Selection and validation of reference genes for quantitative real-time PCR in Artemisia sphaerocephala based on transcriptome sequence data

Selection and validation of appropriate reference genes for RT-qPCR analysis of Nitraria sibirica under various abiotic stresses

BACKGROUND

Nitraria sibirica Pall. is a halophytic shrub with strong environmental adaptability that can survive in extremely saline-alkali and drought-impacted environments. Gene expression analysis aids in the exploration of the molecular mechanisms of plant responses to abiotic stresses. RT-qPCR is the most common technique for studying gene expression. Stable reference genes are a prerequisite for obtaining accurate target gene expression results in RT-qPCR analysis.

RESULTS

In this study, a total of 10 candidate reference genes were selected from the transcriptome of N. sibirica, and their expression stability in leaves and roots under different treatment conditions (salt, alkali, drought, cold, heat and ABA) was evaluated with the geNorm, NormFinder, BestKeeper, comparative ΔCt and RefFinder programs. The results showed that the expression stability of the candidate reference genes was dependent on the tissue and experimental conditions tested. ACT7 combined with R3H, GAPDH, TUB or His were the most stable reference genes in the salt- or alkali-treated leaves, salt-treated roots and drought-treated roots, respectively; R3H and GAPDH were the most suitable combination for drought-treated leaves, heat-treated root samples and ABA-treated leaves; DIM1 and His maintained stable expression in roots under alkali stress; and TUB combined with R3H was stable in ABA-treated roots. TBCB and GAPDH exhibited stable expression in heat-treated leaves; TBCB, R3H, and ERF3A were stable in cold-treated leaves; and the three most stable reference genes for cold-treated roots were TBCB, ACT11 and DIM1. The reliability of the selected reference genes was further confirmed by evaluating the expression patterns of the NsP5CS gene under the six treatment conditions.

CONCLUSION

This study provides a theoretical reference for N. sibirica gene expression standardization and quantification under various abiotic stress conditions and will help to reveal the molecular mechanisms that confer stress tolerance to N. sibirica.

Expression of potential reference genes in response to macronutrient stress in rice and soybean

Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.

Transcriptomic Analysis Reveals Key Genes Involved in Oil and Linoleic Acid Biosynthesis during Artemisia sphaerocephala Seed Development

Artemisia sphaerocephala seeds are rich in polysaccharides and linoleic acid (C18:2), which have been widely used as traditional medicine and to improve food quality. The accumulation patterns and molecular regulatory mechanisms of polysaccharides during A. sphaerocephala seed development have been studied. However, the related research on seed oil and C18:2 remain unclear. For this study, A. sphaerocephala seeds at seven different development stages at 10, 20, 30, 40, 50, 60, and 70 days after flowering (designated as S1~S7), respectively, were employed as experimental samples, the accumulation patterns of oil and fatty acids (FA) and the underlying molecular regulatory mechanisms were analyzed. The results revealed that oil content increased from 10.1% to 20.0% in the early stages of seed development (S1~S2), and up to 32.0% in mature seeds, of which C18:2 accounted for 80.6% of the total FA. FA and triacylglycerol biosynthesis-related genes jointly involved in the rapid accumulation of oil in S1~S2. Weighted gene co-expression network analysis showed that transcription factors FUS3 and bHLH played a critical role in the seed oil biosynthesis. The perfect harmonization of the high expression of FAD2 with the extremely low expression of FAD3 regulated the accumulation of C18:2. This study uncovered the gene involved in oil biosynthesis and molecular regulatory mechanisms of high C18:2 accumulation in A. sphaerocephala seeds; thus, advancing research into unsaturated fatty acid metabolism in plants while generating valuable genetic resources for optimal C18:2 breeding.

Identification of Ginger (Zingiber officinale Roscoe) Reference Genes for Gene Expression Analysis

Quantitative real-time PCR (qRT-PCR) is widely used in the detection of gene expression level. However, there is no suitable ginger reference gene for qPCR analysis. Therefore, it is the primary task to select and validate the appropriate ginger reference gene to normalize the expression of target genes. In this study, 14 candidate reference genes were selected and analyzed in different tissues (leaf, and rhizome), different development stages, different varieties, and abiotic stress (ABA and salt stress). Expression stability was calculated using geNorm and NormFinder, Bestkeeper, and RefFinder. For abiotic stress and total conditions, 28S and COX were identified as the most stable genes. In addition, RPII was the most stable in the different development stages and different varieties. TEF2 and RPL2 were the least stably expressed in the tissue and all the conditions. In order to verify the feasibility of these genes as reference genes, we used the most stable and least stable reference genes to normalize the expression levels of ZoSPS genes under different conditions. This work can provide theoretical support for future research on ginger gene expression.

Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus)

BACKGROUND

In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat (Capra hircus) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology.

RESULTS

Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3 + SDHA + PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released.

CONCLUSION

This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3 + SDHA + PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

Identification and evaluation of reference genes for quantitative real-time PCR analysis in Passiflora edulis under stem rot condition

Passion fruit (Passiflora edulis), an important tropical and subtropical fruit, has a high edible and medicinal value. Stem rot disease is one of the most important diseases of passion fruit. An effective way for control and prevention of this disease is to identify the genes associated with resistance to this disease. Quantitative real-time PCR (RT-qPCR) has mainly been widely applied to detect gene expression because of its simplicity, fastness, low cost and high sensitivity. One of the requirements for RT-qPCR is the availability of suitable reference genes for normalization of gene expression. However, currently, no Passiflora edulis reference genes have been identified andthus it has hindered the gene expression studies in this plant. The present study aimed to address this issue. We analyzed sixteen candidate reference genes, including nine common (GAPDH, UBQ, ACT1, ACT2, EF-1α-1, EF-1α-2, TUA, NADP, and GBP) and seven novel genes (C13615, C24590, C27182, C10445, C21209, C22199, and C22526), in different tissues (stem, leaf, flower and fruit) of two accessions under stem rot condition. We calculated the expression stability in twenty-four samples using the ΔCt, GeNorm, NormFinder, BestKeeper and RefFinder. The results showed that both C21209 and EF-1α-2 were sufficient to normalize gene expression under stem rot, whereas the commonly used reference genes, GAPDH and UBQ, were the least stable ones. The expression patterns of PeUFC under stem rot condition normalized by stable and unstable reference genes indicated the suitability of using the optimal reference genes. To our knowledge, this is the first systematic study of reference genes in Passiflora edulis, which identified a number of reliable reference genes suitable for gene expression studies in Passiflora edulis by RT-qPCR.

Selection and validation of reference genes of Paeonia lactiflora in growth development and light stress

The stem of Paeonia lactiflora will bend when it grows in greenhouse at a low light intensity. It is important to explore causes of morphological changes of peony to improve its quality. Gene expression can be evaluated by quantitative real-time PCR, based on reference gene. However, systematic selection of reference genes under weak lighting for herbaceous peony is lacking. To address this problem, we first selected 10 candidate reference genes based on a coefficient of variation of gene expression from peony stem transcriptome data. Then, geNorm, NormFinder and BestKeeper were applied to assess the stability of the genes, and RankAggreg was used to give a comprehensive ranking. The results show that there are some differences in optimal reference genes among samples from different organs and under the two lighting conditions, and the optimal number of suitable reference genes is distinct. Two selected suitable reference genes were then used to normalize target genes, and the results were compared with transcriptome data. Consistent gene expression trends were obtained, indicating the reliability of the method. To the best of our knowledge, this is the first time reference genes for herbaceous peony were selected in different organs, developmental stages and under two kinds of lighting conditions. The findings can provide a practical method for selecting reference genes for peony under these conditions and demonstrate a useful combination of reference genes.

[Rapid preimplantation genetic diagnosis of α-thalassemia SEA deletion with blastocyst cell whole genome amplification and short fragment Gap-PCR method]

OBJECTIVE

To develop a rapid preimplantation genetic diagnosis method for α-thalassemia SEA deletion based on blastocyst cell whole genome amplification (WGA) combined with short fragment Gap-PCR.

METHODS

Using multiple displacement amplification (MDA) WGA technique, we established a double-fluorescent PCR system of the housekeeping genes GAPDH and β-actin for WGA quality testing, and a genotyping PCR system of mutant and normal short sequences for α-thalassemia SEA deletion. The sensitivity and accuracy of this method for diagnosis of α-thalassemia SEA deletion were evaluated by detecting lymphocyte samples containing different cell numbers from carriers of SEA deletion. The applicability of this method was evaluated by testing of 12 blastocyst biopsy samples.

RESULTS

Detection of lymphocyte samples with different cell numbers using the method developed in this study revealed no ADO in 3-cell samples, and the product quantity of WGA became stable for 4-cell samples. Genotyping of the 10 blastocyst biopsy samples with successful WGA showed a genotype of --^SEA/αα in 5 samples and αα/αα in the other 5 samples, which were consistent with the verification results.

CONCLUSIONS

The method developed in this study is a complete testing process for 4-6 blastocyst biopsy cells to allow rapid, accurate, and cost-effective PGD genotyping of α-thalassemia SEA deletion using short fragment gap-PCR.