Molecular Plant最新文献

Soybean is one of the most important crops in the world and its production needs to be significantly increased to meet the escalating global demand. Elucidating the genetic regulatory networks underlying soybean organ development is critical for breeding elite and resilient varieties to ensure an increase in soybean production under the changing climates. Integrated transcriptomic atlas that leverages multiple types of transcriptomic data can facilitate the characterization of temporal-spatial expression patterns of most organ development-related genes and thereby help understand organ developmental processes. Here, we constructed a comprehensive integrated transcriptomic atlas for soybean, integrating bulk RNA-seq dataset from 314 samples across the soybean life cycle, along with snRNA-seq and Stereo-seq datasets from five organs: root, nodule, shoot apical, leaf and stem. Taking the investigations of genes related to organ specificity, blade development and nodule formation as examples, we show that the atlas has robust power for exploring key genes involved in organ formation. In addition, we built a user-friendly panoramic database for the transcriptomic atlas, facilitating easy access and queries, which will serve as a valuable resource to significantly advance future soybean functional studies.

A complete reference genome is crucial for biology research and genetic improvement. Owing to its large size and highly repetitive nature, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome. Here, we generated a 14.46 Gb near-completed assembly of the CS genome, with a contig N50 over 266 Mb and an overall base accuracy of 99.9963%. Among the 290 gaps that remained (26, 257 and 7 gaps from the A, B and D subgenomes, respectively), 278 gaps were extremely high-copy tandem repeats, whereas the remaining 12 were TE-associated gaps. Four chromosomes were completely gap-free, including chr1D, chr3D, chr4D and chr5D. Extensive annotation of the near-complete genome revealed 151,405 high-confidence genes, of which 59,180 high-confidence genes were newly annotated, including 7,602 newly assembled genes. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled. Our near-complete assembly revealed that the extent of tandem repeats, such as SSRs, was highly uneven among different subgenomes. Similarly, the repeat compositions of the centromeres also varied among the three subgenomes. With the genome sequences of all six types of seed storage proteins fully assembled, the expression of ω-gliadin was found to be contributed entirely by the B subgenome, whereas the expression of the other 5 types of SSPs was most abundant from the D subgenome. The near-complete CS genome will serve as a valuable resource for the research and breeding of wheat as well as its related species.

Plant cell expansion is regulated by hormones and driven by turgor pressure, which stretches the cell wall and can potentially cause wall damage or rupture. How plant cells avoid cell wall rupture during hormone-induced rapid cell expansion remains poorly understood. Here, we show that the wall-sensing receptor kinase FERONIA (FER) plays an essential role in maintaining cell wall integrity during brassinosteroid (BR)-induced cell elongation. Compared to the wild type, the BR-treated fer mutants display an increased initial acceleration of cell elongation, increased cell wall damage and rupture, reduced production of reactive oxygen species (ROS), and enhanced cell wall acidification. Long-term treatments of fer with high concentrations of BR cause stress responses and reduce growth, whereas osmolytes, reducing turgor, alleviate the defects. These results show that BR-induced cell elongation causes damage to cell walls and the release of cell wall fragments that activate FER, which promotes ROS production, attenuates apoplastic acidification, and slows cell elongation, thereby preventing further cell wall damage and rupture. Furthermore, we show that BR signaling promotes FER accumulation at the plasma membrane (PM). When the BR level is low, the GSK3-like kinase BIN2 phosphorylates FER to reduce FER accumulation and translocation from the endoplasmic reticulum to PM. BR-induced inactivation of BIN2 leads to dephosphorylation and PM accumulation of FER. Thus, BR signaling enhances FER-mediated cell wall integrity surveillance while promoting cell expansion, whereas FER acts as a brake to maintain a safe cell elongation rate. Our study reveals a vital signaling circuit that coordinates hormone signaling with mechanical sensing to prevent cell rupture during hormone-induced cell expansion.

Barley (Hordeum vulgare ssp. vulgare) is one of the oldest founder crops in human civilization and has been widely dispersed across the globe to support human society as a livestock feed and a raw material for the brewing industries. Since the early half of the 20th century, it has been used for innovative research on cytogenetics, biochemistry, and genetics, facilitated by its mode of reproduction through self-pollination and its true diploid status, which have contributed to the accumulation of numerous germplasm and mutant resources. In the era of molecular genomics and biology, a multitude of barley genes and their related regulatory mechanisms have been identified and functionally validated, providing a paradigm for equivalent studies in other Triticeae crops. This review highlights important advances on barley research over the past decade, focusing mainly on genomics and genomics-assisted germplasm exploration, genetic dissection of developmental and adaptation-related traits, and the complex dynamics of yield and quality formation. In the coming decade, the prospect of integrating these innovations in barley research and breeding shows great promise. Barley is proposed as a reference Triticeae crop for the discovery and functional validation of new genes and the dissection of their molecular mechanisms. The application of precise genome editing as well as genomic prediction and selection, further enhanced by artificial intelligence-based tools and applications, is expected to promote barley improvement to efficiently meet the evolving global demands for this important crop.

Medicago, a genus in the Leguminosae or Fabaceae family, includes the most globally significant forage crops, notably alfalfa (Medicago sativa). Its close diploid relative Medicago truncatula serves as an exemplary model plant for investigating legume growth and development, as well as symbiosis with rhizobia. Over the past decade, advances in Medicago genomics have significantly deepened our understanding of the molecular regulatory mechanisms that underlie various traits. In this review, we comprehensively summarize research progress on Medicago genomics, growth and development (including compound leaf development, shoot branching, flowering time regulation, inflorescence development, floral organ development, and seed dormancy), resistance to abiotic and biotic stresses, and symbiotic nitrogen fixation with rhizobia, as well as molecular breeding. We propose avenues for molecular biology research on Medicago in the coming decade, highlighting those areas that have yet to be investigated or that remain ambiguous.

Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet further increase in global maize production faces mounting challenges in a changing world. In this Perspective paper, we overview the historical successes of maize breeding that laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology approaches. A transition toward a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.