Plant Physiology最新文献

Soybean cyst nematode (SCN, Heterodera glycines [HG]) causes significant soybean yield losses. The Rhg1 locus is a major contributor to SCN resistance and contains 3 genes that mediate this trait, including Rhg1-GmAAT (Glyma.18G022400), which encodes the putative amino acid transporter AATRhg1. The molecular function of AATRhg1 in SCN resistance is not understood. In this study, rhg1-b soybean lines with Rhg1-GmAAT silencing demonstrated that Rhg1-GmAAT can contribute to resistance against HG 0 SCN and also against problematic HG 2.5.7 populations that partially overcome rhg1-b-mediated resistance. When 2 previously characterized AATRhg1 mutants with contrasting effects on amino acid and betalain accumulation were tested for SCN resistance, the AATRhg1 Y268L mutant complemented SCN resistance in Rhg1-GmAAT-silenced plants, while the D122A mutant did not. Overexpression of Rhg1-GmAAT was not sufficient to enhance SCN resistance, suggesting that AATRhg1 requires coordinated activity with other proteins or pathways. Confocal microscopy demonstrated that AATRhg1 localizes to the tonoplast in soybean root cells. Amino acid, transcriptomic, and metabolomic profiles were determined for root segments collected 3 d after mock or SCN inoculation. In Rhg1-GmAAT-silenced rhg1-b plants relative to fully resistant (non-silenced) rhg1-b plants, levels of leucine, isoleucine, and tyrosine were significantly elevated. Rhg1-GmAAT silencing reduced SCN-responsive transcript abundances for multiple processes, significantly including genes for mitogen-activated protein kinase (MAPK) signaling, ethylene-associated responses, and starch and sucrose metabolism. The most common identified metabolomic changes were in amino acid derivatives, shikimate/phenylpropanoid/isoflavonoid compounds, terpenoids, and especially fatty acids. These findings can guide further investigation into the mechanisms by which AATRhg1 contributes to SCN resistance.

The emergence of clustered regularly interspaced short palindromic repeats (CRISPR) technology has revolutionized plant genome engineering over the past decade. This review begins by highlighting 4 seminal early CRISPR studies published in Plant Physiology that laid critical foundations for crop genome editing and tool development. We then summarize major advances in optimizing CRISPR performance, expanding targeting scope, and developing strategies for transgene removal and transient editing. We also discuss a wide array of innovative applications beyond gene knockout, such as gene targeting, chromosome engineering, synthetic apomixis, and gene drive. Furthermore, we introduce key CRISPR-derived tools, including base editors, prime editors, and programmable transcriptional and epigenetic regulators. Finally, we outline remaining challenges to stimulate future exploration of the full potential of CRISPR toolkits.

Alien chromosome addition lines hold significant value for breeding and genetic research. However, the genetic interaction between the recipient genome(s) and the alien chromosomes remains largely unclear. Here, we analyzed the genomic composition and gene expression of 2 purple-leaved Brassica napus alien addition lines carrying chromosome B05 from B. juncea: the monosomic line ZYCB3 (MAAL, 2n = 39, AACC + 1B05) and the disomic line ZY52 (DAAL, 2n = 40, AACC + 2B05). We assembled a chromosome-level genome of the DAAL ZY52 disomic line and characterized its genomic variation and chromosome introgression patterns. In addition to chromosome B05, multiple introgressed fragments derived from the donor B. juncea line ZYJC were identified, revealing extensive genome remodeling during distant hybridization and backcross breeding. We then used multi-omics approaches to explore chromosomal interactions and the regulation of anthocyanin biosynthesis. Notably, the addition of chromosome B05 was associated with stronger repression of homoeologous genes on C-subgenome chromosomes than on A-subgenome chromosomes. In ZY52, homoeologous genes on chromosome C01 showed reduced expression, whereas in the ZYCB3 monosomic line reduced expression was observed on both C01 and C02. Comparative transcriptomic and metabolomic analyses further showed that highly expressed anthocyanin biosynthesis genes (ABGs) on chromosome B05contributed to anthocyanin accumulation and the purple-leaf phenotype in both addition lines. Overall, this study provides new insights into interchromosomal interactions, genome remodeling, and phenotypic variation in alien addition lines.

Numerous pathogens invade plants through stomata, and plants, on the other hand, could close the stomata after sensing the pathogen-associated molecular patterns (PAMPs). Subsequently, pathogens could overcome this plant immune response with their phytotoxins and effectors. A previous study showed that Plasmopara viticola, a strictly obligate biotrophic oomycete, could inhibit the Vitis vinifera stomatal closure to promote infection. However, the underlying mechanism stimulating the stomata movement is still poorly understood. Here we demonstrate that PvRxLR24, an effector from P. viticola, functions analogously to a phosphatase by directly inhibiting the kinase activity of OPEN STOMATA 1 (OST1), a central regulator of abscisic acid (ABA) signaling and stomatal closure. This inhibition subsequently abolishes the activation of the slow-type anion channel SLAC1, resulting in a "stomatal lock" open state. Our study demonstrated that OST1 is the direct target of pathogen effectors, shedding light on a new mechanism by which pathogens could manipulate the plant ABA signaling pathways to influence stomatal movement for successful invasion.

Plant-virus protein-protein interactions (PPIs) play crucial roles in viral infection and host immune responses. However, large-scale experimental characterization of plant-virus PPIs is costly and labor-intensive, suggesting the need to develop computational methods. Recent advances in biological sequence language models are offering unprecedented opportunities to develop machine learning-based plant virus PPI predictors. In this study, we collected publicly available PPI data between Arabidopsis thaliana (A. thaliana) and viruses, establishing a robust dataset for method development. Based on this dataset, we developed AraVirusPPI, a machine learning framework for predicting A. thaliana virus PPIs. AraVirusPPI employs the protein language model ESM Cambrian (ESMC) to encode sequence features and combines these representations with Extreme Gradient Boosting (XGBoost) to build the prediction model. Furthermore, we systematically evaluated multiple protein and genomic language models combined with various classification algorithms, thereby justifying the optimal model architecture adopted in AraVirusPPI. We applied AraVirusPPI to predict PPIs in the A. thaliana-Cabbage leaf curl virus (CabLCV) system. Predicted viral target proteins were compared with experimental datasets from A. thaliana-Turnip mosaic virus (TuMV) and A. thaliana-Pseudomonas syringae (Psy) systems. Network topology and functional enrichment analyses showed that the predicted CabLCV targets in A. thaliana were more similar to TuMV than Psy targets. These results suggest potential shared and distinct host-targeting patterns among pathogens and provide computational evidence supporting the biological significance of the proposed AraVirusPPI predictor.

Alternative polyadenylation (APA) serves as a critical cotranscriptional regulatory mechanism that shapes messenger RNA fate and protein function. POLY(A) POLYMERASE 1 (PAPS1) contributes to poly(A) tail synthesis; however, its relationship to poly(A) site choice is less well characterized. Here, we profiled PAPS1-associated poly(A) site usage across Arabidopsis (Arabidopsis thaliana) tissues using unique molecular identifier-quantified poly(A) tag sequencing. Across tissues, paps1-4 showed tissue-dependent shifts in poly(A) site usage, with pronounced effects in pollen. In the paps1-4 mutant, polyadenylated transcripts were biased toward longer isoforms with significantly longer 3' untranslated regions, and poly(A) signal usage was altered in distinct ways: a U-to-A shift immediately downstream of poly(A) sites occurred in leaves and flower buds, whereas pollen showed more complex motif combinations with reduced usage of canonical cis-elements. In pollen, differentially expressed APA genes included multiple genes previously linked to a pollen developmental regulatory module involving AT-RICH INTERACTING DOMAIN-CONTAINING PROTEIN 1 (ARID1), RETINOBLASTOMA RELATED 1 (RBR1), and DUO POLLEN1 (DUO1), showing coordinated changes in APA and expression. Flowering time-related terms were also enriched among genes with significantly altered APA in paps1-4, including regulators connected to FLOWERING LOCUS C (FLC) and photoperiod responses, and these changes were more consistent with poly(A) site selection differences than with widespread poly(A) tail length changes. Notably, multiple poly(A) factors in pollen switched between single- and multi-poly(A) site usage patterns in paps1-4, representing a major component of PAPS1-associated regulation. Together, these findings reveal tissue-specific APA alterations associated with PAPS1 and highlight pollen and flowering pathways as key contexts of its regulatory influence.

The development of perpetual flowering (PF) cultivars revolutionized octoploid strawberry (Fragaria  ×  ananassa) cultivation by enabling nearly year-round fruit production and doubling fruit yields compared to historic seasonal flowering (SF) cultivars, which flower in spring. Most commercial PF cultivars result from the introgression of a dominant PERPETUAL FLOWERING (PF) allele at the PERPETUAL FLOWERING RUNNERING (PFRU) locus. PFRU has been genetically and physically mapped to chromosome 4B, but the causal gene(s) remain unknown. Here we used the haplotype-phased "UCD Royal Royce" (PFpf) genome, next-generation sequencing-based k-mer genome-wide association study (k-mer GWAS), and RNAseq to investigate PFRU. We narrowed the locus down to a precise physical address and revealed abundant genetic and transcriptomic differences in the locus and associated with flowering. Outside the PFRU locus, flowering regulation diverges at expression of TERMINAL FLOWER 1 (TFL1) in all 4 subgenomes, analogous to diploid Fragaria vesca. This critical step of the flowering pathway is altered by PF in diverse cultivars, and gene editing knockout of TFL1 is sufficient to induce flowering under long days in a seasonal flowering cultivar. Together, these results shed light on the mechanism of flowering regulation by the PF locus and expand biotechnological approaches to achieve extended flowering in any strawberry cultivar.