Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions Gómez Martín, Cristina Medina Muñoz, José María Hackenberg, Michael miRNAs Wheat Issue-specific Genome conservation Differential expression miRNA function Drought Kukri RAC875 Excalibur The following are available online at https://www.mdpi.com/article/ 10.3390/biom13030440/s1. Figure S1: Fraction of different RNA species. Figure S2: Read length distribution of all genome mapped reads (a) from total reads (redundant reads) and (b) from unique reads (non-redundant reads. Figure S3: Library normalized RPM values distribution per sample of novel miRNAs. Figure S4: qRT-PCR analysis of the expression of novel miRNA Tae-mir-novel54-5p and known miRNA Tae-miR827c in 10 samples. Figure S5: Network analysis of (a) target genes by drought downregulated miRNAs and (b) drought upregulated miRNAs in leaves. Table S1: Quality and read mapping report. Table S2: Fraction of different RNA species. Table S3: Read length distribution of all genome mapped reads from total reads (redundant reads). Table S4: Read length distribution of all genome mapped reads from unique reads (non-redundant reads. Table S5: All miRNAs expression matrix. Table S6: Expression matrix of all the miRNAs in the SRA datasets. Table S7: miRNA expression matrix of all miRNAs in the Zea mays SRA datasets. Table S8: Degradome based target-gene predicted interactions. Table S9: qRT-PCR assay information. Table S10: Enrichment of functional annotations in miRNA target genes. Table S11: Mature and hairpin sequences of predicted miRNAs. Table S12: Degradome miRNA-target interaction predictions using CleaveLand4. Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced small RNA (sRNA) libraries from the leaves and roots of three wheat cultivars (Kukri, RAC875 and Excalibur) under water and drought conditions. A total of 636 known miRNAs and 294 novel miRNAs were identified, of which 34 miRNAs were tissue- or cultivar-specific. Among these, 314 were significantly regulated under drought conditions. miRNAs that were drought-regulated in all cultivars displayed notably higher expression than those that responded in a cultivar-specific manner. Cultivar-specific drought response miRNAs were mainly detected in roots and showed significantly different drought regulations between cultivars. By using wheat degradome library, 6619 target genes were identified. Many target genes were strongly enriched for protein domains, such as MEKHLA, that play roles in drought response. Targeting analysis showed that drought-downregulated miRNAs targeted more genes than drought- upregulated miRNAs. Furthermore, such genes had more important functions. Additionally, the genes targeted by drought-downregulated miRNAs had multiple interactions with each other, while the genes targeted by drought-upregulated miRNAs had no interactions. Our data provide valuable information on wheat miRNA expression profiles and potential functions in different tissues, cultivars and drought conditions. 2023-05-16T06:33:22Z 2023-05-16T06:33:22Z 2023-02-26 journal article Gómez-Martín, C.; Zhou, H.; Medina, J.M.; Aparicio-Puerta, E.; Shi, B.; Hackenberg, M. Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions. Biomolecules 2023, 13, 440. [https://doi.org/10.3390/ biom13030440] https://hdl.handle.net/10481/81545 10.3390/biom13030440 eng http://creativecommons.org/licenses/by/4.0/ open access Atribución 4.0 Internacional MDPI