The genetic architecture of cell type–specific cis regulation in maize

IF 45.8 1区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Science Pub Date : 2025-04-18 DOI:10.1126/science.ads6601

Alexandre P. Marand, Luguang Jiang, Fabio Gomez-Cano, Mark A. A. Minow, Xuan Zhang, John P. Mendieta, Ziliang Luo, Sohyun Bang, Haidong Yan, Cullan Meyer, Luca Schlegel, Frank Johannes, Robert J. Schmitz

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Abstract

Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of more than 0.7 million nuclei across 172 Zea mays (maize) inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and revealed how historical transposon activity has shaped the cis-regulatory landscape. Leveraging population genetics principles, we fine-mapped about 22,000 chromatin accessibility–associated genetic variants with widespread cell type–specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR–binding sites were the most prevalent determinants of chromatin accessibility. Finally, integrating chromatin accessibility–associated variants, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular contexts to alter maize flowering.

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玉米细胞类型特异性顺式调控的遗传结构

基因表达和复杂表型是由顺式调控元件的活性决定的。然而，对现存遗传变异如何影响顺式调控的理解仍然有限。在这里，我们利用172个Zea mays（玉米）自交系的70多万个细胞核的单细胞基因组学研究了顺式调控多样性的后果。我们的分析明确了与驯化玉米不同的顺式调控元件，并揭示了历史上转座子活动如何塑造顺式调控景观。利用群体遗传学原理，我们精细绘制了大约22,000个与染色质可及性相关的遗传变异，这些变异具有广泛的细胞类型特异性效应。TEOSINTE BRANCHED1/CYCLOIDEA/增殖细胞因子结合位点的变异是染色质可及性的最普遍决定因素。最后，整合染色质可及性相关变异、有机性状变异和群体分化，揭示了局部适应如何在独特的细胞环境中重新连接调控网络，从而改变玉米开花。

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来源期刊

Science 综合性期刊-综合性期刊

CiteScore

61.10

自引率

0.90%

发文量

审稿时长

2.1 months

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