Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

Yang, Xinglu; Hua, Xu; Li, Wenhui; Li, L e; Sun, Jinyue; Li, Yaxuan; Yan, Yueming; Hu, Yingkao

doi:10.1186/1471-2164-12-513

Cited by 9 publications

(7 citation statements)

References 30 publications

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“…This indicates that as early as 2 days after anthesis, marked transcriptional activity dedicated to the synthesis of nutrient components (storage proteins) occurs, together with the transcription of genes coding for protease-inhibitors and alpha-amylase inhibitors intended to protect these two components from degradation by different hydrolases. This finding is consistent with that of Yang et al, who identified these gene families as wheat seed-specific genes [ 52 ]. No enriched biological process was observed at the 240-260°Cdays transition.…”

Section: Discussionsupporting

confidence: 93%

“…These genes are protease inhibitors and protect cereal seed from attack by endogenous hydrolase. Thus, during the grain filling stage, in addition to the transcript accumulation of genes encoding storage proteins, genes involved in protecting the main nutritional resource of the developing seed from both endogenous and exogenous degradation are also active [ 52 ]. This phenomenon therefore appears to be important as it constitutes the significant change seen during the first transition (see above).…”

Section: Discussionmentioning

confidence: 99%

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Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development

et al. 2012

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BackgroundWheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction.ResultsA NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile.ConclusionsThe differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development

et al. 2012

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“…We found 436 transcripts (3.3%) that were over-expressed at least 10-fold in the resistant branch, while 970 transcripts (7.4%) were similarly over-expressed in the susceptible branch (Table 2). This difference compares to the variation in gene expression found between functionally distinct tissues in the same organism [29]. …”

Section: Resultsmentioning

confidence: 96%

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

et al. 2013

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BackgroundLong-lived trees can accumulate mutations throughout their lifetimes that may influence biotic and abiotic interactions. For example, some Eucalyptus trees display marked variation in herbivore defence within a single canopy. These “mosaic” trees support foliage with distinct chemotypes which are differentially favoured by insect and vertebrate herbivores, resulting in susceptible and resistant branches within a single canopy. These mosaic trees provide a unique opportunity to explore the biosynthesis and genetic regulation of chemical defences in the foliage. The biosynthesis of the principal defence compounds, terpenoid-dominated essential oils, is well understood. However, the regulation of the genes involved and thus the control of phenotypic variation within a single tree canopy remains a mystery.ResultsWe sequenced the transcriptomes of the leaves of the two different chemotypes of a chemically mosaic Eucalyptus melliodora tree using 454 pyrosequencing technology. We used gene set enrichment analysis to identify differentially expressed transcripts and found the proportion of differentially expressed genes in the resistant and susceptible foliage similar to the transcript difference between functionally distinct tissues of the same organism, for example roots and leaves. We also investigated sequence differences in the form of single nucleotide polymorphisms and found 10 nucleotides that were different between the two branches. These are likely true SNPs and several occur in regulatory genes.ConclusionWe found three lines of evidence that suggest changes to a ‘master switch’ can result in large scale phenotypic changes: 1. We found differential expression of terpene biosynthetic genes between the two chemotypes that could contribute to chemical variation within this plant. 2. We identified many genes that are differentially expressed between the two chemotypes, including some unique genes in each branch. These genes are involved in a variety of processes within the plant and many could contribute to the regulation of secondary metabolism, thus contributing to the chemical variation. 3. We identified 10 SNPs, some of which occur in regulatory genes that could influence secondary metabolism and thus contribute to chemical variation. Whilst this research is inherently limited by sample size, the patterns we describe could be indicative of other plant genetic mosaics.

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“…The wheat embryo and endosperm samples from four germination periods were ground into fine powder in liquid nitrogen. Then, total RNA was extracted from each sample and reverse-transcribed into cDNA according to the procedures in Yang et al [ 86 ]. Gene-specific primers were designed using online Primer3Plus ( http://primer3.ut.ee/ ) according to Untergasser et al [ 87 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination

Zhu

Dong

et al. 2015

BMC Plant Biol

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BackgroundWheat seeds provide a staple food and an important protein source for the world’s population. Seed germination is vital to wheat growth and development and directly affects grain yield and quality. In this study, we performed the first comparative proteomic analysis of wheat embryo and endosperm during seed germination.ResultsThe proteomic changes in embryo and endosperm during the four different seed germination stages of elite Chinese bread wheat cultivar Zhengmai 9023 were first investigated. In total, 74 and 34 differentially expressed protein (DEP) spots representing 63 and 26 unique proteins were identified in embryo and endosperm, respectively. Eight common DEP were present in both tissues, and 55 and 18 DEP were specific to embryo and endosperm, respectively. These identified DEP spots could be sorted into 13 functional groups, in which the main group was involved in different metabolism pathways, particularly in the reserves necessary for mobilization in preparation for seed germination. The DEPs from the embryo were mainly related to carbohydrate metabolism, proteometabolism, amino acid metabolism, nucleic acid metabolism, and stress-related proteins, whereas those from the endosperm were mainly involved in protein storage, carbohydrate metabolism, inhibitors, stress response, and protein synthesis. During seed germination, both embryo and endosperm had a basic pattern of oxygen consumption, so the proteins related to respiration and energy metabolism were up-regulated or down-regulated along with respiration of wheat seeds. When germination was complete, most storage proteins from the endosperm began to be mobilized, but only a small amount was degraded during germination. Transcription expression of six representative DEP genes at the mRNA level was consistent with their protein expression changes.ConclusionWheat seed germination is a complex process with imbibition, stirring, and germination stages, which involve a series of physiological, morphological, and proteomic changes. The first process is a rapid water uptake, in which the seed coat becomes softer and the physical state of storage materials change gradually. Then the germinated seed enters the second process (a plateau phase) and the third process (the embryonic axes elongation). Seed embryo and endosperm display distinct differentially expressed proteins, and their synergistic expression mechanisms provide a basis for the normal germination of wheat seeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0471-z) contains supplementary material, which is available to authorized users.

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Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

Cited by 9 publications

References 30 publications

Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development

Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development

Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory

Comparative proteome analysis of embryo and endosperm reveals central differential expression proteins involved in wheat seed germination

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