Molecular Plant最新文献

The molecular regulatory mechanisms underlying spike development critically influence wheat (Triticum aestivum) grain yield but remain incompletely understood. Using spatial transcriptomic analysis at single-cell resolution, we comprehensively mapped the spatiotemporal transcriptomes across five key stages of wheat spike development. Our approach enabled the identification and annotation of nine distinct cell types, revealing the spatiotemporal distribution of hormonal and metabolic signaling pathways across multiple cell populations. Notably, we observed variations in biosynthesis and signaling responses among key phytohormones, particularly cytokinin and auxin. We demonstrated that the rachis cell population plays a crucial role in nutrient and energy supply during spike morphogenesis. The pseudotime and RNA velocity analyses revealed cell populations with distinct differentiation states, highlighting the potential influence of spikelet primordium base (SPB) cells on lateral organ development and grain number determination. By integrating single-nucleus RNA sequencing from the W3.5 stage, gene regulatory relationships, and GWAS data from public databases, we constructed a co-expression regulatory network for wheat spike development and identified a key gene module that regulates multiple spike-related traits. Subsequent investigations characterized heterogeneous subpopulations of SPB cells and identified a novel gene cluster that substantially regulates grain number per spike. Based on spatial transcriptomics data, we have developed a publicly accessible online platform that allows users to interactively query and visualize spatiotemporal gene expression patterns during wheat spike development. Collectively, our study provides a comprehensive molecular framework for early spike development in wheat, offering valuable genetic resources and public data for functional genomics research. These data and knowledge may have significant implications for breeding efforts to optimize spike architecture and enhance wheat's grain yield potential.

Centromeres are indispensable for accurate chromosome segregation, but are subject to rapid sequence turnover while maintaining conserved functions--a paradox in genome evolution. To unravel this paradox, we integrated over 400 fully resolved centromeres from 17 diploid angiosperms spanning 180 million years of divergence, along with 1,000+ pan-genomic assemblies, resequencing datasets, and congeneric whole-genome sequences. We showed that angiosperm centromere organization is determined by lineage-specific combinations of satellite repeats and transposable elements (TEs), which, in turn, shape distinct epigenetic landscapes and evolutionary trajectories within centromeres. In particular, TE insertion patterns were found to be key drivers of structural diversification and positional shift of centromeres in angiosperms. Intriguingly, population-level analyses revealed considerable plasticity in centromere sequences across species, with satellite repeats serving as focal points of evolutionary change and exhibiting species-specific heterogeneity patterns. Temporal reconstructions across congeneric species revealed the emergence and subsequent differentiation of centromeric repeats, outlining a dynamic continuum from gradual sequence diversification to complete turnover during speciation, often accompanied by karyotype reorganization. By integrating intra- and inter-species comparisons, we propose a unifying framework in which centromere innovation is governed by a delicate interplay between genome evolution, chromosomal shuffling, and selection constraints, resulting in phylogenomic signatures of centromere-driven speciation.

Histone methylation is involved in a wide range of biological regulation in plants, and is conducted by three major components, including methyltransferases, demethylases, and histone readers. Compared with the other two components, research on histone readers is relatively limited. In this study, we demonstrate that OsSHH5 functions as an H3K9me1 reader to regulate rice disease resistance, tillering, and grain yield. Loss of OsSHH5 function significantly enhances both grain yield and disease resistance. Mechanistically, OsSHH5 recruits the H3K9 methyltransferase SGD733 and binds to H3K9me1, thereby maintaining H3K9me1 enrichment and facilitating gene silencing. In leaves, OsSHH5 interacts with the transcriptional factor HPY1 to target the resistance-related genes OsWAKg52 and OsWRKY81, maintaining their H3K9me1 levels and suppressing multiple PAMP-triggered immune responses, which ultimately reduces rice disease resistance. In tiller buds, OsSHH5 interacts with the transcriptional factor TCP19 to target the tillering-related gene OsNGR5, maintaining its H3K9me1 enrichment and inhibition of tillering, leading to reduced yield. Collectively, these findings reveal that OsSHH5 plays a vital role in integrating immune response, tillering, and grain yield in rice, providing new insights into the function of histone readers and offering a new strategy to improve rice yield and disease resistance.

Aroma differentiation is a key trait that distinguishes citrus and other horticultural crops from staple crops. However, the mechanistic basis and sensory features of the distinctive and varied citrus-like aromas of citrus remain poorly understood. In this study, we demonstrated that γ-terpinene determines tangerine-like aroma, affects consumer preference, and has pest-repellent properties. Both forward and reverse genetic analyses uncovered the pivotal role of CreTPS3a in γ-terpinene biosynthesis. In addition, we identified a solo long terminal repeat (solo-LTR) insertion upstream of the CreTPS3a promoter in MD1-type domesticated mandarins. We found that the transcription factor CreARF2 specifically binds to this solo-LTR and positively regulates CreTPS3a expression and γ-terpinene accumulation. Notably, this regulatory mechanism may be associated with the geographic distribution patterns of tangerine germplasms. By integrating sensory evaluation with insect behavioral assays, we identified a γ-terpinene sensory threshold of approximately 50 μg/g, which optimally balances pest-repellent properties with consumer preference. Collectively, these findings reveal the molecular mechanisms that underlie the production of tangerine-like aroma, illustrate the complex interactions among citrus plants, human beings, and insects, and offer new possibilities for the development of innovative, eco-friendly strategies that may simultaneously enhance fruit aroma and strengthen plant defense against pests.

Potato is an important crop for ensuring global food and nutritional security. The metabolic transitions and underlying genetic mechanisms that occurred during potato domestication from wild progenitors remain not fully understood. In this study, we used a multi-omics approach to decipher its domestication footprint. The metabolomic remodeling of potato tubers featured a decrease in diversity and content of bitter steroidal glycoalkaloids (SGAs) and an increase in nutritional flavonoid content. Two biosynthesis genes affecting the structural divergence of SGAs and two transcription factors that regulate SGA content in potato were characterized. Two tandem MYB transcription factors were shown to modulate the phenylpropanoid flux between phenolic acids and flavonoids. Furthermore, we uncovered that selection of coding and cis-regulatory variations has substantially reshaped tuber metabolite diversity and content, respectively. Through dissection of the genetic architecture of 2046 loci for 568 metabolites, we identified 2745 epistatic interactions and 268 pleiotropic effects, providing a roadmap for metabolic manipulation in tubers. Taken together, these findings deepen our understanding of potato domestication and offer genetic strategies for developing cultivars with improved quality.

Rice yield remains limited by trade-offs between effective panicle number, grain number per panicle, and grain weight. However, the molecular mechanisms linking auxin transport to panicle formation in rice remain largely unknown. In this study, we conducted genome-wide association studies and identified Suppressor of Effective Panicle 1 (SEP1), which encodes a basic helix-loop-helix transcription factor that negatively regulates effective panicle number and yield. SEP1 directly activates OsPIN1a and OsPIN1b, two auxin efflux carriers that modulate auxin transport and distribution in tiller buds. Natural variation in SEP1 alters the transcriptional activation capacity of SEP1, and the SEP1^Hap2 allelic variant exhibits weaker transcriptional activation of OsPIN1a and OsPIN1b, correlating with its prevalence in Xian cultivars with relatively higher panicle numbers. Furthermore, we discovered that Gnp4/LAX PANICLE 2, a RING finger and WD40-associated ubiquitin-like domain-containing protein, destabilizes SEP1 via ubiquitin-proteasome degradation, fine-tuning auxin transport and tiller bud elongation. Notably, knockout of SEP1 in Xian/Geng cultivars significantly increases yield in field trials. Collectively, our study reveals a molecular mechanism for regulating rice yield and provides a practical strategy for breeding high-yield rice.