Exploring the diversity of promoter and 5'UTR sequences in ancestral, historic and modern wheat

Bioinformatics analysis and development of functional markers for TaMYB4-1A in wheat

MYB transcription factors play crucial roles in various stages of plant growth and development. Bioinformatics analysis revealed that wheat TaMYB4-1A contains two conserved MYB domain. The coding region of TaMYB4-1A is 792 bp, encoding 263 amino acids. TaMYB4-1A is a hydrophilic protein, and its encoded protein is localized in the cell nucleus. Evolutionary tree analysis indicates that the TaMYB4 protein shares the closest relationship with Aegilops, barley, and rye. Tissue-specific expression analysis revealed that TaMYB4-1A is expressed in wheat roots, stems, leaves, and seeds 14 days post-flowering, with the highest expression in the seeds. Promoter cis-acting element analysis showed that the promoter region of TaMYB4-1A contains various cis-acting elements, including meristem regulatory elements, drought-induced elements, and hormone response elements. qRT-PCR analysis showed that the expression of TaMYB4-1A is suppressed under high salinity and PEG treatment, suggesting that TaMYB4-1A may play a critical regulatory role in response to salt and drought stress. There are two haplotypes of TaMYB4-1A, namely Hap-1A-I and Hap-1A-II. The average plant height of varieties with haplotype Hap-1A-I is significantly higher than that of varieties with haplotype Hap-1A-II. This research provides a basis for future in-depth investigation of the biological function of the TaMYB4-1A gene and offers promising candidate genes for molecular marker-assisted wheat breeding.

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.

A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives

As genome resources for wheat (Triticum L.) expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat and other Triticeae species. The core target space includes sequences from 2-Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.0) and regions of open chromatin identified with an assay for transposase-accessible chromatin using sequencing from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of nucleotide basic local alignment search tool (BLASTN) searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216.5 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species.