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Arabidopsis research requires a critical re-evaluation of genetic tools

Natalia Nikonorova (UGent) , Kun Yue (UGent) , Tom Beeckman (UGent) and Ive De Smet (UGent)
(2018) JOURNAL OF EXPERIMENTAL BOTANY. 69(15). p.3541-3544
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Abstract
An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re) investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.
Keywords
ACR4, Arabidopsis thaliana, loss-of-function lines, SAIL, self-criticism, QRT1, RECEPTOR-LIKE KINASE, TETRAD ANALYSIS, ROOT, ACR4, ORGANIZATION, MUTATION, MUTANTS, SEPAL

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Chicago
Nikonorova, Natalia, Kun Yue, Tom Beeckman, and Ive De Smet. 2018. “Arabidopsis Research Requires a Critical Re-evaluation of Genetic Tools.” Journal of Experimental Botany 69 (15): 3541–3544.
APA
Nikonorova, N., Yue, K., Beeckman, T., & De Smet, I. (2018). Arabidopsis research requires a critical re-evaluation of genetic tools. JOURNAL OF EXPERIMENTAL BOTANY, 69(15), 3541–3544.
Vancouver
1.
Nikonorova N, Yue K, Beeckman T, De Smet I. Arabidopsis research requires a critical re-evaluation of genetic tools. JOURNAL OF EXPERIMENTAL BOTANY. 2018;69(15):3541–4.
MLA
Nikonorova, Natalia, Kun Yue, Tom Beeckman, et al. “Arabidopsis Research Requires a Critical Re-evaluation of Genetic Tools.” JOURNAL OF EXPERIMENTAL BOTANY 69.15 (2018): 3541–3544. Print.
@article{8562939,
  abstract     = {An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re) investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.},
  author       = {Nikonorova, Natalia and Yue, Kun and Beeckman, Tom and De Smet, Ive},
  issn         = {0022-0957},
  journal      = {JOURNAL OF EXPERIMENTAL BOTANY},
  keyword      = {ACR4,Arabidopsis thaliana,loss-of-function lines,SAIL,self-criticism,QRT1,RECEPTOR-LIKE KINASE,TETRAD ANALYSIS,ROOT,ACR4,ORGANIZATION,MUTATION,MUTANTS,SEPAL},
  language     = {eng},
  number       = {15},
  pages        = {3541--3544},
  title        = {Arabidopsis research requires a critical re-evaluation of genetic tools},
  url          = {http://dx.doi.org/10.1093/jxb/ery161},
  volume       = {69},
  year         = {2018},
}

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