Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

Benjamin W. Campbell; Anna N. Hofstad; Suma Sreekanta; Fengli Fu; Thomas J Y Kono; Jamie A. O’Rourke; Carroll P. Vance; Gary J. Muehlbauer; Robert M. Stupar

doi:10.1007/s00122-016-2735-x

Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

Benjamin W. Campbell, Anna N. Hofstad, Suma Sreekanta, Fengli Fu, Thomas J Y Kono, Jamie A. O’Rourke, Carroll P. Vance, Gary J. Muehlbauer, Robert M. Stupar

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Abstract

Key message: Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. Abstract: A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1–2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.

Original language	English (US)
Pages (from-to)	1725-1738
Number of pages	14
Journal	Theoretical and Applied Genetics
Volume	129
Issue number	9
DOIs	https://doi.org/10.1007/s00122-016-2735-x
State	Published - Sep 1 2016

Bibliographical note

Funding Information:
The authors are grateful to Dan Szymanski for providing seed for the Arabidopsis grl-4 mutant, Yung-Tsi Bolon and Jeff Roessler for early identification of the soybean gnarled mutant, Bruna Bucciarelli for assisting with the RNA-seq experiments, and both Junqi Liu and Jean-Michel Michno for their advice regarding the GmNAP1 construct creation. The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. URL: http://www.msi.umn.edu . Microscopy imaging and analysis was performed at the University Imaging Centers, University of Minnesota. The authors would also like to thank the Minnesota Soybean Research and Promotion Council, United Soybean Board, and the National Science Foundation for their help and support. We would also like to thank the National Science Foundation for supporting BWC through the Graduate Research Fellowship Program (NSF-GRFP).

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© 2016, The Author(s).

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title = "Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes",

abstract = "Key message: Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. Abstract: A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1–2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.",

author = "Campbell, {Benjamin W.} and Hofstad, {Anna N.} and Suma Sreekanta and Fengli Fu and Kono, {Thomas J Y} and O{\textquoteright}Rourke, {Jamie A.} and Vance, {Carroll P.} and Muehlbauer, {Gary J.} and Stupar, {Robert M.}",

note = "Funding Information: The authors are grateful to Dan Szymanski for providing seed for the Arabidopsis grl-4 mutant, Yung-Tsi Bolon and Jeff Roessler for early identification of the soybean gnarled mutant, Bruna Bucciarelli for assisting with the RNA-seq experiments, and both Junqi Liu and Jean-Michel Michno for their advice regarding the GmNAP1 construct creation. The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. URL: http://www.msi.umn.edu . Microscopy imaging and analysis was performed at the University Imaging Centers, University of Minnesota. The authors would also like to thank the Minnesota Soybean Research and Promotion Council, United Soybean Board, and the National Science Foundation for their help and support. We would also like to thank the National Science Foundation for supporting BWC through the Graduate Research Fellowship Program (NSF-GRFP). Publisher Copyright: {\textcopyright} 2016, The Author(s).",

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AU - Campbell, Benjamin W.

AU - Hofstad, Anna N.

AU - Sreekanta, Suma

AU - Fu, Fengli

AU - Kono, Thomas J Y

AU - O’Rourke, Jamie A.

AU - Vance, Carroll P.

AU - Muehlbauer, Gary J.

AU - Stupar, Robert M.

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Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

Abstract

Bibliographical note

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Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

Abstract

Bibliographical note

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Equipment

Electron Microscopy

HItachi S3500N Variable Pressure SEM

University Imaging Centers

Cite this