scholarly journals Identification and evaluation of the novel genes for transcript normalization during female gametophyte development in sugarcane

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12298
Author(s):  
Maokai Yan ◽  
Xingyue Jin ◽  
Yanhui Liu ◽  
Huihuang Chen ◽  
Tao Ye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sexual Reproduction ◽  
Reference Genes ◽  
Female Gametophyte ◽  
Developmental Stages ◽  
Reproductive Organs ◽  
The Novel ◽  
Biofuel Feedstock ◽  
Gametophyte Development ◽  
Female Gametophyte Development

Background Sugarcane (Saccharum spontaneum L.), the major sugar and biofuel feedstock crop, is cultivated mainly by vegetative propagation worldwide due to the infertility of female reproductive organs resulting in the reduction of quality and output of sugar. Deciphering the gene expression profile during ovule development will improve our understanding of the complications underlying sexual reproduction in sugarcane. Optimal reference genes are essential for elucidating the expression pattern of a given gene by quantitative real-time PCR (qRT-PCR). Method In this study, based on transcriptome data obtained from sugarcane ovule, eighteen candidate reference genes were identified, cloned, and their expression levels were evaluated across five developmental stages ovule (AC, MMC, Meiosis, Mitosis, and Mature). Results Our results indicated that FAB2 and MOR1 were the most stably expressed genes during sugarcane female gametophyte development. Moreover, two genes, cell cycle-related genes REC8 and CDK, were selected, and their feasibility was validated. This study provides important insights into the female gametophyte development of sugarcane and reports novel reference genes for gene expression research on sugarcane sexual reproduction.

scholarly journals Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 909
Author(s):  
Anyela Valentina Camargo Rodriguez
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Computational Modelling ◽  
Plant Morphology ◽  
Reproductive Organs ◽  
Biological Trait ◽  
Cereal Grain ◽  
Plant Level

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Pollination triggers female gametophyte development in immature Nicotiana tabacum flowers

2015 ◽  
Vol 6 ◽  
Author(s):  
Michael S. Brito ◽  
Lígia T. Bertolino ◽  
Viviane Cossalter ◽  
Andréa C. Quiapim ◽  
Henrique C. DePaoli ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Female Gametophyte ◽  
Gametophyte Development ◽  
Female Gametophyte Development

scholarly journals Maternal Control of PIN1 Is Required for Female Gametophyte Development in Arabidopsis

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66148 ◽  
Author(s):  
Luca Ceccato ◽  
Simona Masiero ◽  
Dola Sinha Roy ◽  
Stefano Bencivenga ◽  
Irma Roig-Villanova ◽  
...  
Keyword(s):  
Female Gametophyte ◽  
Maternal Control ◽  
Gametophyte Development ◽  
Female Gametophyte Development

scholarly journals Selecting and validating reference genes for quantitative real-time PCR in Plutella xylostella (L.)

Genome ◽  
2018 ◽  
Vol 61 (5) ◽  
pp. 349-358 ◽  
Author(s):  
Yanchun You ◽  
Miao Xie ◽  
Liette Vasseur ◽  
Minsheng You
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Plutella Xylostella ◽  
Real Time Pcr ◽  
Reference Genes ◽  
Developmental Stages ◽  
Quantitative Real Time Pcr ◽  
Experimental Conditions ◽  
Expression Studies ◽  
Gene Expression Studies

Gene expression analysis provides important clues regarding gene functions, and quantitative real-time PCR (qRT-PCR) is a widely used method in gene expression studies. Reference genes are essential for normalizing and accurately assessing gene expression. In the present study, 16 candidate reference genes (ACTB, CyPA, EF1-α, GAPDH, HSP90, NDPk, RPL13a, RPL18, RPL19, RPL32, RPL4, RPL8, RPS13, RPS4, α-TUB, and β-TUB) from Plutella xylostella were selected to evaluate gene expression stability across different experimental conditions using five statistical algorithms (geNorm, NormFinder, Delta Ct, BestKeeper, and RefFinder). The results suggest that different reference genes or combinations of reference genes are suitable for normalization in gene expression studies of P. xylostella according to the different developmental stages, strains, tissues, and insecticide treatments. Based on the given experimental sets, the most stable reference genes were RPS4 across different developmental stages, RPL8 across different strains and tissues, and EF1-α across different insecticide treatments. A comprehensive and systematic assessment of potential reference genes for gene expression normalization is essential for post-genomic functional research in P. xylostella, a notorious pest with worldwide distribution and a high capacity to adapt and develop resistance to insecticides.

scholarly journals Selection and validation of reference genes for quantitative gene expression analyses in persimmon (Diospyros kaki Thunb.) using real-time quantitative PCR

2019 ◽  
Vol 70 (4) ◽  
pp. 261-267
Author(s):  
Gaigai Du ◽  
Liyuan Wang ◽  
Huawei Li ◽  
Peng Sun ◽  
Jianmin Fu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Reference Gene ◽  
Reference Genes ◽  
Developmental Stages ◽  
Suitable Reference Gene ◽  
Diospyros Kaki ◽  
Stable Gene ◽  
Expression Studies ◽  
Gene Expression Studies

Background and aims Persimmon (Diospyros kaki) is an economically important fruit tree species with complex flowering characteristics. To obtain accurate expression pattern analysis results, it is vital to select a reliable gene for the normalization of real-time quantitative polymerase chain reaction data. The aim of this study was to identify the optimal internal control gene among six candidate genes for gene expression analysis in different persimmon organs and developmental stages. Materials and methods This analysis was conducted using geNorm and NormFinder software to show differences in the stability of the six reference genes among tissues and floral developmental stages of the same plant. Results Although genes that exhibited moderate expression in NormFinder revealed slightly different expression stabilities than those obtained by geNorm, both sets of results showed that GAPDH was the best reference gene in different organs and floral buds at different developmental stages, whereas 18SrRNA was the least stable gene. Conclusions Based on the overall ranking, GAPDH is the most suitable reference gene and is highly recommended for gene expression studies in different organs and different developmental stages of persimmon. This study provides useful reference data for future gene expression studies and will contribute to improving the accuracy of gene expression results in persimmon.

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