Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum

Genome ◽  
2015 ◽  
Vol 58 (6) ◽  
pp. 305-313 ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Sapna Devi ◽  
S. Sundaresha ◽  
Poonam Chandel ◽  
Nilofer Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Microarray Analysis ◽  
Somatic Hybrid ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Gene Expression Patterns ◽  
Potato Tuberization ◽  
Solanum Etuberosum

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.

scholarly journals Deafness Gene Expression Patterns in the Mouse Cochlea Found by Microarray Analysis

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e92547 ◽  
Author(s):  
Hidekane Yoshimura ◽  
Yutaka Takumi ◽  
Shin-ya Nishio ◽  
Nobuyoshi Suzuki ◽  
Yoh-ichiro Iwasa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Deafness Gene

Photosynthetic Gene Expression in Amaranth, an NAD-ME Type C4 Dicot

1997 ◽  
Vol 24 (4) ◽  
pp. 423 ◽  
Author(s):  
James O. Berry ◽  
Dennis J. McCormac ◽  
John J. Long ◽  
Joseph Boinski ◽  
Amy C. Corey
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Metabolic Enzyme ◽  
Gene Expression Patterns ◽  
Control Mechanisms ◽  
Multiple Control ◽  
Amaranthus Hypochondriacus ◽  
Specific Accumulation ◽  
Post Transcriptional Regulation

Post-transcriptional regulation determines initial C4 gene expression patterns in developing leaves of Amaranthus hypochondriacus, an NAD-ME type C4 dicot. RuBPCase, PEPCase, and PPdK mRNAs are abundant in meristems and in leaf primordia, but are utilised only during specific developmental stages. While each enzyme shows independent patterns of initial mRNA and polypeptide accumulation, cell-specific localisation of the polypeptides occurs prior to cell-specific localisation of the mRNAs. In mature three-coloured leaves of A. tricolor, loss of photosynthetic activity correlates with reductions in the transcription rates of some plastid-encoded genes, reduction and loss of coordination in the translation of RuBPCase polypeptides, and loss of cell-specific accumulation of RuBPCase mRNAs (but not the polypeptides). The mitochondrial NAD-dependent malic enzyme (NAD-ME) provides an example of a basic metabolic enzyme that has acquired specialised gene expression patterns allowing it to function in the C4 pathway. NAD-ME occurs preferentially in photosynthetic tissues, and is specific to bundle sheath cells throughout development. NAD-ME synthesis is regulated by light and development at transcriptional and post-transcriptional levels. The findings summarised here indicate that C4 genes are independently regulated by multiple control mechanisms in response to developmental, environmental, and metabolic signals.

scholarly journals Evolution of gene expression across species and specialized zooids in Siphonophora

2021 ◽  
Author(s):  
Catriona Munro ◽  
Felipe Zapata ◽  
Mark Howison ◽  
Stefan Siebert ◽  
Casey W Dunn
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Trees ◽  
Species Trees ◽  
Examine Gene Expression ◽  
Specialized Tissue ◽  
Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

scholarly journals Reference genes for qRT-PCR normalisation in different tissues, developmental stages, and stress conditions of Hypericum perforatum

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7133 ◽  
Author(s):  
Wen Zhou ◽  
Shiqiang Wang ◽  
Lei Yang ◽  
Yan Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Hypericum Perforatum ◽  
Developmental Stages ◽  
Pcr Analysis ◽  
Potential Candidate ◽  
Qrt Pcr ◽  
Expression Studies ◽  
Different Tissues

Hypericum perforatum L. is a widely known medicinal herb used mostly as a remedy for depression because it contains high levels of naphthodianthrones, phloroglucinols, alkaloids, and some other secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is essential for the interpretation of qRT-PCR data. In this study, we investigated the expression of 14 candidate genes, including nine housekeeping genes (HKGs) (ACT2, ACT3, ACT7, CYP1, EF1-α, GAPDH, TUB-α, TUB-β, and UBC2) and five potential candidate genes (GSA, PKS1, PP2A, RPL13, and SAND). Three programs—GeNorm, NormFinder, and BestKeeper—were applied to evaluate the gene expression stability across four different plant tissues, four developmental stages and a set of abiotic stress and hormonal treatments. Integrating all of the algorithms and evaluations revealed that ACT2 and TUB-β were the most stable combination in different developmental stages samples and all of the experimental samples. ACT2, TUB-β, and EF1-α were identified as the three most applicable reference genes in different tissues and stress-treated samples. The majority of the conventional HKGs performed better than the potential reference genes. The obtained results will aid in improving the credibility of the standardization and quantification of transcription levels in future expression studies on H. perforatum.

scholarly journals Chasing the Apomictic Factors in the Ranunculus auricomus Complex: Exploring Gene Expression Patterns in Microdissected Sexual and Apomictic Ovules

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 728 ◽  
Author(s):  
Marco Pellino ◽  
Diego Hojsgaard ◽  
Elvira Hörandl ◽  
Timothy F. Sharbel
Keyword(s):  
Gene Expression ◽  
Asexual Reproduction ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Dominant Factor ◽  
Gene Expression Patterns ◽  
Future Studies ◽  
Dosage Effects ◽  
Differential Gene ◽  
Parent Of Origin

Apomixis, the asexual reproduction via seeds, is associated to polyploidy and hybridization. To identify possible signatures of apomixis, and possible candidate genes underlying the shift from sex to apomixis, microarray-based gene expression patterns of live microdissected ovules at four different developmental stages were compared between apomictic and sexual individuals of the Ranunculus auricomus complex. Following predictions from previous work on mechanisms underlying apomixis penetrance and expressivity in the genus, gene expression patterns were classified into three categories based on their relative expression in apomicts compared to their sexual parental ancestors. We found evidence of misregulation and differential gene expression between apomicts and sexuals, with the highest number of differences detected during meiosis progression and emergence of aposporous initial (AI) cells, a key developmental stage in the ovule of apomicts where a decision between divergent reproductive pathways takes place. While most of the differentially expressed genes (DEGs) could not be annotated, gene expression was classified into transgressive, parent of origin and ploidy effects. Genes related to gametogenesis and meiosis demonstrated patterns reflective of transgressive and genome dosage effects, which support the hypothesis of a dominant factor controlling apomixis in Ranunculus and modulated by secondary modifiers. Three genes with probable functions in sporogenesis and gametogenesis development are identified and characterized for future studies.

scholarly journals Microarray Analysis Reveals Differential Gene Expression Patterns in Tumors of the Pineal Region

2006 ◽  
Vol 65 (7) ◽  
pp. 675-684 ◽  
Author(s):  
Michelle Fèvre-Montange ◽  
Jacques Champier ◽  
Alexandru Szathmari ◽  
Anne Wierinckx ◽  
Carmine Mottolese ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Microarray Analysis ◽  
Expression Patterns ◽  
Pineal Region ◽  
Gene Expression Patterns ◽  
Differential Gene

scholarly journals Deciphering the dynamic gene expression patterns of pollen abortion in a male sterile line of Avena sativa through transcriptome analysis at different developmental stages

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lijun Zhang ◽  
Mingchuan Ma ◽  
Lin Cui ◽  
Longlong Liu
Keyword(s):  
Gene Expression ◽  
Male Sterility ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Hybrid Breeding ◽  
Gene Expression Patterns ◽  
Hybrid Seed Production ◽  
Isogenic Line ◽  
Male Sterile ◽  
Pollen Abortion

Abstract Background Male sterility (MS) has important applications in hybrid seed production, and the abortion of anthers has been observed in many plant species. While most studies have focused on the genetic factors affecting male sterility, the dynamic gene expression patterns of pollen abortion in male sterile lines have not been fully elucidated. In addition, there is still no hybrid oat that is commercially planted due to the lack of a suitable system of male sterility for hybrid breeding. Results In this study, we cultivated a male sterile oat line and a near-isogenic line by crossbreeding to elucidate the expression patterns of genes that may be involved in sterility. The first reported CA male sterile (CAMS) oat line was used for cross-testing and hybridization experiments and was confirmed to exhibit a type of nuclear sterility controlled by recessive genes. Oat stamens of two lines were sampled at four different developmental stages separately. Paired-end RNA sequencing was performed for each sample and generated 252.84 Gb sequences. There were 295,462 unigenes annotated in public databases in all samples, and we compared the histological characteristics and transcriptomes of oat stamens from the two oat lines at different developmental stages. Our results demonstrate that the sterility of the male sterile oat line occurs in the early stage of stamen development and is primarily attributable to abnormal meiosis and the excessive accumulation of superoxide. Conclusions To the best of our knowledge, this study is the first to decipher the dynamic expression profiles of pollen abortion CAMS and CA male fertile (CAMF) oat lines, which may represent a valuable resource for further studies attempting to understand pollen abortion and anther development in oats.

Sign in / Sign up

Export Citation Format

Share Document