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Identification and validation of reference genes for quantitative real-time PCR studies in alligatorweed (Alternanthera philoxeroides)

Published online by Cambridge University Press:  21 April 2021

Junliang Yin Open the ORCID record for Junliang Yin [Opens in a new window] ,
Lu Hou ,
Xinchen Jiang ,
Jie Yang ,
Yang He ,
Xiaokang Zhou ,
Xiongmeng Zhu ,
Andong Gong ,
Yongxing Zhu  and
Zhongyi Chen
Junliang Yin
Affiliation:
Researcher, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou, Hubei, China
Lu Hou
Affiliation:
Associate Professor, Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province/State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
Xinchen Jiang
Affiliation:
Graduate Research Assistant, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
Jie Yang
Affiliation:
Graduate Research Assistant, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
Yang He
Affiliation:
Graduate Research Assistant, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
Xiaokang Zhou
Affiliation:
Graduate Research Assistant, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
Xiongmeng Zhu
Affiliation:
Graduate Research Assistant, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
Andong Gong
Affiliation:
Associate Professor, College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
Yongxing Zhu*
Affiliation:
Associate Professor, College of Horticulture and Gardening, Jingzhou, Hubei, China
Zhongyi Chen*
Affiliation:
Professor, College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
*
Authors for correspondence: Yongxing Zhu, College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, Hubei, China (Email: yongxingzhu@yangtzeu.edu.cn); Zhongyi Chen, College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, Hubei, China. (Email: czy@yangtzeu.edu.cn)
Authors for correspondence: Yongxing Zhu, College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, Hubei, China (Email: yongxingzhu@yangtzeu.edu.cn); Zhongyi Chen, College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, Hubei, China. (Email: czy@yangtzeu.edu.cn)
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Abstract

Alligatorweed [Alternanthera philoxeroides (Mart.) Griseb.] is an invasive semiaquatic weed that poses a serious threat to agricultural production and ecological balance worldwide. However, information about genetic factors associated with the adaptation and invasion mechanisms of this species is limited. Screening for appropriate reference genes is important for gene expression and functional analysis research in A. philoxeroides. In this study, 30 candidate genes that showed stable expression in different A. philoxeroides tissues under various treatments in RNA-seq data were chosen to design quantitative real-time PCR (qRT-PCR) primers. After the amplification specificity validation, 25 candidates were selected and further evaluated in a diverse set of A. philoxeroides samples, including leaf, stem, and root tissues under drought, salinity, heat, chilling, five herbicides, and corresponding untreated controls using qRT-PCR. The delta-CT method, geNorm, NormFinder, BestKeeper, and RefFinder algorithms were used to identify stable reference genes from A. philoxeroides samples. Overall, CoA, RFI2, Tubby, SRP19, and V-ATPase were the top five ideal reference genes in all organs and conditions. Tubby and CoA were the most stable reference genes in the leaf/stem; and RFI2, ERprr, and SPR19 were suitable reference genes for the roots. This work provided a foundation for exploring gene expression profiling of A. philoxeroides, especially those adaptation- and invasion-related genes, which may help in management of this invasive weed.

Keywords

Housekeeping geneinternal controlqRT-PCRRefFinder
Type
Research Article
Information
Weed Science , Volume 69 , Issue 4 , July 2021 , pp. 404 - 411
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Copyright
© The Author(s), 2021. Published by Cambridge University Press on behalf of the Weed Science Society of America

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Footnotes

Associate Editor: Te-Ming Paul Tseng, Mississippi State University

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