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A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding

View ORCID ProfileGen Xu, Jing Lyu, View ORCID ProfileToshihiro Obata, View ORCID ProfileSanzhen Liu, View ORCID ProfileYufeng Ge, View ORCID ProfileJames C. Schnable, View ORCID ProfileJinliang Yang
doi: https://doi.org/10.1101/2022.02.09.479784
Gen Xu
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Jing Lyu
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
3Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Toshihiro Obata
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
4Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Sanzhen Liu
5Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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Yufeng Ge
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
6Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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James C. Schnable
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Jinliang Yang
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
2Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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  • For correspondence: jinliang.yang@unl.edu
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ABSTRACT

Understanding the patterns of selection during plant evolution and recent crop improvement processes is the central topic in plant breeding and genetics. As an essential macronutrient for plant growth and development, nitrogen (N) is a key factor in affecting plant adaptation and crop improvement. The widespread adoption of less expensive industrial N fixation has dramatically reshaped plant morphology by favoring compact maize plants to tolerant crowding stress. The associated genetic changes, however, have not been systematically studied. Here, we investigated maize inbred lines developed before and after the 1960s — the time point when inorganic N fertilizer started to be widely used for maize production. We identified a strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) and New-Era (post-1960s) inbred lines. Further study revealed population genetics statistics in the sweep exhibited patterns consistent with historical balancing selection. This balanced genomic interval is associated with a number of morphological, physiological, and metabolite traits related to vegetative N responses. A cluster of three glutamate receptor-like (GLR) genes is located within the region targeted by selection. Functional characterizations suggested differences in transcriptional activity of the GLR genes between the haplotypes carried by Old-Era and New-Era inbred lines likely play an essential role in mediating distinct N responses. The identification of both targets of selection and changes in the regulation of N responsive genes between maize lines developed in different eras sheds light on the N sensing and regulation pathways and paves the way to developing N resilient crops.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted February 10, 2022.
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A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding
Gen Xu, Jing Lyu, Toshihiro Obata, Sanzhen Liu, Yufeng Ge, James C. Schnable, Jinliang Yang
bioRxiv 2022.02.09.479784; doi: https://doi.org/10.1101/2022.02.09.479784
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A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding
Gen Xu, Jing Lyu, Toshihiro Obata, Sanzhen Liu, Yufeng Ge, James C. Schnable, Jinliang Yang
bioRxiv 2022.02.09.479784; doi: https://doi.org/10.1101/2022.02.09.479784

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