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We conclude that APC/CTE plays a key role in regulating plant architecture by mediating the signaling cross talks between ABA and GA. © 2020 American Society of Plant Biologists. All rights reserved.Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for 1000 accessions of Arabidopsis thaliana were focused on small variations and did not include CNVs. Here, we performed a genome-wide analysis and identified large indels (50-499 bp) and CNV