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Intraspecific genetic variation is essential for plant responses and adaption to evolutionary challenges, such as changing environmental conditions.Self-incompatible species, such as apple, have higher levels of genetic variation, and the use of highly heterozygous Malus genotypes has allowed us to demonstrate that a TATA-box insertion in the promoter of Iron-Regulated Transporterl (IRT1) gene in the regulation of Fe homeostasis contributes to Fe-efficiency, creates a novel regulatory mechanism.