Abstract:In Arabidopsis thaliana, IQM family is a calmodulin-binding protein family containing IQ motifs, IQM3 mutation can increase main root length, CO (CONSTANS) is an important member of photoperiodic floral regulation pathway, CO mutation can shorten taproot length. The genetic relationship between IQM3 and CO gene was studied by constructing double mutants of IQM3 and CO. The results showed that the first exon in co-12 sequence of the new CO mutant was missing 9 base ACTTGCTAG, which contains the restriction endonucrenase BfaI restriction site CTAG. A molecular marker was established to identify the mutant. When the cross-coding PCR product was cleaved by BfaI enzyme, four fragments were obtained from wild-type Col because it had three sites, three fragments were obtained from co-12 because it had only two sites, and five fragments were obtained from CO/co-12 heterozygote. Under long sunshine, the main root length of co-12 was shorter than that of wild type Col, and that of iqm3-2 was longer than that of wild type, while the phenotype of double mutant co-12 iqm3-2 was more favorable to iqm3-2. Therefore, IQM3 acts downstream of CO to regulate main root length under long day in Arabidopsis.