Sucrose nonfermenting 2 (Snf2) family proteins, as the catalytic core of ATP-dependent chromatin remodeling complexes, play important roles in nuclear processes as diverse as DNA replication, transcriptional regulation, and DNA repair and recombination. The Snf2 gene family has been characterized in several plant species; some of its members regulate flower development in Arabidopsis. However, little is known about the members of the family in barley (Hordeum vulgare). Here, 38 Snf2 genes unevenly distributed among seven chromosomes were identified from the barley (cv. Morex) genome. Phylogenetic analysis categorized them into 18 subfamilies. They contained combinations of 21 domains and consisted of 3 to 34 exons. Evolution analysis revealed that segmental duplication contributed predominantly to the expansion of the family in barley, and the duplicated gene pairs have undergone purifying selection. About eight hundred Snf2 family genes were identified from 20 barley accessions, ranging from 38 to 41 genes in each. Most of these genes were subjected to purification selection during barley domestication. Most were expressed abundantly during spike development. This study provides a comprehensive characterization of barley Snf2 family members, which should help to improve our understanding of their potential regulatory roles in barley spike development.

Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.

SUMMARY: Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ‐specific transcriptome atlas for wild barley floral organs. Genome‐wide transcription profiles indicated that 22 838 protein‐coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ‐enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ‐enriched expression influence the biological processes in floral organs. The co‐expression regulatory network showed that the expression of 690 genes targeted by MADS‐box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.

The NAC transcription factor family is pivotal in regulating plant development and stress responses, yet its diversity and evolutionary dynamics in barley (Hordeum vulgare) remain underexplored. In this study, we performed a comprehensive pan-genome analysis to identify and characterize the HvNACs across 20 barley accessions. A ranging from 127 to 149 HvNACs were identified in each genome, in which the Morex genome harbored the highest count. These HvNACs were classified into 201 orthogroups, further stratified into core (102), soft-core (18), shell (25), and lineage-specific (56) categories. Phylogenetic analysis delineated them into 12 subfamilies, of which the core genes have undergone strong purifying selection, by contrast, the shell and lineage-specific genes were under relaxed selection constraint, suggesting functional diversification in barley. Genomic variation, such as PAVs and CNVs, largely driven by TEs, highlighted the dynamic nature of NAC loci. Furthermore, transcriptome profiling of the HvNACs demonstrated diverse tissue expression patterns and different response characteristics under salt stress. These findings elucidate the evolutionary and functional dynamics of HvNACs, offering valuable insights for genetic improvement of breeding programs in barley as well as in other crops.

Background: Crown root is the main part of root system, which performs an important role in rice growth and development, especially in nutrition and water assimilation. Previously, we reported negative feedback regulation loop between Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11) and cytokinin by Oryza sativa CYTOKININ OXIDASE/DEHYDROGENASE 4 (OsCKX4) in rice development. Methods: Reverse transcription quantitative RT-PCR analyses was used to analyze the related gene transcript level. Nitrogen and hormone were measured by CHN-Nitrogen analyser and Liquid chromatography mass spectrometer, respectively. Exogenous application of cytokinin and [13C] sucrose labeled stable isotope uptake experiments help us to explain the relationship between OsDOF11 and cytokinin. Results: We demonstrate the role of OsDOF11 in root development. We note that the loss function of OsDOF11 displays the reduced crown roots number, low activity of nitrogen assimilation and low content of cytokinin and auxin. The expression level of WUSCHEL-related homeobox (OsWOX11), A-type response regulator 2 (OsRR2), OsRR3, and OsCKX4 were decreased in osdof11-1, as well as in OsDOF11 RNA interference 9 mutants (RNAi-9 lines). Through Exogenous application of multiple concentrations of cytokinin as treatment to osdof11-1 mutant, RNAi-9 lines, and wild type (WT). We found that the crown roots number of osdof11-1 plants were rescued as the cytokinin concentration increased gradually from 1 μM to 10 μM, but the effect was weaker in RNAi-9 line. And cytokinin inhibited sucrose uptake activity from Murashige-Skoog medium with 3.0% sucrose (MS30) by OsDOF11 in rice root. Conclusions: OsDOF11 promotes crown root formation via cytokinin in oryza sativa. These results provide a physiological basis for further analysis of the OsDOF11 function of in rice root development.