The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding.

Remorin genes encode plant-specific and plasma-membrane-associated proteins that play important roles in several plant physiological processes and adaptations to environmental adaptations. However, little is known regarding the remorin gene family in foxtail millet (Setaria italica), a traditional drought-resistant crop that grows in China. In this study, 21 remorin genes in the foxtail millet genome were identified, renamed according to their chromosomal distribution, and classified into four main groups based on their phylogenetic relationships and structural features. Additionally, we found that SiREM gene family expansion was primarily because of whole- genome duplication and segmental duplication events. Evolutionary changes in the remorin family in Poaceae crops were clarified via synteny analyses. Gene expression analyses through RT-PCR and qRT-PCR indicated that SiREM genes influenced millet growth and development, particularly SiREM1, 4, 11, and 12. Concurrently, SiREM genes expression showed inconsistent response to phytohormone treatments and abiotic stresses, suggesting that they are regulated by different signaling pathways. This systematic reanalysis remorin gene family in the foxtail millet provides fundamental information about the biological functions associated with growth, development, and stress tolerance and evolutionary characteristics, thus helping in elucidating the molecular mechanism and improving the agricultural traits of this crop in the future.

Valine–glutamine (VQ) motif-containing proteins are transcriptional regulatory cofactors that play critical roles in plant growth and response to biotic and abiotic stresses. However, information on the VQ gene family in foxtail millet (Setaria italica L.) is currently limited. In this study, a total of 32 SiVQ genes were identified in foxtail millet and classified into seven groups (I–VII), based on the constructed phylogenetic relationships; the protein-conserved motif showed high similarity within each group. Gene structure analysis showed that most SiVQs had no introns. Whole-genome duplication analysis revealed that segmental duplications contributed to the expansion of the SiVQ gene family. The cis-element analysis demonstrated that growth and development, stress response, and hormone-response-related cis-elements were all widely distributed in the promoters of the SiVQs. Gene expression analysis demonstrated that the expression of most SiVQ genes was induced by abiotic stress and phytohormone treatments, and seven SiVQ genes showed significant upregulation under both abiotic stress and phytohormone treatments. A potential interaction network between SiVQs and SiWRKYs was predicted. This research provides a basis to further investigate the molecular function of VQs in plant growth and abiotic stress responses.