Genome-wide characterization and expression analysis of Dof family genes in sweetpotato

Abstract

<p id="C3">DNA-binding One Zinc Finger (Dof) transcription factors are widely involved in various life activities of plants. Forty-six <italic>IbDof</italic> genes from sweetpotato cv. Taizhong 6 with a highly conserved Dof domain structured as a C2C2-type zinc finger were identified and named from<italic> IbDof1</italic> to <italic>IbDof46 </italic>according to their position on the chromosomes. IbDof family could be divided into four subgroups (A-D), which shared the similar motifs and gene structures. Motif 1 and Motf 2 occurred in all of the identified IbDofs, Motif 5 and Motif 9 only occurred in subgroup A, and Motif 6-Motif 8 and Motif 10 only occurred in subgroup D. Twelve segment duplicated gene pairs and five tandem duplicated gene pairs of <italic>IbDofs</italic> (<italic>IbDof2/IbDof3</italic>,<italic> IbDof12/IbDof13</italic>,<italic> IbDof9/IbDof10</italic>,<italic> IbDof28/IbDof29</italic>, and<italic> IbDof32/IbDof33</italic>) contributed to the expansion of IbDof family in sweetpotato. The average divergence times of segmental duplication gene pairs and tandem duplicated gene pairs seemed to have emerged 35.22 MYA and 1.86 MYA, and the Ka/Ks ratios of the paralogous<italic> IbDofs </italic>were range from 0.07 (<italic>IbDof12/IbDof13</italic>) to 0.68 (<italic>IbDof6/IbDof25</italic>). Tirty-eight orthologous <italic>IbDof</italic> gene pairs between sweetpotato and their wild relative species <italic>Ipomoea trifida</italic> were involved in duplicated genomic blocks based on synteny analysis. Transcriptome analysis indicated different subgroups expressed specifically in various tissues, and <italic>IbDofs</italic> in the same subgroup also revealed different expression tends. Various hormones and stresses response element were identified in the promoters of <italic>IbDof</italic> genes, and qRT-PCR demonstrated specific<italic> IbDof </italic>genes responded to various environmental stresses, including cold, drought, salt, and H₂O₂. Most <italic>IbDof</italic> genes were regulated by cold treatment; <italic>IbDof10</italic> and<italic> IbDof14</italic> were up-regulated by drought treatment;<italic> IbDof-2</italic>, <italic>-14</italic>,<italic> -37</italic>,<italic> -41</italic>, <italic>-43</italic> were up regulated by high salt stress; and <italic>IbDof-8</italic>,<italic> -10</italic>,<italic> -25</italic>,<italic> -41</italic> were up regulated by H₂O₂ treatment. In summary, our result indicated that <italic>IbDof</italic> family genes coordinately regulated the growth and development of sweetpotato and been involved in the various abiotic stresses process.