Sorghum, the fifth most important food crop globally, is a source of silage forage, fiber, syrup, and biofuel. Moreover, it is widely recognized as an ideal model crop for studying stress biology becaused of its ability to tolerate multiple abiotic stresses, including high salt-alkali conditions, drought, and heat. However, functional genomics studies on sorghum have been challenging, primarily due to the limited availability of genetic resources and effective genetic transformation techniques. In this study, we developed the Sorghum Genomics and Mutation Database (SGMD), aiming to advance the genetic understanding of sorghum. Our effort encompassed a telomere-to-telomere genome assembly of an inbred sorghum line, E048, yielding 729.46 Mb of sequence data representing the complete genome. Alongside the high-quality sequence data, a gene expression atlas covering 13 distinct tissues was developed. We constructed a saturated ethyl methane sulfonate mutant library comprising 13,226 independent mutants. Causal genes in chlorosis and leafy mutants from the library were easily identified by leveraging the MutMap and MutMap+ methodologies, demonstrating the powerful application of this library for identifying functional genes. To facilitate sorghum research, we performed whole-genome sequencing of 179 M mutant lines, resulting in 2,291,074 mutations that covered 97.54% of all genes. In addition, an Agrobacterium-mediated sorghum transformation platform was established for gene function studies. In summary, this work establishes a comprehensive platform and provides valuable resources for functional genomics investigations and genetic improvement of sorghum.

Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has bred numerous cultivated varieties over the last decades that are well adapted to diverse growing regions. However, the genomic bases that underlie the phenotypes of modern cultivars are poorly characterized, limiting access to this vast resource for breeding of specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major growing regions in China. Genomic and phenotypic analyses of this diversity panel revealed regional preferences for genomic backgrounds and specific traits, such as heading date, biotic/abiotic stress resistance, and grain shape, associated with adaptation to local growing conditions and consumer preferences. We identified 3131 QTLs associated with 53 phenotypes across 212 datasets under different environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We rapidly improved the grain shape of the Suigeng4 cultivar using the RiceAtlas breeding design function. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.

Human adiponectin receptors (AdipoRs) and membrane progestin receptors (mPRs, members of the progestin and adipoQ receptor [PAQR] family) are seven-transmembrane receptors involved in the regulation of metabolism and cancer development, which share structural similarities with G protein-coupled receptors. Plant PAQR-like sensors (PLSs) are homologous to human PAQRs but their molecular functions remain unclear. In this study, we found that PLSs associate with cell surface receptor-like kinases through KIN7 and positively regulate plant immune responses, stomatal defense, and disease resistance. Moreover, PLSs activate heterotrimeric G proteins (Gαβγ) to transduce immune signals and regulate the exchange of GDP for GTP on GPA1. Further analyses revealed that the immune function of PLSs is conserved in rice and soybean and contributes to resistance against multiple diseases. Notably, heterologous expression of human AdipoRs in Arabidopsis replicates the immune functions of PLSs. Collectively, our findings demonstrate that PLSs are key modulators of plant immunity via the G-protein pathway and highlight the potential application of human genes in enhancing plant disease resistance.

Coordinated gene transcription in plastid and nucleus is essential for the photosynthetic apparatus assembly during chloroplast biogenesis. Despite identification of several transcription factors regulating the transcription of nuclear-encoded photosynthetic genes,no transcription factor regulating plastid gene transcription has been discovered. Here we report that BAI1 ("albino" in Chinese), a nucleus-plastid dual-targeted C2H2-type zinc finger transcription factor in Arabidopsis, positively regulates and orchestrates the transcription of nuclear and plastid genes. The knockout of BAI1 leads to the blockage of chloroplast formation, albino seedling, and lethality. In plastid, BAI1 is a newly identified functional component of the pTAC (transcriptionally active chromosome complex), which physically interacts with another pTAC component, pTAC12/PAP5/HMR to enable the effective assembly of PEP (plastid-encoded RNA polymerase) complex. The transcript levels of investigated PEP-dependent genes were reduced in the bai1 mutant, while the accumulation of NEP (nuclear-encoded RNA polymerase)-dependent transcripts was increased, indicating that BAI1 plays a vital role in maintaining PEP activity. BAI1 directly binds to the promoter regions of RbcSs, a nuclear gene, and RbcL, a plastid gene, to activate their expression for efficient RubisCO assembly. AtBAI1 homologs TaBAI1, GmBAI1a and GmBAI1b from both monocot and dicot can fully complement the defects of Arabidopsis bai1 mutant. In contrast, PpBAI1, from Physcomitrium patens, only partially complements the bai1 mutant. The phylogenetic analysis of BAI1 and HMR elucidated that both components originated from late-diverging streptophyte algae, following the conservative evolutionary path during plant terrestrialization. In summary, this work unveils a BAI1-mediated transcription regulatory mechanism synchronizing transcription of nuclear and plastid genes, which is required for hybrid photosynthetic complex assembly and could be an intrinsic feature facilitating plant terrestrialization.

Genome editing using CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies. SuperDecode comprises three modules, DSDecodeMS, HiDecode, and LaDecode, each designed to automatically decode mutations from Sanger, high-throughput short-read, and long-read sequencing data, respectively, from targeted PCR amplicons. By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons, HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex target-site editing in a cost-effective manner. We demonstrate the efficacy of SuperDecode by analyzing mutations produced using different genome editing tools (CRISPR/Cas, base editing, and prime editing) in different materials (diploid and tetraploid rice and protoplasts), underscoring its versatility in decoding genome editing outcomes across different applications. Furthermore, this toolkit can be used to analyze other genetic variations, as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene. SuperDecode offers both a standalone software package and a web-based version, ensuring its easy access and broad compatibility across diverse computer systems. Thus, SuperDecode provides a comprehensive platform for analyzing a wide array of mutations, advancing the utility of genome editing for scientific research and genetic engineering.

Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole, we meticulously constructed a transcriptomic atlas and identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members encoding cytokinin oxidase/dehydrogenase (CKX) gene family, was identified as key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as "Pioneer" activator, and GhMYB108, acting as "Successor" activator, orchestrate a sequential modulation GhWRKY70/GhMYB108-GhRLF1-cytokinin (CTK) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines exhibiting rapid leaf falling and requiring less defoliant, while maintaining unaffected cotton yield, were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability.

Genetic transformation is a crucial tool for investigating gene function and advancing molecular breeding in crops, with Agrobacterium tumefaciens-mediated transformation being the primary method for plant genetic modification. However, this approach exhibits significant genotypic dependence in maize. Therefore, to overcome these limitations, we herein combined dynamic transcriptome analysis and genome-wide association study (GWAS) to identify the key genes controlling Agrobacterium infection frequency (AIF) in immature maize embryos. Transcriptome analysis of Agrobacterium-infected embryos uncovered 8483 and 1580 genotype-specific response genes in 18-599R (low AIF) and A188 (high AIF), respectively. A weighted gene co-expression network analysis (WGCNA) further revealed five and seven stage-specific co-expression modules in each corresponding line. Basd on a self-developed AIF quantitation method, the GWAS revealed 30 AIF-associated single nucleotide polymorphisms and 315 candidate genes under multiple environments. Integration of GWAS and WGCNA further identified 12 key genes associated with high AIF in A188, among which, ZmHRGP, encoding a hydroxyproline-rich glycoprotein, was functionally validated as a key factor of AIF in immature embryos. Knockout of ZmHRGP further enabled to establish a high-efficiency genetic transformation system for the 18-599R line, with the transformation frequency being approximately 80%. Moreover, transient reduction of ZmHRGP expression significantly enhanced the AIF of maize calluses and leaves. Overall, these findings advance our understanding of plant factors controlling Agrobacterium infection and contribute to the development of more efficient Agrobacterium-mediated transformation systems in crops.

Edible maize is an important food crop that provides energy and nutrients to meet human health and nutritional requirements. However, how environmental pressures and human activity have shaped the metabolome of edible maize remains unclear. In this study, we collected 452 diverse edible maize accessions worldwide, including waxy, sweet, and field maize. A total of 3020 non-redundant metabolites, including 802 annotated metabolites, were identified using a two-step optimized approach, which generated the most comprehensive annotated metabolite dataset in plants to date. Although specific metabolite differentiation was detected between field and sweet maize and between field and waxy maize, convergent metabolite differentiation was the dominant pattern. We identified hub genes in all metabolite classes by hotspot analysis in a metabolite genome-wide association study. Seventeen and 15 hub genes were selected as the key differentiation genes for flavonoids and lipids, respectively. Surprisingly, almost all of these genes were under diversifying selection, suggesting that diversifying selection was the main genetic mechanism of convergent metabolic differentiation. Further genetic and molecular studies revealed the roles and genetic diversifying selection mechanisms of ZmGPAT11 in convergent metabolite differentiation in the lipid pathway. On the basis of our research, we established the first edible maize metabolome database, EMMDB (https://www.maizemdb.site/home/). We successfully used EMMDB for precision improvement of nutritional and flavor traits and bred the elite inbred line 6644_2, with greatly increased contents of flavonoids, lysophosphatidylcholines, lysophosphatidylethanolamines, and vitamins. Collectively, our study sheds light on the genetic mechanisms of metabolite differentiation in edible maize and provides a database for breeding improvement of flavor and nutritional traits in edible maize by metabolome precision design.

ABA INSENSITIVE 1 (ABI1) and ABI2 are co-receptors of the phytohormone abscisic acid (ABA). Studies have demonstrated that phosphorylation of multiple amino acids on ABI1/2 augments their ability to inhibit ABA signaling in planta. However, it is currently unknown whether there exists a mechanism to regulate the dephosphorylation of ABI1/2 that enhances the plant's sensitivity to ABA. In this study, we identified two protein phosphatases, designated ABI1 Dephosphorylating E clade PP2C 1 (ADEP1) and ADEP2, that interact with ABI1/2. Mutants lacking ADEP1, ADEP2, or both (adep1/2) exhibited reduced sensitivity to ABA-inhibited seed germination, root growth and ABA-induced stomatal closure. Additionally, ABA-induced accumulation of ABI5 protein and the expression of downstream target genes were reduced in the adep1/2 mutant compared to the wild-type. These findings suggest that ADEP1/2 function as positive regulators of the ABA signaling pathway. Mass spectrometry analysis and two-dimensional electrophoresis identified Ser as a major ABA-induced phosphorylation site on ABI1 protein. ADEP1/2 can dephosphorylate Ser, leading to the destabilization of ABI1 protein and increased sensitivity to ABA in plants. Moreover, ABA treatment decreases the abundance of ADEP1/2 proteins. Overall, our study discovers two novel regulatory proteins that modulate ABA signaling and provides new insights into the regulatory network that fine-tune plant ABA responses.