Genome-wide identification and validation of optimal reference genes for gene expression normalization in pear peel

Chen, Changmei; Wang, Tengyun; Cai, Zhenmei; Xie, Guifeng; Chen, Zhiyi; Yuan, Yafang; Wang, Wei; Xie, Qian; Guan, Xiayu; Chen, Qing‐Xi

doi:10.1007/s10725-020-00634-z

Cited by 5 publications

(6 citation statements)

References 61 publications

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“…1A), which had relatively stable expression in the developmental stages fruit of three pear cultivars. The value of CV% < 20 was the basic requirement for reference gene [25,27]. Based on the transcript abundance and CV of gene expression, potential reference genes were selected to test, which had FPKM > 40 and CV% < 20.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, accurate and reliable analysis of expression patterns helps to reveal the gene functions and related molecular mechanisms. However, characterization of reference genes in pear has been only reported in limited tissues and cultivars[6, [24][25][26][27][28][29]. Accordingly, identi cation of appropriate reference genes in pear is in demand for obtaining reliable and accurate gene expression analysis data.…”

Section: Introductionmentioning

confidence: 99%

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Identification and testing of reference genes for qRT-PCR analysis during pear fruit development

et al. 2022

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Background: Quantitative real-time PCR (qRT-PCR) is currently one of the most reliable and improved tools for analyzing gene expression. Various studies have shown that housekeeping genes was varied with cultivars, tissues and treatment. The reliable and stable reference genes were necessarily identi ed and evaluated according to different experimental requirements.Result: In this study, 10 candidate reference genes were initially screened based on the transcriptome sequencing data of four pear fruit development stages of three different pear cultivars, including a candidate housekeeping gene PbrTUB. Furthermore, we ranked the expression stability of 10 candidate reference genes using algorithms GeNorm, NormFinder, BestKeeper and ReFinder. Finally, the result showed that Pbr028511, Pbr038418 and Pbr041114 were the most stable reference gene in Cuiguan, Housui and Xueqing fruit, respectively. Concludion: Thee results provide a valuable resource that serve as signi cant reference for gene function explorations and molecular mechanism studies in fruit development and ripening of different pear cultivars.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification and testing of reference genes for qRT-PCR analysis during pear fruit development

et al. 2022

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“…In leaf, SKD1and ARM were the most apropos single reference genes for leave of the 'training_period' and 'training_space', respectively [29]. In pear peel, ACT6/7/8/9 and NAP1 were recommended as the optimal reference genes [27]. Reference genes in pear fruit were studied relatively more, PbPDI.F1 presented the highest expression stability during pear fruit developmental [44], the housekeeping gene EF1α members showed an obviously unstable expression in pear fruits at different developmental stages [28], SOX2 and PP2A showed most highly and stably expression in pear fruit [25], and BPS1 and ICDH1 were the high stable expressed genes [26].…”

Section: Discussionmentioning

confidence: 99%

Identification and Testing of Reference Genes for qRT-PCR Analysis During Pear Fruit Development

Wang

Guo

Wang

et al. 2021

Preprint

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Background: Quantitative real-time PCR (qRT-PCR) is currently one of the most reliable and improved tools for analyzing gene expression. Various studies have shown that housekeeping genes was varied with cultivars, tissues and treatment. The reliable and stable reference genes were necessarily identified and evaluated according to different experimental requirements. Result: In this study, 10 candidate reference genes were initially screened based on the transcriptome sequencing data of four pear fruit development stages of three different pear cultivars, including a candidate housekeeping gene PbrTUB. Furthermore, we ranked the expression stability of 10 candidate reference genes using algorithms GeNorm, NormFinder, BestKeeper and ReFinder. Finally, the result showed that Pbr028511, Pbr038418 and Pbr041114 were the most stable reference gene in Cuiguan, Housui and Xueqing fruit, respectively. Concludion: Thee results provide a valuable resource that serve as significant reference for gene function explorations and molecular mechanism studies in fruit development and ripening of different pear cultivars.

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“…Over the past few years, an increasing number of studies have shown that the traditional housekeeping gene could not work as stable normalization factors. Meanwhile, the selection of reference genes at the transcriptome level has found many novel genes which can be expressed stably, such as with apple (Storch et al, 2015), pineapple sexual organs (Jin et al, 2020), pear peel (Chen et al, 2020), and papaya (Zhu et al, 2012). Jin et al (2020) revealed novel identified genes CCR and RPS4 behave better than the traditional housekeeping genes in pineapple ovule and stamen normalization.…”

Section: Introductionmentioning

confidence: 99%

“…Jin et al (2020) revealed novel identified genes CCR and RPS4 behave better than the traditional housekeeping genes in pineapple ovule and stamen normalization. Chen et al (2020) identified a novel gene named NAP1 (Nucleosome Assembly Protein 1) that performed better in pear peel. Taken together, genome-wide identification work could provide new candidate reference genes and avoid the inappropriate selection of internal reference genes.…”

Section: Introductionmentioning

confidence: 99%

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

Yan

Jin

Liu

et al. 2021

PeerJ

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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.

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Genome-wide identification and validation of optimal reference genes for gene expression normalization in pear peel

Cited by 5 publications

References 61 publications

Identification and testing of reference genes for qRT-PCR analysis during pear fruit development

Identification and testing of reference genes for qRT-PCR analysis during pear fruit development

Identification and Testing of Reference Genes for qRT-PCR Analysis During Pear Fruit Development

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

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