Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure

Yang, Piao; Li, Yaxing; He, Chongsheng; Yan, Jindong; Zhang, Wei; Li, Xin; Xiang, Fujiang; Zuo, Zecheng; Li, Xinmei; Zhu, Yonghua; Liu, Xuanming; Zhao, Xiaoying

doi:10.1016/j.jprot.2019.103621

Cited by 20 publications

(10 citation statements)

References 42 publications

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“…Volcano plot and protein abundance data showed the differential expression of proteins between CK and TM in each group of plants ( Figure 4 A–C and Table 1 ). According to the variance analysis with p < 0.05 and 1.3- or 0.7-fold change, a commonly used stringent parameter setting for TMT-based comparative proteomics [ 36 , 37 , 38 ], in total, 59, 82, and 111 quantified proteins were considered to be upregulated, and 29, 31, and 57 proteins were considered to be downregulated proteins at the protein level by ER stress in Col, L er , and DM plants, respectively ( Figure 4 D–F, Table S1 ). The enrichment of gene ontology (GO) analysis showed that similar biological process (BP) or molecular function (MF) were enriched in Col and L er , in which GO terms related to protein folding and degradation were commonly found ( Figures S2 and S3 ).…”

Section: Resultsmentioning

confidence: 99%

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis thaliana

Lyu

Shao

Yang

et al. 2020

IJMS

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Accumulation of unfolded and misfolded proteins in endoplasmic reticulum (ER) elicits a well-conserved response called the unfolded protein response (UPR), which triggers the upregulation of downstream genes involved in protein folding, vesicle trafficking, and ER-associated degradation (ERAD). Although dynamic transcriptomic responses and the underlying major transcriptional regulators in ER stress response in Arabidopsis have been well established, the proteome changes induced by ER stress have not been reported in Arabidopsis. In the current study, we found that the Arabidopsis Landsberg erecta (Ler) ecotype was more sensitive to ER stress than the Columbia (Col) ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that, in total, 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC > 1.3 or <0.7, p < 0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly upregulated in Col and Ler, among which 10 were not upregulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically upregulated proteins in Col, as compared with that in Ler, components in ERAD, N-glycosylation, vesicle trafficking, and molecular chaperones were represented. Quantitative RT-PCR showed that transcripts of eight out of 19 proteins were not upregulated (FC > 1.3 or <0.7, p < 0.05) by ER stress in Col ecotype, while transcripts of 11 out of 19 proteins were upregulated by ER stress in both ecotypes with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at the proteome level in plants and revealed differentially regulated proteins that may contribute to the differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.

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Section: Resultsmentioning

confidence: 99%

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis thaliana

Lyu

Shao

Yang

et al. 2020

IJMS

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“…Ten plants from plot were randomly selected for agronomic traits analysis. The plant height (PH), internode length (IL), internode number (IN), first branch height (FBH), main inflorescence length (MIL), number of effective primary branches (NPB), number of siliques on raceme (NSR), siliques per plant (SPP), length of siliques (LS), seeds per silique (SPS), thousand-seed weight (TSW) and yield per plant (YPP), were measured and counted as previously described [49,50]. Significant differences were determined by Student's t-test using SPSS version 25 (SPSS Inc., Chicago).…”

Section: Agronomic Traits Analysismentioning

confidence: 99%

Characterization and fine mapping of a new dwarf mutant in Brassica napus

Xiang

Zhang

et al. 2021

BMC Plant Biol

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Background Plant height is an important plant characteristic closely related to yield performance of many crops. Reasonable reduction of plant height of crops is beneficial for improving yield and enhancing lodging resistance. Results In the present study, we described the Brassica napus dwarf mutant bnd2 that was isolated using ethyl methanesulfonate (EMS) mutagenesis. Compared to wild type (WT), bnd2 exhibited reduced height and shorter hypocotyl and petiole leaves. By crossing the bnd2 mutant with the WT strain, we found that the ratio of the mutant to the WT in the F2 population was close to 1:3, indicating that bnd2 is a recessive mutation of a single locus. Following bulked segregant analysis (BSA) by resequencing, BND2 was found to be located in the 13.77–18.08 Mb interval of chromosome A08, with a length of 4.31 Mb. After fine mapping with single nucleotide polymorphism (SNP) and insertion/deletion (InDel) markers, the gene was narrowed to a 140-Kb interval ranging from 15.62 Mb to 15.76 Mb. According to reference genome annotation, there were 27 genes in the interval, of which BnaA08g20960D had an SNP type variation in the intron between the mutant and its parent, which may be the candidate gene corresponding to BND2. The hybrid line derived from a cross between the mutant bnd2 and the commercial cultivar L329 had similar plant height but higher grain yield compared to the commercial cultivar, suggesting that the allele bnd2 is beneficial for hybrid breeding of lodging resistant and high yield rapeseed. Conclusion In this study, we identified a novel dwarf mutant of rapeseed with a new locus, which may be useful for functional analyses of genetic mechanisms of plant architecture and grain yield in rapeseed.

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“…Ten plants from plot were randomly selected for agronomic traits analysis. The plant height (PH), internode length (IL), internode number (IN), rst branch height (FBH), main in orescence length (MIL), number of effective primary branches (NPB), number of siliques on raceme (NSR), siliques per plant (SPP), length of siliques (LS), seeds per silique (SPS), thousand-seed weight (TSW) and yield per plant (YPP), were measured and counted as previously described [39,40]. Signi cant differences were determined by Student's t-test using SPSS version 25 (SPSS Inc, Chicago).…”

Section: Agronomic Traits Analysismentioning

confidence: 99%

Characterization and Fine Mapping of a New Dwarf Mutant in Brassica Napus

Xiang

Zhang

et al. 2020

Preprint

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Background: Plant height is an important plant architecture character closely related to yield performance of many crops. Reasonable reduction of plant height of crops is beneficial for enhancing lodging resistance and improving yield. Results: In the present study, we described a Brassica napus dwarf mutant bnd2 induced by ethyl methanesulfonate (EMS) mutagenesis. Compared to wild type, bnd2 showed shorter stature, shorter hypocotyl, as well as shorter petiole leaves. We crossed the bnd2 mutant with its wild type and found that the ratio of the mutant to the wild type in the F2 population was close to 1:3, indicating that bnd2 is a recessive mutation of a single locus. Following bulked segregant analysis (BSA) by resequencing, BND2 was located into the 13.77 Mb-18.08 Mb interval of chromosome A08, with a length of 4.31 Mb. After fine mapping with SNP and InDel markers, the gene was narrowed to a 140-Kb interval ranging from 15.62 Mb to 15.76 Mb. According to reference genome annotation, there are 27 genes in the interval, and one of them BnaA08g20960D has a SNP type variation in the intron between the mutant and its parent, which may be the candidate gene conferring to BND2. The hybrid line derived from a cross between the mutant bnd2 and a commercial cultivar L329 has similar plant height but higher grain yield than the commercial cultivar, suggesting that the allele bnd2 is benefit for hybrid breeding of lodging resistance and high yield in rapeseed.Conclusion: In this study, we found a fresh resource and a new locus for dwarf in rapeseed, which may be benefit for functional analysis of genetic mechanism of plant architecture and grain yield in rapeseed.

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Phenotype and TMT-based quantitative proteomics analysis of Brassica napus reveals new insight into chlorophyll synthesis and chloroplast structure

Cited by 20 publications

References 42 publications

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis thaliana

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis thaliana

Characterization and fine mapping of a new dwarf mutant in Brassica napus

Characterization and Fine Mapping of a New Dwarf Mutant in Brassica Napus

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