the view of the whole transcriptome by using RNA-Seq method. In total, 19,442 genes were detected during rice grain development. Genes involved in starch synthesis, grain storage and grain development were interrogated in particular in superior and inferior grains. Of the genes involved in sucrose to starch transformation process, most were expressed at lower level in inferior grains at early filling stage compared to that of superior grains. But at late filling stage, the expression of those genes was higher in inferior grains and lower in superior grains. The same trends were observed in the expression of grain storage protein genes. While, evidence that genes involved in cell cycle showed higher expression in inferior grains during whole period of grain filling indicated that cell proliferation was active till the late filling stage. In conclusion, delayed expression of most starch synthesis genes in inferior grains and low capacity of sink organ might be two important factors causing low filling rate of inferior grain at early filling stage, and shortage of carbohydrate supply was a limiting factor at late filling stage.
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Affiliation(s)
- Hongzheng Sun
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Ting Peng
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yafan Zhao
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yanxiu Du
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Jing Zhang
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Junzhou Li
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Zeyu Xin
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Quanzhi Zhao
- Collaberative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China
- Rice Engineer Center, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China
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33
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Dong M, Gu J, Zhang L, Chen P, Liu T, Deng J, Lu H, Han L, Zhao B. Data in support of comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification. Data Brief 2015. [PMID: 26217686 PMCID: PMC4459568 DOI: 10.1016/j.dib.2014.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We provide the raw data for protein and peptide identification and quantization of superior and inferior spikelets in hybrid rice during grain filling. The mass spectrometry proteomics data have been deposited to the Proteome Xchange Consortium via the PRIDE partner repository with the dataset identifier PXD001046. Our data presented here is also related to the article “Comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification ”in the Journal of Proteomics [1].
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Affiliation(s)
- Minghui Dong
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Junrong Gu
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Li Zhang
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Peifeng Chen
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Tengfei Liu
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Jinhua Deng
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Haoqian Lu
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Liyu Han
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
| | - Buhong Zhao
- Suzhou Academy of Agricultural Science, Suzhou, 215155, PR China
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Koh J, Chen G, Yoo MJ, Zhu N, Dufresne D, Erickson JE, Shao H, Chen S. Comparative Proteomic Analysis of Brassica napus in Response to Drought Stress. J Proteome Res 2015; 14:3068-81. [PMID: 26086353 DOI: 10.1021/pr501323d] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Drought is one of the most widespread stresses leading to retardation of plant growth and development. We examined proteome changes of an important oil seed crop, canola (Brassica napus L.), under drought stress over a 14-day period. Using iTRAQ LC-MS/MS, we identified 1976 proteins expressed during drought stress. Among them, 417 proteins showed significant changes in abundance, and 136, 244, 286, and 213 proteins were differentially expressed in the third, seventh, 10th, and 14th day of stress, respectively. Functional analysis indicated that the number of proteins associated with metabolism, protein folding and degradation, and signaling decreased, while those related to energy (photosynthesis), protein synthesis, and stress and defense increased in response to drought stress. The seventh and 10th-day profiles were similar to each other but with more post-translational modifications (PTMs) at day 10. Interestingly, 181 proteins underwent PTMs; 49 of them were differentially changed in drought-stressed plants, and 33 were observed at the 10th day. Comparison of protein expression changes with those of gene transcription showed a positive correlation in B. napus, although different patterns between transcripts and proteins were observed at each time point. Under drought stress, most protein abundance changes may be attributed to gene transcription, and PTMs clearly contribute to protein diversity and functions.
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Affiliation(s)
| | - Gang Chen
- §Yangzhou University, Yangzhou, 225009 Jiangsu, China
| | | | | | - Daniel Dufresne
- ⊥Palm Beach Central High School, Wellington, Florida 33411, United States
| | | | - Hongbo Shao
- #Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003 Shandong, China
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