Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids. Results Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

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Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

10.21203/rs.3.rs-29700/v4 ◽

2020 ◽

Author(s):

Daoping Wang ◽

Yongying Mu ◽

Xiaojiao Hu ◽

Bo Ma ◽

Zhibo Wang ◽

...

Keyword(s):

Stress Response ◽

Stress Responses ◽

Proteomic Analysis ◽

Agronomic Traits ◽

Female Parent ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Label Free ◽

Maize Hybrids ◽

Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

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Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

10.21203/rs.3.rs-29700/v3 ◽

2020 ◽

Author(s):

Daoping Wang ◽

Yongying Mu ◽

Xiaojiao Hu ◽

Bo Ma ◽

Zhibo Wang ◽

...

Keyword(s):

Stress Response ◽

Stress Responses ◽

Proteomic Analysis ◽

Agronomic Traits ◽

Female Parent ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Label Free ◽

Maize Hybrids ◽

Comparative Proteomic Analysis

Abstract Background Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. ‘Zhongdan808’ (ZD808) and ‘Zhongdan909’ (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.Results Over 2,000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value. Conclusions Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

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Comparative Proteomic Analysis Reveals That the Heterosis of Two Maize Hybrids is Related to Enhancement of Stress Response and Photosynthesis Respectively

10.21203/rs.3.rs-29700/v1 ◽

2020 ◽

Author(s):

Daoping Wang ◽

Yongying Mu ◽

Xiaojiao Hu ◽

Bo Ma ◽

Zhibo Wang ◽

...

Keyword(s):

Stress Responses ◽

Proteomic Analysis ◽

Molecular Mechanisms ◽

Agronomic Traits ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Label Free ◽

Maize Production ◽

Maize Hybrids ◽

Comparative Proteomic Analysis

Abstract BackgroundMaize is a major crop worldwide and heterotic hybrids play important roles in global maize production. Heterosis refers hybrid progeny of species or varieties exhibiting superior traits compared with those of their parents and much attention has been paid to heterosis associated genes recently. The hybridization between parents can change the expression pattern of some proteins such as non-additive proteins which might lead to heterosis, so that comparative proteomic analysis of maize hybrid and its parents is helpful for understanding the mechanism of heterosis.ResultsSecond seedling leaves of maize hybrids "Zhongdan 808" and "Zhongdan 909" and their parents were collected at three-leaf stage for protein extractions. Over 2,000 protein groups were accurately assessed in the two hybrids and their parents by label-free quantification. Quantitative data analyses of the proteomes revealed that the two hybrids were more similar to their female parents. Additionally, pathway enrichment analysis showed that most non-additive proteins in Zhongdan 808 were mainly enriched in stress-related pathways, while those in Zhongdan 909 were mainly enriched in photosynthesis. ConclusionsIn comparison with their parents, the excellent agronomic traits of hybrid Zhongdan 808 was correlated with the high expression levels of some proteins related to stress responses and and metabolic functions, while those of Zhongdan 909 was correlated with photosynthesis. Our proteomics results supported previous physiological and morphological research. This work may provide useful information for understanding of the molecular mechanisms involved in the heterosis of hybrid maize.

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Comparative Proteomic Analysis of Molecular Differences between Leaves of Wild-Type Upland Cotton and Its Fuzzless-Lintless Mutant

Molecules ◽

10.3390/molecules24203769 ◽

2019 ◽

Vol 24 (20) ◽

pp. 3769

Author(s):

Liping Zhu ◽

Bowen Zheng ◽

Wangyang Song ◽

Chengcheng Tao ◽

Xiang Jin ◽

...

Keyword(s):

Proteomic Analysis ◽

Upland Cotton ◽

Interaction Network ◽

Enrichment Analysis ◽

Gossypol Content ◽

Pathway Enrichment Analysis ◽

Protein Accumulation ◽

Wild Type ◽

Protein Protein Interaction ◽

Comparative Proteomic Analysis

Fuzzless-lintless mutant (fl) ovules of upland cotton have been used to investigate cotton fiber development for decades. However, the molecular differences of green tissues between fl and wild-type (WT) cotton were barely reported. Here, we found that gossypol content, the most important secondary metabolite of cotton leaves, was higher in Gossypium hirsutum L. cv Xuzhou-142 (Xu142) WT than in fl. Then, we performed comparative proteomic analysis of the leaves from Xu142 WT and its fl. A total of 4506 proteins were identified, of which 103 and 164 appeared to be WT- and fl-specific, respectively. In the 4239 common-expressed proteins, 80 and 74 were preferentially accumulated in WT and fl, respectively. Pathway enrichment analysis and protein–protein interaction network analysis of both variety-specific and differential abundant proteins showed that secondary metabolism and chloroplast-related pathways were significantly enriched. Quantitative real-time PCR confirmed that the expression levels of 12 out of 16 selected genes from representative pathways were consistent with their protein accumulation patterns. Further analyses showed that the content of chlorophyll a in WT, but not chlorophyll b, was significantly increased compared to fl. This work provides the leaf proteome profiles of Xu142 and its fl mutant, indicating the necessity of further investigation of molecular differences between WT and fl leaves.

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Comparative Proteomic Analysis of Non-small-cell Lung Cancer and Normal Controls Using Serum Label-Free Quantitative Shotgun Technology

Lung ◽

10.1007/s00408-008-9093-7 ◽

2008 ◽

Vol 186 (4) ◽

pp. 255-261 ◽

Cited By ~ 23

Author(s):

Jun Pan ◽

Hai-Quan Chen ◽

Yi-Hua Sun ◽

Jun-Hua Zhang ◽

Xiao-Yang Luo

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Proteomic Analysis ◽

Small Cell ◽

Label Free ◽

Small Cell Lung ◽

Comparative Proteomic Analysis ◽

Normal Controls

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Label-free based comparative proteomic analysis of whey proteins between different milk yields of Dezhou donkey

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2018.11.130 ◽

2019 ◽

Vol 508 (1) ◽

pp. 237-242 ◽

Cited By ~ 2

Author(s):

Xinhao Zhang ◽

Haijing Li ◽

Jie Yu ◽

Xiangshan Zhou ◽

Chuanliang Ji ◽

...

Keyword(s):

Proteomic Analysis ◽

Whey Proteins ◽

Label Free ◽

Comparative Proteomic Analysis

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Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

Frontiers in Plant Science ◽

10.3389/fpls.2021.744654 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pajaree Sonsungsan ◽

Pheerawat Chantanakool ◽

Apichat Suratanee ◽

Teerapong Buaboocha ◽

Luca Comai ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Stress Responses ◽

Time Course ◽

Rice Variety ◽

Enrichment Analysis ◽

Normal Growth ◽

Growth Conditions ◽

Pathway Enrichment Analysis ◽

Key Genes

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

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Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

10.21203/rs.3.rs-20923/v1 ◽

2020 ◽

Author(s):

Bolin Wu ◽

Haitao Shang ◽

Xitian Liang ◽

Huajing Yang Huajing Yang ◽

Hui Jing ◽

...

Keyword(s):

Protein Interactions ◽

Interaction Analysis ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Differentially Expressed Proteins ◽

Label Free ◽

Protein Protein Interaction ◽

Study Results ◽

Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

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Exploring microRNAs, Target mRNAs and their Functions in Leguminous PlantArachis hypogaea

MicroRNA ◽

10.2174/2211536608666181105114154 ◽

2019 ◽

Vol 8 (2) ◽

pp. 135-146 ◽

Cited By ~ 1

Author(s):

Anjana Rajendiran ◽

Saravanan Vijayakumar ◽

Archana Pan

Keyword(s):

Comparative Genomics ◽

Stress Responses ◽

Unsaturated Fatty Acids ◽

Enrichment Analysis ◽

Antibiotic Biosynthesis ◽

Pathway Enrichment Analysis ◽

Transcriptional Level ◽

Biological Databases ◽

Biotic And Abiotic Stress ◽

Genome Survey

Background:MicroRNAs (miRNAs) are a class of small non-coding, endogenous RNAs that regulate gene expression at post-transcriptional level. In plants, miRNAs are usually of 18-24 nucleotide in length and play humongous role by aiding in development, growth, defense, biotic and abiotic stress responses, etc.Objective:Arachis hypogaea is an economically important oil seed crop and human dietary source cultivated mostly in tropical and subtropical regions. In the present study, an initiative was taken to uncover miRNAs, their targets and functions in this important plant species. </P><P> Method: Comparative genomics strategy coupled with bioinformatics approaches was deployed for the identification of miRNAs, their corresponding targets and functions by exploiting biological databases and tools.Results:The study was able to identify 34 conserved miRNA candidates, belonging to 17 miRNA families, contributed by 23 and 3 precursor miRNAs from A. hypogaea Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS), respectively. As well, 495 EST and 917 unigene sequences were predicted as targets for the identified miRNAs. Herein, psRNAtarget server and TargetFinder tool were used to predict unigene targets, whereas comparative genomics strategy was used for identifying EST targets. Functional annotation of the identified targets revealed that the identified miRNAs regulate mRNAs that participate in key biological and metabolic processes. Pathway enrichment analysis using KEGG database also revealed that they regulate important metabolic pathways including antibiotic biosynthesis, biosynthesis of unsaturated fatty acids, amino acids metabolism and flavonoid biosynthesis.Conclusion:The outcome of the study would aid experimental biologists to focus on these miRNAs to facilitate improved crop development and yield.

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