Determination of Suitable Candidate Genes as Endogenous Control for Gene Expression Analysis in Local Capsicum Annuum MC11

2021 ◽  
Vol 12 (3) ◽  
pp. 1011-1017
Author(s):  
Marina Mokhtar Et.al
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Capsicum Annuum ◽  
Reference Genes ◽  
Data Normalization ◽  
Plant Parts ◽  
Qrt Pcr ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Suitable Reference

Quantitative real-time polymerase chain reaction (qRT-PCR) is one of the most common methods for gene expression studies. Data normalization based on reference genes is essential for qRT-PCR assays. This study identifies suitable reference genes for local chilli, Capsicum annuum var MC11 under incident of Cucumber mosaic virus infection. Six candidate genes actin, tub, EF1α, GAPDH, TEF1α and 18SrRNA and three validated Capsicum reference genes UBI-3 ref, β-tub ref and gapdhref were tested against five chilli plant parts stem, shoot, leave, flower and root.  The PCR/qRT-PCR results demonstrate only five candidate references genes actin, EF1α, GAPDH, 18SrRNA, and TEF1α that show specific single band of amplicon, without primer dimers and at the targeted sizes. Through qRT-PCR, GAPDH gives single peak in dissociation curve in all plant parts used further fulfilling the characteristic of reference genes.Previous work on validation of reference genes in pepper shows that only UBI-3 suits to C. annuum var MC11 infected CMV, thus we suggest that GAPDH has a potential to be a validated reference gene for C. annuum var MC11 and can be used together UBI-3 for the purpose of data normalization. 

scholarly journals Identification of Suitable Reference Genes for gene Expression Studies by qRT-PCR in the Blister BeetleMylabris cichorii

2014 ◽  
Vol 14 (94) ◽  
pp. 1-10 ◽  
Author(s):  
Yu Wang ◽  
Zhong-Kang Wang ◽  
Yi Huang ◽  
Yu-Feng Liao ◽  
You-Ping Yin
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Qrt Pcr ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Suitable Reference

scholarly journals Identification and Validation of Reference Genes for qRT-PCR Studies of Gene Expression inDioscorea opposita

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xiting Zhao ◽  
Xiaoli Zhang ◽  
Xiaobo Guo ◽  
Shujie Li ◽  
Linlin Han ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Developmental Stages ◽  
Chain Reaction ◽  
Qrt Pcr ◽  
Expression Studies ◽  
Tuber Crop ◽  
Polymerase Chain ◽  
Gene Expression Studies ◽  
Suitable Reference

Quantitative real-time polymerase chain reaction (qRT-PCR) is one of the most common methods for gene expression studies. Data normalization based on reference genes is essential for obtaining reliable results for qRT-PCR assays. This study evaluated potential reference genes of Chinese yam (Dioscorea oppositaThunb.), which is an important tuber crop and medicinal plant in East Asia. The expression of ten candidate reference genes across 20 samples from different organs and development stages was assessed. We identified the most stable genes for qRT-PCR studies using combined samples from different organs. Our results also suggest that different suitable reference genes or combinations of reference genes for normalization should be applied according to different organs and developmental stages. To validate the suitability of the reference genes, we evaluated the relative expression ofPE2.1andPE53, which are two genes that may be associated with microtuber formation. Our results provide the foundation for reference gene(s) selection inD. oppositaand will contribute toward more accurate gene analysis studies of the genusDioscorea.

scholarly journals Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa

2020 ◽  
Author(s):  
Nathaly Maldonado-Taipe ◽  
Dilan Sarange ◽  
Sandra Schmöckel ◽  
Christian Jung ◽  
Nazgol Emrani
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Expression Patterns ◽  
Data Normalization ◽  
Potential Candidate ◽  
Polypyrimidine Tract Binding Protein ◽  
Expression Studies ◽  
Diurnal Expression ◽  
Gene Expression Studies

AbstractQuinoa depicts high nutritional quality and abiotic stress resistance attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns, and that our novel approach overcomes failures related to stability-based selection of reference genes. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.

scholarly journals Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0233821
Author(s):  
Nathaly Maldonado-Taipe ◽  
Dilan S. R. Patirange ◽  
Sandra M. Schmöckel ◽  
Christian Jung ◽  
Nazgol Emrani
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Expression Patterns ◽  
Data Normalization ◽  
Potential Candidate ◽  
Polypyrimidine Tract Binding Protein ◽  
Expression Studies ◽  
Diurnal Expression ◽  
Gene Expression Studies

Quinoa depicts high nutritional quality and abiotic stress resistance, attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. Moreover, we validated our reference genes by normalizing two known diurnally regulated genes, BTC1 and BBX19. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.

scholarly journals In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

2007 ◽  
Vol 8 (1) ◽  
pp. 47 ◽  
Author(s):  
Monika Jung ◽  
Azizbek Ramankulov ◽  
Jan Roigas ◽  
Manfred Johannsen ◽  
Martin Ringsdorf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Real Time Pcr ◽  
Renal Cell ◽  
Reference Genes ◽  
Human Renal Cell Carcinoma ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Suitable Reference
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