As a major adverse environmental factor in most parts of the world, drought causes substantial crop yield losses. Rice (Oryza sativa) is one of the staple foods for more than one-half of the world’s population. Rice plants are sensitive to even mild drought stress and need almost twice the amount of water compared to wheat (Triticum aestivum) or maize (Zea mays). Arabidopsis (Arabidopsis thaliana) small GTPase Nucleolar GTP-binding protein 1 (AtNOG1) plays a role in biotic stress tolerance. Here, we created transgenic rice lines constitutively overexpressing AtNOG1-1 or AtNOG1-2. We also developed rice RNA interference (RNAi) lines that show downregulation of OsNOG1. AtNOG1-1 and AtNOG1-2 overexpressors showed enhanced drought tolerance without compromising grain yield, whereas OsNOG1-RNAi was more susceptible to drought when compared to wild-type plants. Analysis of physiological parameters showed increased cell sap osmolality, relative water content, and abscisic acid (ABA) level, but decreased leaf water loss in AtNOG1-1 or AtNOG1-2 overexpressor lines compared to the control. We found upregulation of several genes involved in ABA and jasmonic acid (JA) signaling, stomata regulation, osmotic potential maintenance, stress protection, and disease resistance in AtNOG1-1 and AtNOG1-2 overexpressor lines compared to the control. We elucidated the role of NOG1-2 and NOG1-1 in regulation of silica body formation around stomata to prevent transpirational water loss. These results provide an avenue to confer drought tolerance in rice.

Background: Cultivated strawberry (Fragaria xananassa Duch.), an allo-octoploid species arising from at least 3 diploid progenitors, poses a challenge for genomic analysis due to its high levels of heterozygosity and the complex nature of its polyploid genome. Results: This study developed the complete haplotype-phased genome sequence from a short-day strawberry, ‘Florida Brilliance’ without parental data, assembling 56 chromosomes from telomere to telomere. This assembly was achieved with high-fidelity long reads and high-throughput chromatic capture sequencing (Hi-C). The centromere core regions and 96,104 genes were annotated using long-read isoform RNA sequencing. Using the high quality of the haplotype-phased reference genome, FaFB1, we identified the causal mutation within the gene encoding Leaf Rust 10 Disease-Resistance Locus Receptor-like Protein Kinase (LRK10) that confers resistance to anthracnose fruit rot (AFR). This disease is caused by the Colletotrichum acutatum species complex and results in significant economic losses in strawberry production. Comparison of resistant and susceptible haplotype assemblies and full-length transcript data revealed a 29-bp insertion at the first exon of the susceptible allele, leading to a premature stop codon and loss of gene function. The functional role of LRK10 in resistance to AFR was validated using a simplified Agrobacterium-based transformation method for transient gene expression analysis in strawberry fruits. Transient knockdown and overexpression of LRK10 in fruit indicate a key role for LRK10 in AFR resistance in strawberry. Conclusions: The FaFB1 assembly along with other resources will be valuable for the discovery of additional candidate genes associated with disease resistance and fruit quality, which will not only advance our understanding of genes and their functions but also facilitate advancements in genome editing in strawberry.

Background: The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle. Results: Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups. Conclusions: These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, 'Florida Brilliance' (FaFB1) and 'Royal Royce' (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries.

Understanding gene function is important for crop improvement and breeding efforts, especially in a genetically complex polyploid plant species such as the octoploid strawberry. Agrobacterium-mediated transient assays are a widely used tool for investigating gene functions and offer a reliable alternative to stable transformation. However, variability in tissue-specific responses and inconsistent applicability of Agrobacterium-mediated transient assay across diverse plant species can be challenging. In this study, we provide a method utilizing Agrobacterium-mediated transient expression to examine the function of genes in octoploid strawberry. Our approach encompasses leaf, root, and fruit tissues, providing a comprehensive strategy for validating gene functions in strawberries. Through meticulous optimization and validation in planta, this method offers valuable insights into gene function in strawberry functional genomics and genetics research. By addressing tissue-specific variability, our methodology serves as a valuable technical resource that could facilitate advancements in identifying gene functions in octoploid strawberry.

Phytophthora crown rot, caused by Phytophthora cactorum , is a soilborne disease with broad impacts on cultivated strawberry ( Fragaria × ananassa ). A resistance locus, RPc2 , was previously identified in octoploid strawberries, but the underlying genomic architecture and causal genes remained uncharacterized. In this study, we fine‐mapped RPc2 from a 1.12 Mb interval to a 546 kb region containing 92 genes by genotyping an association panel of 339 accessions with high‐resolution subgenome‐specific markers. To discover candidate genes, a chromosome‐scale haplotype‐phased genome of the resistant breeding line FL16.33‐8 was assembled and validated with a high‐density genetic map and comparative analyses with high‐quality phased octoploid reference genomes, Florida Brilliance and Royal Royce. Transcriptome profiling following pathogen inoculation combined with comparative genomics identified wall‐associated kinase 1 ( WAK1 ) and cyclic nucleotide‐gated channel ( CNGC1 CNGC2 ) as strong candidates within the RPc2 region. Using an efficient Agrobacterium ‐mediated transient expression assay, we confirmed their role in resistance to P . cactorum in strawberry. RNA interference knockdown of these genes increased disease severity, while overexpression of WAK1 or CNGC1 reduced crown rot symptoms in susceptible backgrounds. Furthermore, population analyses of 1029 global accessions revealed that the predominant‐resistant haplotype ( RPc2 ‐ H3 ) is common in modern cultivars and shows evidence of positive selection in breeding programs. Taken together, our study refines the genomic region of RPc2 , identifies and functionally validates WAK1 and CNGC1/2 for the resistance to Phytophthora crown rot, and demonstrates that RPc2‐H3 has been selected globally. These findings from this study would facilitate the advancement of genome‐assisted breeding strategies for resistance to Phytophthora crown rot in strawberry.