THERMOSENSITIVE BARREN PANICLE (TAP) is required for rice panicle and spikelet development at high ambient temperature

Mining Genetic Variations Reveals the Differentiation of Gene Alternative Polyadenylation Involving in Rice Panicle Architecture Regulation

Panicle architecture is a critical determinant of rice yield and resilience, yet the genetic and environmental factors shaping this trait remain incompletely understood. Here, we applied an integrative genomic approach combining multi-locus association mapping, transcriptome analysis and population genomics to dissect the genetic basis of key panicle traits in rice. We identified robust genetic loci underlying the number of primary branches, panicle length and spikelets per panicle, with many showing sensitivity to temperature, underscoring the importance of gene-environment interactions for yield stability. Notably, we discovered that variation in alternative polyadenylation (APA) of specific transcripts is associated with panicle trait diversity at the population level, suggesting that regulatory mechanisms such as APA are significant contributors to phenotypic plasticity and adaptation. These findings deliver both novel candidate genes in panicle development and mechanistic insights to support the breeding of rice varieties with enhanced productivity and climate resilience.

The MADS6, JAGGED, and YABBY proteins synergistically determine floral organ development in rice

MADS6, JAGGED (JAG), and DROOPING LEAF (DL) are key regulators of floral organ patterns in rice (Oryza sativa); however, how they work together in specifying floral organs remains to be determined. Here, we extensively analyzed the coordination mechanism. Genetic interactions showed that all double/triple mutant combinations of mads6-5 with jag and/or dl-sup7 generated an inflorescence from the spikelet center and lemma-like organs (LLOs) at the periphery, indicating that these genes synergistically promote floral organ specification, inhibit inflorescence initiation, and terminate the floral meristem (FM). Particularly, a fully developed mads6-5 jag spikelet appeared as a large bouquet composed of numerous multifloral complexes (MFC), while the triple mutant was generally similar to mads6-5 jag, except for a longer pedicel and fewer MFCs. Expression analysis revealed that JAG directly inhibits the transcription of MADS6 in stamens but not in pistils, as JAG and DL co-express in pistils and form a JAG-DL complex, indicating that JAG and DL may coordinate the transcription of MADS6 in sexual organs. Protein interactions revealed that MADS6 and JAG bind to 5 spikelet-related YABBY proteins (including DL), forming 10 heterodimers, suggesting that they may promote floral differentiation through various pathways. However, MADS6 and JAG neither bound together nor formed a heterotrimer with any of the 5 YABBY proteins. These findings revealed specific synergistic patterns between MADS6, JAGGED, and YABBY proteins, which may contribute to the unique characteristics of rice spikelets and provide insights into the diversity regulation mechanisms of floral specification in plants.

Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays

A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the Zea mays FARL protein family. This study identifies and characterizes fifteen ZmFARL genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The ZmFARL genes' exon-intron and motif distribution were conserved based on their evolutionary group. The fifteen ZmFARL genes were distributed over seven of the ten Z. mays chromosomes, although no duplication was discovered. Cis-element analysis reveals that ZmFARL genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes ZmFARL2 and ZmFARL5 were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in Z. mays and related species will be aided by the characterization of the FARL genes.

MADS1-regulated lemma and awn development benefits barley yield

Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthate to developing grain. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, affecting grain size and weight. Cytological data indicates that HvMADS1 promotes awn and lemma growth by promoting cell proliferation, while multi-omics data reveals that HvMADS1 target genes are associated with cell cycle, phytohormone signaling, and developmental processes. We define two potential targets of HvMADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants. Additionally, we demonstrate that HvMADS1 interacts with APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development in barley. Notably, we find that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development and provide insights for Triticeae crop improvement strategies.

Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize

As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.