Transcription factors (TFs) are important regulators of numerous gene expressions due to their ability to recognize and combine cis-elements in the promoters of target genes. The INDETERMINATE DOMAIN (IDD) gene family belongs to a subfamily of C2H2 zinc finger proteins and has been identified only in terrestrial plants. Nevertheless, little study has been reported concerning the genome-wide analysis of the IDD gene family in maize. In total, 22 ZmIDD genes were identified, which can be distributed on 8 chromosomes in maize. On the basis of evolutionary relationships and conserved motif analysis, ZmIDDs were categorized into three clades (1, 2, and 3), each owning 4, 6, and 12 genes, respectively. We analyzed the characteristics of gene structure and found that 3 of the 22 ZmIDD genes do not contain an intron. Cis-element analysis of the ZmIDD promoter showed that most ZmIDD genes possessed at least one ABRE or MBS cis-element, and some ZmIDD genes owned the AuxRR-core, TCA-element, TC-rich repeats, and LTR cis-element. The Ka:Ks ratio of eight segmentally duplicated gene pairs demonstrated that the ZmIDD gene families had undergone a purifying selection. Then, the transcription levels of ZmIDDs were analyzed, and they showed great differences in diverse tissues as well as abiotic stresses. Furthermore, regulatory networks were constructed through the prediction of ZmIDD-targeted genes and miRNAs, which can inhibit the transcription of ZmIDDs. In total, 6 ZmIDDs and 22 miRNAs were discovered, which can target 180 genes and depress the expression of 9 ZmIDDs, respectively. Taken together, the results give us valuable information for studying the function of ZmIDDs involved in plant development and climate resilience in maize.

Aluminum toxicity is a major abiotic stress on acidic soils, leading to restricted root growth and reduced plant yield. Long non-coding RNAs are crucial signaling molecules regulating the expression of downstream genes, particularly under abiotic stress conditions. However, the extent to which lncRNAs participate in the response to aluminum (Al) stress in barley remains largely unknown. Here, we conducted RNA sequencing of root samples under aluminum stress and compared the lncRNA transcriptomes of two Tibetan wild barley genotypes, XZ16 (Al-tolerant) and XZ61 (Al-sensitive), as well as the aluminum-tolerant cultivar Dayton. In total, 268 lncRNAs were identified as aluminum-responsive genes on the basis of their differential expression profiles under aluminum treatment. Through target gene prediction analysis, we identified 938 candidate lncRNA-messenger RNA (mRNA) pairs that function in a cis-acting manner. Subsequently, enrichment analysis showed that the genes targeted by aluminum-responsive lncRNAs were involved in diterpenoid biosynthesis, peroxisome function, and starch/sucrose metabolism. Further analysis of genotype differences in the transcriptome led to the identification of 15 aluminum-responsive lncRNAs specifically altered by aluminum stress in XZ16. The RNA sequencing data were further validated by RT-qPCR. The functional roles of lncRNA-mRNA interactions demonstrated that these lncRNAs are involved in the signal transduction of secondary messengers, and a disease resistance protein, such as RPP13-like protein 4, is probably involved in aluminum tolerance in XZ16. The current findings significantly contribute to our understanding of the regulatory roles of lncRNAs in aluminum tolerance and extend our knowledge of their importance in plant responses to aluminum stress.

Background: INDETERMINATE DOMAIN ( IDD ) is a unique C2H2 zinc finger protein subfamily in plants. It has been thoroughly studied in Arabidopsis and is widely involved in the growth and development of various plants and stress response. Following wheat, maize and rice, barley stands as the fourth major cereal crop. In contrast, there are limited studies on the IDD gene family in Hordeum vulgare . Therefore, this study comprehensively identified and analyzed the barley IDD gene family by bioinformatics methods. Results: A total of 13 HvIDD family genes were detected and classified into three subfamilies. Ten conserved motifs were identified by motif analysis. Through chromosome localization analysis, 13 HvIDD genes were found to be located on multiple chromosomes, of which 4 HvIDD s were found on chromosomes 3 and 4, respectively. In addition, analysis of cis-acting element in promoter revealed a variety of elements, such as O2-site, ARE, LTR, TGA-element and MRE, which play an important role in regulating gene expression. In our study, six miRNAs were predicted to interact with HvIDDs and HvIDD4/5/7/9/13 could regulate 72 genes expression, which enriched in membrane-binding pathways. Conclusion: In summary, these findings provide valuable insights for future functional verification of HvIDDs and contribute to a deeper understanding of the role of HvIDDs in response to stress conditions in barley.

Rapid alkalinization factors (RALFs) are plant-derived cysteine-rich peptides that have been widely studied in Arabidopsis, where they regulate pollen tube