scholarly journals iTRAQ-based quantitative proteome analysis insights into cold stress of Winter Rapeseed (Brassica rapa L.) grown in the field

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zaoxia Niu ◽  
Lijun Liu ◽  
Yuanyuan Pu ◽  
Li Ma ◽  
Junyan Wu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Brassica Rapa ◽  
Molecular Mechanisms ◽  
Glutathione Transferase ◽  
Soluble Sugars ◽  
Freezing Stress ◽  
Transferase Activity ◽  
Oilseed Crop ◽  
Winter Rapeseed ◽  
Collar Diameter

AbstractWinter rapeseed (Brassica rapa L.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. However, not much is known about the role of differentially accumulated proteins (DAPs) during the chilling and freezing stress. In this study, isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. To explore the molecular mechanisms of cold stress tolerance at the cellular and protein levels, the morphological and physiological differences in the shoot apical meristem (SAM) of two winter rapeseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were explored in field-grown plants. Compared to Lenox, Longyou 7 had a lower SAM height and higher collar diameter. The level of malondialdehyde (MDA) and indole-3-acetic acid (IAA) content was also decreased. Simultaneously, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase (POD) activity, soluble protein (SP) content, and collar diameter were increased in Longyou 7 as compared to Lenox. A total of 6330 proteins were identified. Among this, 98, 107, 183 and 111 DAPs were expressed in L7 CK/Le CK, L7 d/Le d, Le d/Le CK and L7 d/L7 CK, respectively. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs was performed for validation. These DAPs were identified based on gene ontology enrichment analysis, which revealed that glutathione transferase activity, carbohydrate-binding, glutathione binding, metabolic process, and IAA response were closely associated with the cold stress response. In addition, some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play an essential role during cold acclimation in the SAM of Brassica rapa. The present study provides valuable information on the involvement of DAPs during cold stress responses in Brassica rapa L, and hence could be used for breeding experiments.

scholarly journals iTRAQ-Based Quantitative Proteome Analysis Insights into Cold Stress of Winter Turnip Rapa (Brassica rapa L.) Grown in the Field

2021 ◽  
Author(s):  
Zaoxia Niu ◽  
Lijun Liu ◽  
Yuanyuan Pu ◽  
Li Ma ◽  
Junyan Wu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Brassica Rapa ◽  
Molecular Mechanisms ◽  
Glutathione Transferase ◽  
Function Analysis ◽  
Chilling Stress ◽  
Freezing Stress ◽  
Transferase Activity ◽  
Oilseed Crop ◽  
Collar Diameter

Abstract Winter Turnip rapa (Brassica rapa L.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. Previous studies have demonstrated that differentially accumulated proteins (DAPs) were expressed in roots and leaves under control chilling stress. In this study, the isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. Two winter rapaseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were used to investigated morphological, physiological, cell and protein levels in the shoot apical meristem (SAM) of field-grown Brassica rapa to reveal the molecular mechanisms of cold stress tolerance. Compared to Lenox, Longyou 7 had a lower SAM of height, higher collar diameter. The level of malondialdehyde (MDA), SAM of height and IAA content were repressed. At the same time, compared to Lenox, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase(POD)activity, soluble protein (SP) content and collar diameter increased in Longyou 7. In total, we identified 6330 proteins, among this, 98 DAPs were expressed in L7 CK/Le CK, 107 DAPs were expressed in L7 d /Le d 183 DAPs were expressed in Le d /Le CK, 111 DAPs were expressed in L7 d /L7 CK. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs were performed for validation. These DAPs were identified from the two winter rapa seed cultivars involved in the biological process, cellular component and molecular function analysis, which revealed glutathione transferase activity, carbohydrate-binding, and glutathione binding, glutathione metabolic process and response IAA were closely associated with the cold stress response. Some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play essential roles cold acclimation in Brassica rapa of SAM. Our work will help to provide valuable information for responding to the cold stress in Brassica rapa L.

scholarly journals Transcriptome Profile Analysis of Winter Rapeseed (Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress

2019 ◽  
Vol 20 (11) ◽  
pp. 2771 ◽  
Author(s):  
Yuanyuan Pu ◽  
Lijun Liu ◽  
Junyan Wu ◽  
Yuhong Zhao ◽  
Jing Bai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Brassica Napus ◽  
Molecular Mechanism ◽  
Stress Responses ◽  
Soluble Sugars ◽  
Enrichment Analysis ◽  
Freezing Stress ◽  
Oilseed Crop ◽  
Brassica Napus L ◽  
Winter Rapeseed

Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line “2016TS(G)10” (freezing-tolerance line) that was exposed to –2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.

scholarly journals iTRAQ-Based Comparative Proteomic Analysis of the Roots of TWO Winter Turnip Rapes (Brassica rapa L.) with Different Freezing-Tolerance

2018 ◽  
Vol 19 (12) ◽  
pp. 4077 ◽  
Author(s):  
Xiucun Zeng ◽  
Yaozhao Xu ◽  
Jinjin Jiang ◽  
Fenqin Zhang ◽  
Li Ma ◽  
...  
Keyword(s):  
Cold Acclimation ◽  
Linolenic Acid ◽  
Brassica Rapa ◽  
Freezing Tolerance ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Freezing Stress ◽  
Turnip Rape ◽  
Mannose Metabolism

The freezing tolerance of roots is crucial for winter turnip rape (Brassica rapa L.) survival in the winter in Northwest China. Cold acclimation (CA) can alleviate the root damage caused by freezing stress. To acknowledge the molecular mechanisms of freezing tolerance in winter turnip rape, two Brassica rapa genotypes, freezing stressed after the induction of cold acclimation, were used to compare the proteomic profiles of roots by isobaric tags for relative and absolute quantification (iTRAQ). Under freezing stress (−4 °C) for 8 h, 139 and 96 differentially abundant proteins (DAPs) were identified in the roots of “Longyou7” (freezing-tolerant) and “Tianyou4” (freezing-sensitive), respectively. Among these DAPs, 91 and 48 proteins were up- and down-accumulated in “Longyou7”, respectively, and 46 and 50 proteins were up- and down-accumulated in “Tianyou4”, respectively. Under freezing stress, 174 DAPs of two varieties were identified, including 9 proteins related to ribosome, 19 DAPs related to the biosynthesis of secondary metabolites (e.g., phenylpropanoid and the lignin pathway), and 22 down-accumulated DAPs enriched in oxidative phosphorylation, the pentose phosphate pathway, fructose and mannose metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, ascorbate and aldarate metabolism. The expressional pattern of the genes encoding the 15 significant DAPs were consistent with the iTRAQ data. This work indicates that protein biosynthesis, lignin synthesis, the reduction of energy consumption and a higher linolenic acid content contribute to the freezing tolerance of winter turnip rape. Functional analyses of these DAPs would be helpful in dissecting the molecular mechanisms of the stress responses in B. rapa.

scholarly journals iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

2018 ◽  
Vol 19 (11) ◽  
pp. 3346 ◽  
Author(s):  
Yaozhao Xu ◽  
Xiucun Zeng ◽  
Jian Wu ◽  
Fenqin Zhang ◽  
Caixia Li ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Pentose Phosphate ◽  
Metabolic Process ◽  
Cellular Process ◽  
Turnip Rape

Winter turnip rape (Brassica rapa L.) is a large-scale winter-only oil crop cultivated in Northwest China. However, its cold-resistant molecular mechanism remains inadequate. Studying the cold adaptation mechanisms of winter turnip rape based on the proteomic technique of isobaric tags for relative and absolute quantification (iTRAQ) offers a solution to this problem. Under cold stress (−4 °C for eight hours), 51 and 94 differently accumulated proteins (DAPs) in Longyou 7 (cold-tolerant) and Tianyou 4 (cold-sensitive) were identified, respectively. These DAPs were classified into 38 gene ontology (GO) term categories, such as metabolic process, cellular process, catalytic activity, and binding. The 142 DAPs identified between the two cold-stressed cultivars were classified into 40 GO terms, including cellular process, metabolic process, cell, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DAPs participated in 10 pathways. The abundance of most protein functions in ribosomes, carbon metabolism, photosynthesis, and energy metabolism including the citrate cycle, pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism decreased, and the proteins that participate in photosynthesis–antenna and isoflavonoid biosynthesis increased in cold-stressed Longyou 7 compared with those in cold-stressed Tianyou 4. The expression pattern of genes encoding the 10 significant DAPs was consistent with the iTRAQ data. This study provides new information on the proteomic differences between the leaves of Longyou 7 and Tianyou 4 plants and explains the possible molecular mechanisms of cold-stress adaptation in B. rapa.

scholarly journals Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

2019 ◽  
Vol 20 (5) ◽  
pp. 1071 ◽  
Author(s):  
Li Ma ◽  
Jeffrey Coulter ◽  
Lijun Liu ◽  
Yuhong Zhao ◽  
Yu Chang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cold Stress ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Ribosome Biogenesis ◽  
Physiological Activity ◽  
Growth Period ◽  
Ambient Air ◽  
Mapk Signaling ◽  
Winter Rapeseed

Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.

scholarly journals Quantitative Proteomic Analysis of the Response to Cold Stress in Jojoba, a Tropical Woody Crop

2019 ◽  
Vol 20 (2) ◽  
pp. 243 ◽  
Author(s):  
Fei Gao ◽  
Pengju Ma ◽  
Yingxin Wu ◽  
Yijun Zhou ◽  
Genfa Zhang
Keyword(s):  
Superoxide Dismutase ◽  
Stress Response ◽  
Cold Stress ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Soluble Sugars ◽  
Pcr Analysis ◽  
Ros Scavenging ◽  
Quantitative Proteomic Analysis ◽  
Woody Crop

Jojoba (Simmondsia chinensis) is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba’s growth, development and yield and limit introduction of jojoba in the vast temperate arid areas. To get insight into the molecular mechanisms of the cold stress response of jojoba, a combined physiological and quantitative proteomic analysis was conducted. Under cold stress, the photosynthesis was repressed, the level of malondialdehyde (MDA), relative electrolyte leakage (REL), soluble sugars, superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) were increased in jojoba leaves. Of the 2821 proteins whose abundance were determined, a total of 109 differentially accumulated proteins (DAPs) were found and quantitative real time PCR (qRT-PCR) analysis of the coding genes for 7 randomly selected DAPs were performed for validation. The identified DAPs were involved in various physiological processes. Functional classification analysis revealed that photosynthesis, adjustment of cytoskeleton and cell wall, lipid metabolism and transport, reactive oxygen species (ROS) scavenging and carbohydrate metabolism were closely associated with the cold stress response. Some cold-induced proteins, such as cold-regulated 47 (COR47), staurosporin and temperature sensitive 3-like a (STT3a), phytyl ester synthase 1 (PES1) and copper/zinc superoxide dismutase 1, might play important roles in cold acclimation in jojoba seedlings. Our work provided important data to understand the plant response to the cold stress in tropical woody crops.

scholarly journals Comparative proteomics analysis reveals the molecular mechanism of enhanced cold tolerance through ROS scavenging in winter rapeseed (Brassica napus L.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0243292
Author(s):  
Wenbo Mi ◽  
Zigang Liu ◽  
Jiaojiao Jin ◽  
Xiaoyun Dong ◽  
Chunmei Xu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Cold Treatment ◽  
Ros Scavenging ◽  
Brassica Napus L ◽  
Membrane Injury ◽  
Data Independent Acquisition ◽  
Winter Rapeseed

Two winter rapeseed cultivars, “NS” (cold tolerant) and “NF” (cold sensitive), were used to reveal the morphological, physiological, and proteomic characteristics in leaves of plants after treatment at -4°C for 12 h(T1) and 24 h(T2), and at room temperature(T0), to understand the molecular mechanisms of cold tolerance. Antioxidant activity and osmotic adjustment ability were higher, and plasma membrane injury was less obvious, in NS than in NF under cold stress. We detected different abundant proteins (DAPs) related to cold tolerance in winter rapeseed through data-independent acquisition (DIA). Compared with NF, A total of 1,235 and 1,543 DAPs were identified in the NSs under T1 and T2, respectively. Compared with NF, 911 proteins were more abundant in NS only after cold treatment. Some of these proteins were related to ROS scavenging through four metabolic pathways: lysine degradation; phenylalanine, tyrosine, and tryptophan; flavonoid biosynthesis; and ubiquinone and other terpenoid-quinone biosynthesis. Analysis of these proteins in the four candidate pathways revealed that they were rapidly accumulated to quickly enhance ROS scavenging and improve the cold tolerance of NS. These proteins were noticeably more abundant during the early stage of cold stress, which was critical for avoiding ROS damage.

scholarly journals Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zaiqing Wang ◽  
Anmin Yu ◽  
Fei Li ◽  
Wei Xu ◽  
Bing Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Castor Bean ◽  
Woody Plants ◽  
Molecular Mechanisms ◽  
Ricinus Communis ◽  
Bulked Segregant Analysis ◽  
Oilseed Crop ◽  
Yeast Transformation ◽  
Dwarf Phenotype ◽  
Genetic Breeding

AbstractPlant dwarfism is a desirable agronomic trait in non-timber trees, but little is known about the physiological and molecular mechanism underlying dwarfism in woody plants. Castor bean (Ricinus communis) is a typical woody oilseed crop. We performed cytological observations within xylem, phloem and cambia tissues, revealing that divergent cell growth in all tissues might play a role in the dwarf phenotype in cultivated castor bean. Based on bulked segregant analyses for a F2 population generated from the crossing of a tall and a dwarf accession, we identified two QTLs associated with plant height, covering 325 candidate genes. One of these, Rc5NG4-1 encoding a putative IAA transport protein localized in the tonoplast was functionally characterized. A non-synonymous SNP (altering the amino acid sequence from Y to C at position 218) differentiated the tall and dwarf plants and we confirmed, through heterologous yeast transformation, that the IAA uptake capacities of Rc5NG4-1Y and Rc5NG4-1C were significantly different. This study provides insights into the physiological and molecular mechanisms of dwarfing in woody non-timber economically important plants, with potential to aid in the genetic breeding of castor bean and other related crops.

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