Development of Reference Genes for Horticultural Plants

Ahmed, Umair; Xie, Qi; Shi, Xueping; Zheng, Bo

doi:10.1080/07352689.2022.2084227

Cited by 4 publications

(3 citation statements)

References 151 publications

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“…Selection of internal reference genes with stable expression levels is the key to accurately analyzing the target gene expression [30]. The screening of the internal reference genes in combination with the plant transcriptome database is one of the most effective methods for the research in nonmodel plants [31]. It has been applied in various plants such as Malpighia emarginata [32], Sinocalycanthus chinensisb [33], and Oryza sativab [34].…”

Section: Discussionmentioning

confidence: 99%

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO4 Treatments in Broussonetia papyrifera

Chen,

Wang,

Hao

et al. 2023

IJMS

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Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO4 treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera.

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Section: Discussionmentioning

confidence: 99%

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO4 Treatments in Broussonetia papyrifera

Chen,

Wang,

Hao

et al. 2023

IJMS

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“…Such understanding can lead to the identification of key molecular mechanisms and regulatory networks in plants, which can significantly influence horticultural practices and crop improvement strategies. Overall, transcriptomics serves as an essential bridge between the genome and the phenotype, contributing significantly to the elucidation of the functional elements of the genome and their roles in horticulture [74][75][76].…”

Section: Overview Of Genomics Transcriptomics Proteomics and Metabolo...mentioning

confidence: 99%

An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture

Cembrowska-Lech,

Krzemińska,

Miller

et al. 2023

Biology

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This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.

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“…RGs are widely used in molecular biology research, such as RT-qPCR, ribonuclease protection assay (RPA), northern blotting, gene chips, Western blotting, etc. [ 3 , 4 , 5 ]. The stability of RGs affects the evaluation of gene expression levels and the accuracy of quantitative analysis [ 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum

Zhang

Zhou

et al. 2022

Genes

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Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.

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Development of Reference Genes for Horticultural Plants

Cited by 4 publications

References 151 publications

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO4 Treatments in Broussonetia papyrifera

Screening and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR under PEG, NaCl and ZnSO4 Treatments in Broussonetia papyrifera

An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture

Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum

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