| Summary: | The control of flowering time has an important impact on biomass and the environmental adaption of legumes. The <i>CCT</i> (<i>CO</i>, <i>COL</i> and <i>TOC1</i>) gene family was elucidated to participate in the molecular regulation of flowering in plants. We identified 36 <i>CCT</i> genes in the <i>M</i>. <i>truncatula</i> genome and they were classified into three distinct subfamilies, <i>PRR</i> (7), <i>COL</i> (11) and <i>CMF</i> (18). Synteny and phylogenetic analyses revealed that <i>CCT</i> genes occurred before the differentiation of monocot and dicot, and <i>CCT</i> orthologous genes might have diversified among plants. The diverse spatial-temporal expression profiles indicated that <i>MtCCT</i> genes could be key regulators in flowering time, as well as in the development of seeds and nodules in <i>M. truncatula</i>. Notably, 22 <i>MtCCT</i> genes with typical circadian rhythmic variations suggested their different responses to light. The response to various hormones of <i>MtCCT</i> genes demonstrated that they participate in plant growth and development via varied hormones dependent pathways. Moreover, six <i>MtCCT</i> genes were dramatically induced by salinity and dehydration treatments, illustrating their vital roles in the prevention of abiotic injury. Collectively, our study provides valuable information for the in-depth investigation of the molecular mechanism of flowering time in <i>M. truncatula</i>, and it also provides candidate genes for alfalfa molecular breeding with ideal flowering time.
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