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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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Peng S, Ali Sabir I, Hu X, Chen J, Qin Y. Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review. Int J Mol Sci 2024; 25:1142. [PMID: 38256212 PMCID: PMC10816256 DOI: 10.3390/ijms25021142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Real-time quantitative polymerase chain reaction (qRT-PCR) has been widely used in gene expression analyses due to its advantages of sensitivity, accuracy and high throughput. The stability of internal reference genes has progressively emerged as a major factor affecting the precision of qRT-PCR results. However, the stability of the expression of the reference genes needs to be determined further in different cells or organs, physiological and experimental conditions. Methods for evaluating these candidate internal reference genes have also evolved from simple single software evaluation to more reliable and accurate internal reference gene evaluation by combining different software tools in a comprehensive analysis. This study intends to provide a definitive reference for upcoming research that will be conducted on fruit trees. The primary focus of this review is to summarize the research progress in recent years regarding the selection and stability analysis of candidate reference genes for different fruit trees.
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Affiliation(s)
- Shujun Peng
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Irfan Ali Sabir
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Xinglong Hu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Jiayi Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Yonghua Qin
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
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Yao J, Zhu G, Liang D, He B, Wang Y, Cai Y, Zhang Q. Reference Gene Selection for qPCR Analysis in Schima superba under Abiotic Stress. Genes (Basel) 2022; 13:genes13101887. [PMID: 36292772 PMCID: PMC9601953 DOI: 10.3390/genes13101887] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Quantitative real-time PCR (qPCR) is an indispensable technique for gene expression analysis in modern molecular biology. The selection and evaluation of suitable reference genes is a prerequisite for accurate gene expression analysis. Schimasuperba is a valuable tree species that is environmentally adaptable and highly fire-resistant. In this study, 12 candidate reference genes were selected to check their stability of gene expression in different tissues under abiotic stresses: cold stress, salt stress, and drought stress by ΔCt, geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that AP-2 was the most stably expressed overall and for the cold stress and drought stress. eIF-5α gene expression was the most stable under the salt stress treatment, while UBQ expression was the most stable across mature leaves, shoots, stems, and roots. In contrast, UBC20, GAPDH, and TUB were the least stably expressed genes tested. This study delivers valid reference genes in S. superba under the different experimental conditions, providing an important resource for the subsequent elucidation of the abiotic stress adaptation mechanisms and genes with biological importance.
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Affiliation(s)
- Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Gang Zhu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dongcheng Liang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yingli Wang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Silviculture Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
- Correspondence: ; Tel.: +86-020-87033420
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Identification of Suitable Reference Genes for qRT-PCR Normalization in Kiwifruit. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reference genes are used for the correction of qRT-PCR data, and it is necessary to investigate the optimum reference gene under certain conditions. The expression levels of seven traditional reference genes ACT1, ACT2, GAPDH, 18S rRNA, UBQ, TUB and CYP were analyzed using qRT-PCR in different varieties, tissues, developmental stages and hormone (or pollen polysaccharide) treatments in kiwifruit. Gene expression stability was assessed with the help of three common software (geNorm, NormFinder, BestKeeper), and the minimum number of reference genes necessary for normalization was also determined. GAPDH, ACT1 and ACT2 were selected as reference genes for different genotypes of kiwifruit. GAPDH and UBQ were the best combinations of reference genes for root, stem, leaf, flower and fruit. GAPDH and ACT1 could be the preferred reference genes for normalization of qRT-PCR data during fruit development. The pairing of ACT1 and UBQ constituted the optimal combination of reference genes in kiwifruit treated with different hormones (or pollen polysaccharide). This study provides a new and reliable option for the use of reference genes in the analysis of gene expression patterns of interest in kiwifruit.
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