Selection and validation of reference genes for quantitative RT-PCR analysis in peach fruit under different experimental conditions

Kou, Xiyi; Zhang, Li; Yang, Shuzhen; Li, Guohuai; Ye, Junli

doi:10.1016/j.scienta.2017.07.004

Cited by 37 publications

(44 citation statements)

References 43 publications

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“…To confirm the RNAseq results qPCR has been selected, highlighting the need of a set of reference genes from endocarp and early fruit developmental stages to help us standardize RNA expression. We identified standard genes from the literature that had been reported for stone [4][5][6][7] and used those to extract the RPM values from our 20 expression libraries representing early plum fruit development and young endocarp tissue. Only a few of these genes appeared to be stably expressed in all the libraries which prompted us to utilize the RNAseq data to generate a specific set of reference genes (Tables 1 and S2).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies on gene expression in peach and plum had used only the 26S rRNA gene as a reference gene [8][9]. Several studies since then presented candidate reference genes for Prunus [4][5][6][7]. The ten primer pairs from Tong et al, [4] were used to BLAST the peach V1.0 version of predicted transcripts.…”

Section: Comparison Of Published Prunus Reference Genes (Ref1-ref13)mentioning

confidence: 99%

“…Expression levels of reference genes REF1 and REF12 were higher in endocarp, while expression levels of REF3, REF4, REF8, REF9 and REF10 were lower in endocarp when compared to whole ovary/fruit. Additional previously described reference genes from plum (Prunus salicina) and peach (Prunus persica) [5][6][7] were also analyzed in a similar fashion. The results of matching reads and nine candidate reference genes from plum early fruit libraries.…”

Section: Comparison Of Published Prunus Reference Genes (Ref1-ref13)mentioning

confidence: 99%

“…It was clear that many of these genes in peach though were not expressed uniformly in all tissues and treatments. Further studies in peach and plum also demonstrated that the expression of these genes varied across tissues and treatments, so additional reference genes were identified [5][6][7]. Kim et al, [5] utilized RNAseq data for Japanese plum (Prunus salicina) flesh, peel and leaf tissues from two different cultivars at two different ripening stages to identify genes.…”

Section: Introductionmentioning

confidence: 99%

“…They concluded that for both room temperature and cold storage CAC, and ACT, and UNK (from Kim et al, [5]), were the optimal combination of reference genes. Similarly, Kou et al, [7] utilized RNAseq data from a peach fruit storage project to select the genes with the lowest CV across different temperature regimes. The overall conclusions of all these studies were that the reference genes are very dependent on the experimental set of RNAs being used.…”

Section: Introductionmentioning

confidence: 99%

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Identification of early fruit development reference genes in plum

et al. 2020

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An RNAseq study of early fruit development and stone development in plum, Prunus domestica, was mined to identify sets of genes that could be used to normalize expression studies in early fruit development. The expression values of genes previously identified from Prunus as reference genes were first extracted and found to vary considerably in endocarp tissue relative to whole fruit tissue. Nine other genes were chosen that varied less than 2fold amongst the 20 RNAseq libraries of early fruit development and endocarp tissues. These gene were tested on a series of developmental plum fruit samples to determine if any could be used as a reference gene in the analyses of fruit-based tissues in plum. The three most stable genes as determined using RefFinder were IPGD (imidazole glycerol-phosphate dehydratase), HAM1 (histone acetyltransferase) and SNX1 (sorting nexin 1). These were further tested to analyze genes expressed differentially in endocarp tissue between normal and minimal endocarp cultivars. To determine the universality of those nine genes as fruit development reference genes, three other data sets of RNAseq from peach and apple were analyzed to determine the reference gene expression. Multiple genes exhibited tissue specific patterns of expression while one gene, the SNX1, emerged as possessing a universal pattern between the Rosaceae species, at all developmental stages, and tissue types tested. The results suggest that the use of existing RNAseq data to identify standard genes can provide stable reference genes for a specific tissues or experimental conditions under exploration.

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Section: Discussionmentioning

confidence: 99%

Section: Comparison Of Published Prunus Reference Genes (Ref1-ref13)mentioning

confidence: 99%

Section: Comparison Of Published Prunus Reference Genes (Ref1-ref13)mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Identification of early fruit development reference genes in plum

et al. 2020

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Selection and validation of reference genes for qRT‐PCR analysis during fruit ripening of red pitaya (Hylocereus polyrhizus)

Zheng

Wang

et al. 2021

FEBS Open Bio

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RNA sequencing analysis was applied to study molecular mechanisms of fruit ripening of red pitaya. The generated stably expressed unigenes are a source of potential reference genes for quantitative real‐time PCR. Herein, the expression stabilities of 12 candidate reference genes were evaluated. Polypyrimidine tract‐binding protein and Chaperone protein dnaJ 49 are suggested as suitable reference genes for quantitative real‐time PCR during red pitaya fruit ripening.

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Selection of suitable reference genes for qRT-PCR analysis of Begonia semperflorens under stress conditions

Wang

et al. 2019

Mol Biol Rep

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Selection and validation of reference genes for quantitative RT-PCR analysis in peach fruit under different experimental conditions

Cited by 37 publications

References 43 publications

Identification of early fruit development reference genes in plum

Identification of early fruit development reference genes in plum

Selection and validation of reference genes for qRT‐PCR analysis during fruit ripening of red pitaya (Hylocereus polyrhizus)

Selection of suitable reference genes for qRT-PCR analysis of Begonia semperflorens under stress conditions

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