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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #345984

Title: The effect of artificial selection on phenotypic plasticity in maize

item GAGE, JOSEPH - University Of Wisconsin
item JARQUIN, DIEGO - University Of Nebraska
item ROMAY, MARIA CINTA - Cornell University
item LORENZ, AARON - University Of Minnesota
item Buckler, Edward - Ed
item KAEPPLER, SHAWN - University Of Wisconsin
item ALKHALIFAH, NASER - Iowa State University
item BOHN, MARTIN - University Of Illinois
item CAMPBELL, DARWIN - Iowa State University
item Edwards, Jode
item ERTL, DAVID - Iowa Corn Promotion Board
item Flint-Garcia, Sherry
item GARDINER, JACK - University Of Missouri
item GOOD, BYRON - University Of Guelph
item HIRSCH, CANDICE - University Of Minnesota
item Holland, Jim - Jim
item HOOKER, DAVID - University Of Guelph
item Knoll, Joseph - Joe
item KOLKMAN, JUDITH - Cornell University
item KRUGER, GREG - University Of Nebraska
item Lauter, Nicholas
item LAWRENCE-DILL, CAROLYN - Iowa State University
item LEE, ELIZABETH - University Of Guelph
item LYNCH, JONATHAN - Pennsylvania State University
item MURRAY, SETH - Texas A&M University
item NELSON, REBECCA - Cornell University
item PETZOLDT, JANE - University Of Wisconsin
item ROCHEFORD, TORBERT - Purdue University
item SCHNABLE, JAMES - University Of Nebraska
item SCHNABLE, PATRICK - Iowa State University
item Scully, Brian
item SMITH, MARGARET - Cornell University
item SPRINGER, NATHAN - University Of Minnesota
item SRINIVASAN, SRIKANT - Iowa State University
item WALTON, RENEE - Iowa State University
item WELDEKIDAN, TECLEMARIAM - University Of Delaware
item WISSER, RANDELL - University Of Delaware
item XU, WENWEI - Texas A&M University
item YU, JIANMING - Iowa State University
item DE LEON, NATALIA - University Of Wisconsin

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2017
Publication Date: 11/7/2017
Citation: Gage, J., Jarquin, D., Romay, M., Lorenz, A., Buckler IV, E.S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D., Edwards, J.W., Ertl, D., Flint Garcia, S.A., Gardiner, J., Good, B., Hirsch, C., Holland, J.B., Hooker, D., Knoll, J.E., Kolkman, J., Kruger, G., Lauter, N.C., Lawrence-Dill, C., Lee, E., Lynch, J., Murray, S., Nelson, R., Petzoldt, J., Rocheford, T., Schnable, J., Schnable, P., Scully, B.T., Smith, M., Springer, N., Srinivasan, S., Walton, R., Weldekidan, T., Wisser, R., Xu, W., Yu, J., De Leon, N. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications. 8:1348.

Interpretive Summary: The expression of an individual’s phenotype is a function of its genotype (G), the environment experienced during its lifetime (E), and the complex relationship established by certain genotypes to specific environmental influences. This variable plastic response is referred to as genotype-by-environment interaction (G×E). In this study, leveraging resources from the Maize G×E project, we tested the following hypotheses: 1) loci that have experienced changes in allele frequency due to selection for high productivity explain less G×E variation than regions that did not undergo selection; and 2) G×E variation is disproportionately controlled by regulatory mechanisms. To test the first hypothesis, we identified SNPs that show high divergence in allele frequency between temperate improved and tropical improved maize lines. We then tested how much G×E variation those SNPs explained relative to a set of SNPs that show little to no divergence. To address the second postulation, we examined the location of polymorphisms associated with G×E in relation to nearby genes to search for enrichment of associations in regulatory, as opposed to genic regions.

Technical Abstract: Remarkable productivity levels have been achieved in crop species through artificial selection and adaptation to modern agronomic practices around the world. The question remains as to whether this intensive selection has also changed the ability of improved cultivars to consistently maintain high productivity across variable environmental conditions. A deeper understanding of the types of genetic architecture and modulation mechanisms controlling phenotypic plasticity and genotype by environment (G×E) interaction will enhance the ability to predict performance of crop varieties grown in diverse environmental conditions. We used the framework of the Genomes to Fields (G2F) G×E Maize project to assess the effect of selection on G×E variation and to characterize polymorphisms associated with plastic response. The G×E Maize project evaluated a collection of over 800 diverse maize hybrids across 21 sites in North America in 2014. Genotypes were evaluated for relevant phenological and agronomic characteristics such as flowering time, plant and ear height, and grain yield. Genomic regions displaying evidence of selection during modern temperate maize breeding were identified by evaluating Fst between pools of temperate and tropical inbred lines. Selected genomic regions explained less of the variability for yield G×E than regions that do not show evidence of selection, indicating that improvement due to breeding efforts may have reduced G×E of modern cultivars. A Finlay-Wilkinson regression was used to quantify and subsequently map hybrid stability. Loci associated with stability were evaluated for distance from the closest annotated gene model to identify trends in genomic position of variants controlling stability. We observed an enrichment of variants 0-5,000 base pairs upstream of genes and a corresponding decrease in genic associations, hypothetically due to control of plasticity by short-range regulatory elements.