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MADS-box transcription factors <i>FLOWERING LOCUS C</i> (<i>FLC</i>) and <i>APETALA1</i> (<i>AP1</i>)/<i>CAULIFLOWER</i> (<i>CAL</i>) have an opposite effect in vernalization-regulated flowering in <i>Arabidopsis</i>. In woody plants, a functional <i>FLC-like</i> gene has not been verified through reverse genetics. To reveal chilling-regulated flowering mechanisms in woody fruit crops, we conducted phylogenetic analysis of the annotated <i>FLC-like</i> proteins of apple and found that these proteins are grouped more closely to <i>Arabidopsis AP1</i> than the <i>FLC</i> group. An <i>FLC3-like</i> MADS-box gene from columnar apple trees (<i>Malus domestica</i>) (<i>MdFLC3-like</i>) was cloned for functional analysis through a constitutive transgenic expression. The <i>MdFLC3-like</i> shows 88% identity to pear&#8217;s <i>FLC-like</i> genes and 82% identity to blueberry&#8217;s <i>CAL1</i> gene (<i>VcCAL1</i>). When constitutively expressed in a highbush blueberry (<i>Vaccinium corymbosum</i> L.) cultivar &#8216;Legacy&#8217;, the <i>MdFLC3-like</i> induced expressions of orthologues of three MADS-box genes, including <i>APETALA1</i>, <i>SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1</i>, and <i>CAL1</i>. As a consequence, in contrast to the anticipated late flowering associated with an overexpressed <i>FLC-like</i>, the <i>MdFLC3-like</i> promoted flowering of transgenic blueberry plants under nonchilling conditions where nontransgenic &#8216;Legacy&#8217; plants could not flower. Thus, the constitutively expressed <i>MdFLC3-like</i> in transgenic blueberries functioned likely as a blueberry&#8217;s <i>VcCAL1</i>. The results are anticipated to facilitate future studies for revealing chilling-mediated flowering mechanisms in woody plants.