The effect of artificial selection on phenotypic plasticity in maize

Joseph L. Gage; Diego Jarquin; Cinta Romay; Aaron Lorenz; Edward S. Buckler; Shawn Kaeppler; Naser Alkhalifah; Martin Bohn; Darwin A. Campbell; Jode Edwards; David Ertl; Sherry Flint-Garcia; Jack Gardiner; Byron Good; Candice N. Hirsch; Jim Holland; David C. Hooker; Joseph Knoll; Judith Kolkman; Greg Kruger; Nick Lauter; Carolyn J. Lawrence-Dill; Elizabeth Lee; Jonathan Lynch; Seth C. Murray; Rebecca Nelson; Jane Petzoldt; Torbert Rocheford; James Schnable; Patrick S. Schnable; Brian Scully; Margaret Smith; Nathan M. Springer; Srikant Srinivasan; Renee Walton; Teclemariam Weldekidan; Randall J. Wisser; Wenwei Xu; Jianming Yu; Natalia De Leon

doi:10.1038/s41467-017-01450-2

The effect of artificial selection on phenotypic plasticity in maize

Joseph L. Gage, Diego Jarquin, Cinta Romay, Aaron Lorenz, Edward S. Buckler, Shawn Kaeppler, Naser Alkhalifah, Martin Bohn, Darwin A. Campbell, Jode Edwards, David Ertl, Sherry Flint-Garcia, Jack Gardiner, Byron Good, Candice N. Hirsch, Jim Holland, David C. Hooker, Joseph Knoll, Judith Kolkman, Greg KrugerNick Lauter, Carolyn J. Lawrence-Dill, Elizabeth Lee, Jonathan Lynch, Seth C. Murray, Rebecca Nelson, Jane Petzoldt, Torbert Rocheford, James Schnable, Patrick S. Schnable, Brian Scully, Margaret Smith, Nathan M. Springer, Srikant Srinivasan, Renee Walton, Teclemariam Weldekidan, Randall J. Wisser, Wenwei Xu, Jianming Yu, Natalia De Leon

Research output: Contribution to journal › Article › peer-review

Abstract

Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0-5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.

Original language	English (US)
Article number	1348
Journal	Nature communications
Volume	8
Issue number	1
DOIs	https://doi.org/10.1038/s41467-017-01450-2
State	Published - Dec 1 2017

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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Gage, J. L., Jarquin, D., Romay, C., Lorenz, A., Buckler, E. S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D. A., Edwards, J., Ertl, D., Flint-Garcia, S., Gardiner, J., Good, B., Hirsch, C. N., Holland, J., Hooker, D. C., Knoll, J., Kolkman, J., ... De Leon, N. (2017). The effect of artificial selection on phenotypic plasticity in maize. Nature communications, 8(1), [1348]. https://doi.org/10.1038/s41467-017-01450-2

The effect of artificial selection on phenotypic plasticity in maize. / Gage, Joseph L.; Jarquin, Diego; Romay, Cinta; Lorenz, Aaron; Buckler, Edward S.; Kaeppler, Shawn; Alkhalifah, Naser; Bohn, Martin; Campbell, Darwin A.; Edwards, Jode; Ertl, David; Flint-Garcia, Sherry; Gardiner, Jack; Good, Byron; Hirsch, Candice N.; Holland, Jim; Hooker, David C.; Knoll, Joseph; Kolkman, Judith; Kruger, Greg; Lauter, Nick; Lawrence-Dill, Carolyn J.; Lee, Elizabeth; Lynch, Jonathan; Murray, Seth C.; Nelson, Rebecca; Petzoldt, Jane; Rocheford, Torbert; Schnable, James; Schnable, Patrick S.; Scully, Brian; Smith, Margaret; Springer, Nathan M.; Srinivasan, Srikant; Walton, Renee; Weldekidan, Teclemariam; Wisser, Randall J.; Xu, Wenwei; Yu, Jianming; De Leon, Natalia.

In: Nature communications, Vol. 8, No. 1, 1348, 01.12.2017.

Research output: Contribution to journal › Article › peer-review

Gage, JL, Jarquin, D, Romay, C, Lorenz, A, Buckler, ES, Kaeppler, S, Alkhalifah, N, Bohn, M, Campbell, DA, Edwards, J, Ertl, D, Flint-Garcia, S, Gardiner, J, Good, B, Hirsch, CN, Holland, J, Hooker, DC, Knoll, J, Kolkman, J, Kruger, G, Lauter, N, Lawrence-Dill, CJ, Lee, E, Lynch, J, Murray, SC, Nelson, R, Petzoldt, J, Rocheford, T, Schnable, J, Schnable, PS, Scully, B, Smith, M, Springer, NM, Srinivasan, S, Walton, R, Weldekidan, T, Wisser, RJ, Xu, W, Yu, J & De Leon, N 2017, 'The effect of artificial selection on phenotypic plasticity in maize', Nature communications, vol. 8, no. 1, 1348. https://doi.org/10.1038/s41467-017-01450-2

Gage, Joseph L. ; Jarquin, Diego ; Romay, Cinta ; Lorenz, Aaron ; Buckler, Edward S. ; Kaeppler, Shawn ; Alkhalifah, Naser ; Bohn, Martin ; Campbell, Darwin A. ; Edwards, Jode ; Ertl, David ; Flint-Garcia, Sherry ; Gardiner, Jack ; Good, Byron ; Hirsch, Candice N. ; Holland, Jim ; Hooker, David C. ; Knoll, Joseph ; Kolkman, Judith ; Kruger, Greg ; Lauter, Nick ; Lawrence-Dill, Carolyn J. ; Lee, Elizabeth ; Lynch, Jonathan ; Murray, Seth C. ; Nelson, Rebecca ; Petzoldt, Jane ; Rocheford, Torbert ; Schnable, James ; Schnable, Patrick S. ; Scully, Brian ; Smith, Margaret ; Springer, Nathan M. ; Srinivasan, Srikant ; Walton, Renee ; Weldekidan, Teclemariam ; Wisser, Randall J. ; Xu, Wenwei ; Yu, Jianming ; De Leon, Natalia. / The effect of artificial selection on phenotypic plasticity in maize. In: Nature communications. 2017 ; Vol. 8, No. 1.

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abstract = "Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0-5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements.",

author = "Gage, {Joseph L.} and Diego Jarquin and Cinta Romay and Aaron Lorenz and Buckler, {Edward S.} and Shawn Kaeppler and Naser Alkhalifah and Martin Bohn and Campbell, {Darwin A.} and Jode Edwards and David Ertl and Sherry Flint-Garcia and Jack Gardiner and Byron Good and Hirsch, {Candice N.} and Jim Holland and Hooker, {David C.} and Joseph Knoll and Judith Kolkman and Greg Kruger and Nick Lauter and Lawrence-Dill, {Carolyn J.} and Elizabeth Lee and Jonathan Lynch and Murray, {Seth C.} and Rebecca Nelson and Jane Petzoldt and Torbert Rocheford and James Schnable and Schnable, {Patrick S.} and Brian Scully and Margaret Smith and Springer, {Nathan M.} and Srikant Srinivasan and Renee Walton and Teclemariam Weldekidan and Wisser, {Randall J.} and Wenwei Xu and Jianming Yu and {De Leon}, Natalia",

note = "Funding Information: The authors would like to thank the entire G2F Consortium for their help with this study and extend a hearty acknowledgment to Tim Beissinger, Bret Payseur, and Jeff Ross-Ibarra for their sound advice. Ms. Lisa Coffey for assistance organizing and conducting field trials at Iowa State University and Dustin Eilert and Marina Borsecnik for assistance organizing and conducting field trials at the University of Wisconsin, Madison. This project was supported by the National Research Initiative for Agriculture and Food Research Initiative Competitive Grants Program grant no. #2012-67013-19460 from the USDA National Institute of Food and Agriculture, USDA Hatch program funds to multiple PIs in this project, NSF Plant Genome Research Project #1238014, the USDA-ARS, the Ontario Ministry of Agriculture, Food, and Rural Affairs, the Iowa Corn Promotion Board, the Nebraska Corn Board, the Minnesota Corn Research and Promotion Council, the Illinois Corn Marketing Board, and the National Corn Growers Association.",

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AU - Gage, Joseph L.

AU - Jarquin, Diego

AU - Romay, Cinta

AU - Lorenz, Aaron

AU - Buckler, Edward S.

AU - Kaeppler, Shawn

AU - Alkhalifah, Naser

AU - Bohn, Martin

AU - Campbell, Darwin A.

AU - Edwards, Jode

AU - Ertl, David

AU - Flint-Garcia, Sherry

AU - Gardiner, Jack

AU - Good, Byron

AU - Hirsch, Candice N.

AU - Holland, Jim

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AU - Lee, Elizabeth

AU - Lynch, Jonathan

AU - Murray, Seth C.

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AU - Petzoldt, Jane

AU - Rocheford, Torbert

AU - Schnable, James

AU - Schnable, Patrick S.

AU - Scully, Brian

AU - Smith, Margaret

AU - Springer, Nathan M.

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AU - Weldekidan, Teclemariam

AU - Wisser, Randall J.

AU - Xu, Wenwei

AU - Yu, Jianming

AU - De Leon, Natalia

N1 - Funding Information: The authors would like to thank the entire G2F Consortium for their help with this study and extend a hearty acknowledgment to Tim Beissinger, Bret Payseur, and Jeff Ross-Ibarra for their sound advice. Ms. Lisa Coffey for assistance organizing and conducting field trials at Iowa State University and Dustin Eilert and Marina Borsecnik for assistance organizing and conducting field trials at the University of Wisconsin, Madison. This project was supported by the National Research Initiative for Agriculture and Food Research Initiative Competitive Grants Program grant no. #2012-67013-19460 from the USDA National Institute of Food and Agriculture, USDA Hatch program funds to multiple PIs in this project, NSF Plant Genome Research Project #1238014, the USDA-ARS, the Ontario Ministry of Agriculture, Food, and Rural Affairs, the Iowa Corn Promotion Board, the Nebraska Corn Board, the Minnesota Corn Research and Promotion Council, the Illinois Corn Marketing Board, and the National Corn Growers Association.

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