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Combining linkage and association mapping identifies RECEPTOR-LIKE PROTEIN KINASE1 as an essential Arabidopsis shoot regeneration gene

Hans Motte (UGent) , Annelies Vercauteren (UGent) , Stephen Depuydt (UGent) , Sofie Landschoot (UGent) , Danny Geelen (UGent) , Stefaan Werbrouck (UGent) , Sofie Goormachtig (UGent) , Marnik Vuylsteke (UGent) and Danny Vereecke (UGent)
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Abstract
De novo shoot organogenesis (i.e., the regeneration of shoots on nonmeristematic tissue) is widely applied in plant biotechnology. However, the capacity to regenerate shoots varies highly among plant species and cultivars, and the factors underlying it are still poorly understood. Here, we evaluated the shoot regeneration capacity of 88 Arabidopsis thaliana accessions and found that the process is blocked at different stages in different accessions. We show that the variation in regeneration capacity between the Arabidopsis accessions Nok-3 and Ga-0 is determined by five quantitative trait loci (QTL): REG-1 to REG-5. Fine mapping by local association analysis identified RECEPTOR-LIKE PROTEIN KINASE1 (RPK1), an abscisic acid-related receptor, as the most likely gene underlying REG-1, which was confirmed by quantitative failure of an RPK1 mutation to complement the high and low REG-1 QTL alleles. The importance of RPK1 in regeneration was further corroborated by mutant and expression analysis. Altogether, our results show that association mapping combined with linkage mapping is a powerful method to discover important genes implicated in a biological process as complex as shoot regeneration.
Keywords
SEED-DERIVED CALLI, TISSUE-CULTURE, IN-VITRO ORGANOGENESIS, RECOMBINANT INBRED LINES, QTG, natural variation, ABA, SNP, regeneration recalcitrance, MAJOR GENES, ROOT EXPLANTS, PATTERN-FORMATION, QUANTITATIVE TRAITS, ABSCISIC-ACID, PLANT-REGENERATION

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Chicago
Motte, Hans, Annelies Vercauteren, Stephen Depuydt, Sofie Landschoot, Danny Geelen, Stefaan Werbrouck, Sofie Goormachtig, Marnik Vuylsteke, and Danny Vereecke. 2014. “Combining Linkage and Association Mapping Identifies RECEPTOR-LIKE PROTEIN KINASE1 as an Essential Arabidopsis Shoot Regeneration Gene.” Proceedings of the National Academy of Sciences of the United States of America 111 (22): 8305–8310.
APA
Motte, H., Vercauteren, A., Depuydt, S., Landschoot, S., Geelen, D., Werbrouck, S., Goormachtig, S., et al. (2014). Combining linkage and association mapping identifies RECEPTOR-LIKE PROTEIN KINASE1 as an essential Arabidopsis shoot regeneration gene. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(22), 8305–8310.
Vancouver
1.
Motte H, Vercauteren A, Depuydt S, Landschoot S, Geelen D, Werbrouck S, et al. Combining linkage and association mapping identifies RECEPTOR-LIKE PROTEIN KINASE1 as an essential Arabidopsis shoot regeneration gene. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2014;111(22):8305–10.
MLA
Motte, Hans, Annelies Vercauteren, Stephen Depuydt, et al. “Combining Linkage and Association Mapping Identifies RECEPTOR-LIKE PROTEIN KINASE1 as an Essential Arabidopsis Shoot Regeneration Gene.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111.22 (2014): 8305–8310. Print.
@article{4443639,
  abstract     = {De novo shoot organogenesis (i.e., the regeneration of shoots on nonmeristematic tissue) is widely applied in plant biotechnology. However, the capacity to regenerate shoots varies highly among plant species and cultivars, and the factors underlying it are still poorly understood. Here, we evaluated the shoot regeneration capacity of 88 Arabidopsis thaliana accessions and found that the process is blocked at different stages in different accessions. We show that the variation in regeneration capacity between the Arabidopsis accessions Nok-3 and Ga-0 is determined by five quantitative trait loci (QTL): REG-1 to REG-5. Fine mapping by local association analysis identified RECEPTOR-LIKE PROTEIN KINASE1 (RPK1), an abscisic acid-related receptor, as the most likely gene underlying REG-1, which was confirmed by quantitative failure of an RPK1 mutation to complement the high and low REG-1 QTL alleles. The importance of RPK1 in regeneration was further corroborated by mutant and expression analysis. Altogether, our results show that association mapping combined with linkage mapping is a powerful method to discover important genes implicated in a biological process as complex as shoot regeneration.},
  author       = {Motte, Hans and Vercauteren, Annelies and Depuydt, Stephen and Landschoot, Sofie and Geelen, Danny and Werbrouck, Stefaan and Goormachtig, Sofie and Vuylsteke, Marnik and Vereecke, Danny},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keyword      = {SEED-DERIVED CALLI,TISSUE-CULTURE,IN-VITRO ORGANOGENESIS,RECOMBINANT INBRED LINES,QTG,natural variation,ABA,SNP,regeneration recalcitrance,MAJOR GENES,ROOT EXPLANTS,PATTERN-FORMATION,QUANTITATIVE TRAITS,ABSCISIC-ACID,PLANT-REGENERATION},
  language     = {eng},
  number       = {22},
  pages        = {8305--8310},
  title        = {Combining linkage and association mapping identifies RECEPTOR-LIKE PROTEIN KINASE1 as an essential Arabidopsis shoot regeneration gene},
  url          = {http://dx.doi.org/10.1073/pnas.1404978111},
  volume       = {111},
  year         = {2014},
}

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