Dataset Information

Evaluation of cold tolerant Saccharum spontaneum and identification of proteins related to cold tolerance by proteomic analysis

ABSTRACT: Saccharum spontaneum L., the main source of tolerance gene in sugarcane variety, is one of the most valuable germplasms for sugarcane breeding. In this study, 22 clones of S.spontaneum L. were selected from more than 690 collections in our preliminary experiment, and the cold tolerance of these clones were evaluated by physiological and biochemical indicators. Then 2 clones which were designated as lines 1027 and 3217,with contrasting cold tolerance ability were selected for further proteome analysis using DIA and PRM technology.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharum Spontaneum

TISSUE(S): Leaf

SUBMITTER: miao huang

LAB HEAD: Bao-Qing Zhang

PROVIDER: PXD038181 | Pride | 2023-03-11

REPOSITORIES: Pride

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Publications

Cold-Induced Physiological and Biochemical Alternations and Proteomic Insight into the Response of <i>Saccharum spontaneum</i> to Low Temperature.

Zhang Bao-Qing BQ Huang Yu-Xin YX Zhou Zhong-Feng ZF Zhou Shan S Duan Wei-Xing WX Yang Cui-Fang CF Gao Yi-Jing YJ Zhang Ge-Min GM Song Xiu-Peng XP Zhang Xiao-Qiu XQ Li Ao-Mei AM Huang Dong-Liang DL Li Yang-Rui YR

International journal of molecular sciences 20221117 22

Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of <i>S. sp ...[more]

PMID: 36430736

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Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.

			Action	DRS
	DIA_1027_8D_1.raw	Raw
	DIA_1027_8D_2.raw	Raw
	DIA_1027_8D_3.raw	Raw
	DIA_1027_CK_1.raw	Raw
	DIA_1027_CK_2.raw	Raw