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Ni Y, Zhang Q, Li W, Cao L, Feng R, Zhao Z, Zhao X. Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens. Fungal Biol 2024; 128:1596-1606. [PMID: 38341265 DOI: 10.1016/j.funbio.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024]
Abstract
Floccularia luteovirens is one of the rare edible fungi with high nutritional value found on the Qinghai-Tibet Plateau. However, research at the molecular level on this species is currently constrained due to the lack of reliable reference genes for this species. Thirteen potential reference genes (ACT, GAPDH, EF-Tu, SAMDC, UBI, CLN1, β-TUB, γ-TUB, GTP, H3, UBC, UBC-E2, and GTPBP1) were chosen for the present study, and their expression under various abiotic conditions was investigated. Stability of gene expression was tested using GeNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder. The results showed that the most suitable reference genes for salt treatment were ACT and EF-Tu. Under drought stress, γ-TUB and UBC-E2 would be suitable for normalization. Under oxidative stress, the reference genes H3 and GAPDH worked well. Under heat stress, the reference genes EF-Tu and γ-TUB were suggested. Under extreme pH stress, UBC-E2 and H3 were appropriate reference genes. Under cadmium stress, the reference genes ACT and UBC-E2 functioned well. In different tissues, H3 and GTPBP1 were appropriate reference genes. The optimal internal reference genes when analyzing all samples were H3 and SAMDC. The expression level of HSP90 was studied to further validate the applicability of the genes identified in this study.
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Affiliation(s)
- Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Luping Cao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Zhiqiang Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Xu Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, 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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Su W, Zhu C, Fan Z, Huang M, Lin H, Chen X, Deng C, Chen Y, Kou Y, Tong Z, Zhang Y, Xu C, Zheng S, Jiang J. Comprehensive metabolome and transcriptome analyses demonstrate divergent anthocyanin and carotenoid accumulation in fruits of wild and cultivated loquats. FRONTIERS IN PLANT SCIENCE 2023; 14:1285456. [PMID: 37900735 PMCID: PMC10611460 DOI: 10.3389/fpls.2023.1285456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
Eriobotrya is an evergreen fruit tree native to South-West China and adjacent countries. There are more than 26 loquat species known in this genus, while E. japonica is the only species yet domesticated to produce fresh fruits from late spring to early summer. Fruits of cultivated loquat are usually orange colored, in contrast to the red color of fruits of wild E. henryi (EH). However, the mechanisms of fruit pigment formation during loquat evolution are yet to be elucidated. To understand these, targeted carotenoid and anthocyanin metabolomics as well as transcriptomics analyses were carried out in this study. The results showed that β-carotene, violaxanthin palmitate and rubixanthin laurate, totally accounted for over 60% of the colored carotenoids, were the major carotenoids in peel of the orange colored 'Jiefangzhong' (JFZ) fruits. Total carotenoids content in JFZ is about 10 times to that of EH, and the expression levels of PSY, ZDS and ZEP in JFZ were 10.69 to 23.26 folds to that in EH at ripen stage. Cyanidin-3-O-galactoside and pelargonidin-3-O-galactoside were the predominant anthocyanins enriched in EH peel. On the contrary, both of them were almost undetectable in JFZ, and the transcript levels of F3H, F3'H, ANS, CHS and CHI in EH were 4.39 to 73.12 folds higher than that in JFZ during fruit pigmentation. In summary, abundant carotenoid deposition in JFZ peel is well correlated with the strong expression of PSY, ZDS and ZEP, while the accumulation of anthocyanin metabolites in EH peel is tightly associated with the notably upregulated expressions of F3H, F3'H, ANS, CHS and CHI. This study was the first to demonstrate the metabolic background of how fruit pigmentations evolved from wild to cultivated loquat species, and provided gene targets for further breeding of more colorful loquat fruits via manipulation of carotenoids and anthocyanin biosynthesis.
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Affiliation(s)
- Wenbing Su
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Changqing Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/State Agriculture Ministry Laboratory of Horticultural Plant Crop Growth and Development, Zhejiang University, Hangzhou, China
| | - Zhongqi Fan
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mingkun Huang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Han Lin
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Xiuping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Chaojun Deng
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Yongping Chen
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Yidan Kou
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Zhihong Tong
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yaling Zhang
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Changjie Xu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology/State Agriculture Ministry Laboratory of Horticultural Plant Crop Growth and Development, Zhejiang University, Hangzhou, China
| | - Shaoquan Zheng
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Jimou Jiang
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou, China
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Liu Y, Zhou J, Qiu Z, Hu P, Chen X, Yang Z. Identification and Validation of Reference Genes for Expression Analysis Using RT-qPCR in Leptocybe invasa Fisher and La Salle (Hymenoptera: Eulophidae). INSECTS 2023; 14:insects14050456. [PMID: 37233084 DOI: 10.3390/insects14050456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Leptocybe invasa (Hymenoptera: Eulophidae) is a globally intrusive pest. Despite extensive research into the physiological responses of this pest, our understanding of the molecular mechanisms still needs to be improved. We want to accurately investigate the expression of L. invasa's target genes, so it is imperative to select fitting reference genes. In this study, eight housekeeping genes' stability (RPS30, ACTR, 18S rRNA, ACT, RPL18, GAPDH, 28S rRNA, and TUB) was tested under five different experimental conditions, including male or female adults, somites (head, thorax, and abdomen), temperatures (0 °C, 25 °C, and 40 °C), diets (starvation, clear water, 10% honey water, Eucalyptus sap), and pesticides (acetone was used as a control, imidacloprid, monosultap). Gene stability was calculated using RefFinder, which integrates four algorithms (the ∆Ct method, geNorm, NormFinder, and BestKeeper). The findings implied that ACT and ACTR were the most accurate when comparing sexes. For analyzing different somites, 28S rRNA and RPL18 were ideal; the 28S rRNA and RRS30 were perfect for analyzing at different temperatures. The combination of ACT and GAPDH helped to analyze gene expression in different diets, and GAPDH and 28S rRNA were suitable for various pesticide conditions. Overall, this research offers a complete list of reference genes from L. invasa for precise analysis of target gene expression, which can improve the trustworthiness of RT-qPCR and lay the foundation for further investigations into the gene function of this pest.
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Affiliation(s)
- Ya Liu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Jing Zhou
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhisong Qiu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Ping Hu
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
| | - Xiao Chen
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhende Yang
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
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Hu A, Yang X, Zhu J, Wang X, Liu J, Wang J, Wu H, Zhang H, Zhang H. Selection and validation of appropriate reference genes for RT-qPCR analysis of Nitraria sibirica under various abiotic stresses. BMC PLANT BIOLOGY 2022; 22:592. [PMID: 36526980 PMCID: PMC9758788 DOI: 10.1186/s12870-022-03988-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
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.
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Affiliation(s)
- Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, 063299, Tangshan, China
- Hebei saline-alkali Land Greening Technology Innovation Center, 063299, Tangshan, China
| | - Jiaxin Liu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Jiping Wang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China
| | - Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, 10091, Beijing, China.
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, 257000, Dongying, China.
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Peng Z, Li W, Gan X, Zhao C, Paudel D, Su W, Lv J, Lin S, Liu Z, Yang X. Genome-Wide Analysis of SAUR Gene Family Identifies a Candidate Associated with Fruit Size in Loquat ( Eriobotrya japonica Lindl.). Int J Mol Sci 2022; 23:13271. [PMID: 36362065 PMCID: PMC9659022 DOI: 10.3390/ijms232113271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 09/28/2023] Open
Abstract
Fruit size is an important fruit quality trait that influences the production and commodity values of loquats (Eriobotrya japonica Lindl.). The Small Auxin Upregulated RNA (SAUR) gene family has proven to play a vital role in the fruit development of many plant species. However, it has not been comprehensively studied in a genome-wide manner in loquats, and its role in regulating fruit size remains unknown. In this study, we identified 95 EjSAUR genes in the loquat genome. Tandem duplication and segmental duplication contributed to the expansion of this gene family in loquats. Phylogenetic analysis grouped the SAURs from Arabidopsis, rice, and loquat into nine clusters. By analyzing the transcriptome profiles in different tissues and at different fruit developmental stages and comparing two sister lines with contrasting fruit sizes, as well as by functional predictions, a candidate gene (EjSAUR22) highly expressed in expanding fruits was selected for further functional investigation. A combination of Indoleacetic acid (IAA) treatment and virus-induced gene silencing revealed that EjSAUR22 was not only responsive to auxin, but also played a role in regulating cell size and fruit expansion. The findings from our study provide a solid foundation for understanding the molecular mechanisms controlling fruit size in loquats, and also provide potential targets for manipulation of fruit size to accelerate loquat breeding.
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Affiliation(s)
- Ze Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wenxiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Gan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Chongbin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Dev Paudel
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL 33598, USA
| | - Wenbing Su
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Juan Lv
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zongli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Su W, Shao Z, Wang M, Gan X, Yang X, Lin S. EjBZR1 represses fruit enlargement by binding to the EjCYP90 promoter in loquat. HORTICULTURE RESEARCH 2021; 8:152. [PMID: 34193858 PMCID: PMC8245498 DOI: 10.1038/s41438-021-00586-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 05/21/2023]
Abstract
Loquat (Eriobotrya japonica) is a subtropical tree that bears fruit that ripens during late spring. Fruit size is one of the dominant factors inhibiting the large-scale production of this fruit crop. To date, little is known about fruit size regulation. In this study, we first discovered that cell size is more important to fruit size than cell number in loquat and that the expression of the EjBZR1 gene is negatively correlated with cell and fruit size. Virus-induced gene silencing (VIGS) of EjBZR1 led to larger cells and fruits in loquat, while its overexpression reduced cell and plant size in Arabidopsis. Moreover, both the suppression and overexpression of EjBZR1 inhibited the expression of brassinosteroid (BR) biosynthesis genes, especially that of EjCYP90A. Further experiments indicated that EjCYP90A, a cytochrome P450 gene, is a fruit growth activator, while EjBZR1 binds to the BRRE (CGTGTG) motif of the EjCYP90A promoter to repress its expression and fruit cell enlargement. Overall, our results demonstrate a possible pathway by which EjBZR1 directly targets EjCYP90A and thereby affects BR biosynthesis, which influences cell expansion and, consequently, fruit size. These findings help to elucidate the molecular functions of BZR1 in fruit growth and thus highlight a useful genetic improvement that can lead to increased crop yields by repressing gene expression.
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Affiliation(s)
- Wenbing Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China
- Fruit Research Institute, Fujian Academy of Agricultural Science, 350013, Fuzhou, China
- Key Laboratory of Loquat Germplasm Innovation and Utilization, Putian University, 351100, Putian, China
| | - Zikun Shao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China
| | - Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China
| | - Xiaoqing Gan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China
| | - Shunquan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources and Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), College of Horticulture, South China Agricultural University, 510642, Guangzhou, China.
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8
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Li LF, Wang ZB, Han CG, Sun HQ, Wang R, Ren YL, Lin JQ, Pang X, Liu XM, Lin JQ, Chen LX. Optimal reference genes for real-time quantitative PCR and the expression of sigma factors in Acidithiobacillus caldus under various conditions. J Appl Microbiol 2021; 131:1800-1812. [PMID: 33754423 DOI: 10.1111/jam.15085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/02/2021] [Accepted: 03/18/2021] [Indexed: 12/01/2022]
Abstract
AIMS Acidithiobacillus caldus is an important sulphur-oxidizing bacterium that plays crucial roles in the bioleaching industry. This study aims to analyse the optimal reference gene for real-time quantitative PCR (RT-qPCR) under different conditions and investigate the transcription levels of the sigma factor genes in the stress response. METHODS AND RESULTS We selected six housekeeping genes and analysed them via RT-qPCR using two energy resources, under four stress conditions. Three statistical approaches BestKeeper, geNorm, and NormFinder were utilized to determine transcription stability of these reference genes. The gapdH gene was the best internal control gene using elemental sulphur as an energy resource and under heat stress, map was the best internal control gene under pH and osmotic stress, era was the best internal control gene for the K2 S4 O6 energy resource, and rpoC was the best internal control gene under Cu2+ stress. Furthermore, the expressional levels of 11 sigma factors were analysed by RT-qPCR in the stress response. CONCLUSIONS Stable internal control genes for RT-qPCR analysis of A. caldus were determined, and the expression patterns of sigma factor genes of A. caldus were investigated. SIGNIFICANCE AND IMPACT OF THE STUDY The identification of the optimal reference gene and analysis of transcription levels of sigma factors in A. caldus can provide clues for reference gene selection and the study of sigma factor function.
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Affiliation(s)
- L F Li
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Z B Wang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - C G Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - H Q Sun
- Department of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - R Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Y L Ren
- Qingdao Longding Biotech Limited Company, Qingdao, China
| | - J Q Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - X Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - X M Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - J Q Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - L X Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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9
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Deng G, Bi F, Liu J, He W, Li C, Dong T, Yang Q, Gao H, Dou T, Zhong X, Peng M, Yi G, Hu C, Sheng O. Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana. BMC PLANT BIOLOGY 2021; 21:125. [PMID: 33648452 PMCID: PMC7923470 DOI: 10.1186/s12870-021-02899-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/21/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Banana plant height is an important trait for horticultural practices and semi-dwarf cultivars show better resistance to damages by wind and rain. However, the molecular mechanisms controlling the pseudostem height remain poorly understood. Herein, we studied the molecular changes in the pseudostem of a semi-dwarf banana mutant Aifen No. 1 (Musa spp. Pisang Awak sub-group ABB) as compared to its wild-type dwarf cultivar using a combined transcriptome and metabolome approach. RESULTS A total of 127 differentially expressed genes and 48 differentially accumulated metabolites were detected between the mutant and its wild type. Metabolites belonging to amino acid and its derivatives, flavonoids, lignans, coumarins, organic acids, and phenolic acids were up-regulated in the mutant. The transcriptome analysis showed the differential regulation of genes related to the gibberellin pathway, auxin transport, cell elongation, and cell wall modification. Based on the regulation of gibberellin and associated pathway-related genes, we discussed the involvement of gibberellins in pseudostem elongation in the mutant banana. Genes and metabolites associated with cell wall were explored and their involvement in cell extension is discussed. CONCLUSIONS The results suggest that gibberellins and associated pathways are possibly developing the observed semi-dwarf pseudostem phenotype together with cell elongation and cell wall modification. The findings increase the understanding of the mechanisms underlying banana stem height and provide new clues for further dissection of specific gene functions.
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Affiliation(s)
- Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Jing Liu
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128 China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Xiaohong Zhong
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128 China
| | - Miao Peng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128 China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Province, Guangzhou, China
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10
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Peng Z, Wang M, Zhang L, Jiang Y, Zhao C, Shahid MQ, Bai Y, Hao J, Peng J, Gao Y, Su W, Yang X. EjRAV1/ 2 Delay Flowering Through Transcriptional Repression of EjFTs and EjSOC1s in Loquat. FRONTIERS IN PLANT SCIENCE 2021; 12:816086. [PMID: 35035390 PMCID: PMC8759039 DOI: 10.3389/fpls.2021.816086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/06/2021] [Indexed: 05/02/2023]
Abstract
Most species in Rosaceae usually need to undergo several years of juvenile phase before the initiation of flowering. After 4-6 years' juvenile phase, cultivated loquat (Eriobotrya japonica), a species in Rosaceae, enters the reproductive phase, blooms in the autumn and sets fruits during the winter. However, the mechanisms of the transition from a seedling to an adult tree remain obscure in loquat. The regulation networks controlling seasonal flowering are also largely unknown. Here, we report two RELATED TO ABI3 AND VP1 (RAV) homologs controlling juvenility and seasonal flowering in loquat. The expressions of EjRAV1/2 were relatively high during the juvenile or vegetative phase and low at the adult or reproductive phase. Overexpression of the two EjRAVs in Arabidopsis prolonged (about threefold) the juvenile period by repressing the expressions of flowering activator genes. Additionally, the transformed plants produced more lateral branches than the wild type plants. Molecular assays revealed that the nucleus localized EjRAVs could bind to the CAACA motif of the promoters of flower signal integrators, EjFT1/2, to repress their expression levels. These findings suggest that EjRAVs play critical roles in maintaining juvenility and repressing flower initiation in the early life cycle of loquat as well as in regulating seasonal flowering. Results from this study not only shed light on the control and maintenance of the juvenile phase, but also provided potential targets for manipulation of flowering time and accelerated breeding in loquat.
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Affiliation(s)
- Ze Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Ling Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, Lushan, China
| | - Yuanyuan Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Chongbin Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yunlu Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Jingjing Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Jiangrong Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
| | - Yongshun Gao
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenbing Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xianghui Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture and Rural Affairs), South China Agricultural University, Guangzhou, China
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11
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Lv Y, Li Y, Liu X, Xu K. Identification of Ginger ( Zingiber officinale Roscoe) Reference Genes for Gene Expression Analysis. Front Genet 2020; 11:586098. [PMID: 33240331 PMCID: PMC7670040 DOI: 10.3389/fgene.2020.586098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
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.
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Affiliation(s)
- Yao Lv
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, China.,Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, China.,State Key Laboratory of Crop Biology, Tai'an, China
| | - Yanyan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China
| | - Xiaohui Liu
- School of Environment, Tsinghua University, Qingdao, China
| | - Kun Xu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Tai'an, China.,Key Laboratory of Biology of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, Tai'an, China.,State Key Laboratory of Crop Biology, Tai'an, China
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12
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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