Replacing chemical nitrogen (N) fertilizer with organic fertilizer is widely considered an effective approach to sustain and enhance crop yields under reduced chemical fertilizer inputs. However, the underlying physiological mechanisms remain unclear. This study quantified source-sink growth dynamics and canopy photosynthetic traits in foxtail millet (Setaria italica L.) under varying N reduction ratios (15%, N-15; 30%, N-30) and organic substitution ratios (15%, N+15org; 30%, N+30org) relative to conventional N application (CT, 150 kg ha-1). The results indicated that moderate N fertilizer reduction (15%) exerted no significant adverse effects on grain yield or quality. However, compared with the CT treatment, the N-30 treatment significantly decreased panicle weight and total grain yield by 5.6—8.9% and 9.5—11.2%, the contents of yellow pigment, starch, and protein were lowered by 15.4—30.1%, 2.7—3.6%, and 5.7—9.2%, source and sink activities were significantly suppressed by 21.9—27.3% and 6.1—14.1%, respectively (p < 0.05). Conversely, replacing 30% of chemical N with organic fertilizer (N+30org) significantly increased grain yield by 17.3—23.5%, grain protein content by 6.6—12.2%, and the amylopectin/amylose ratio by 7.5—17.9% relative to CT (p < 0.05). The N+30org treatment enhanced the leaf area index (LAI, 7.0—11.3%), net photosynthetic rate (Pn, 10.6—21.2%), transpiration rate (Tr, 12.1—24.4%), stomatal conductance (Gs, 9.6—16.4%), and the actual quantum efficiency of PSII (ΦPSII, 13.2—15.7%) during the late grain-filling stage (30—40 days after anthesis). Concurrently, the time required to reach peak sink activity (tm,o) was prolonged by 6—11 days by the organic substitution strategy, which also boosted both source and sink activities, expanded the maximum sink biomass (Wmax,h) by 9.8—15.7%, and increased the sink-to-source ratio by 8.7—11.4%. Random Forest importance assessment and partial least squares path modeling (PLS-PM) revealed that grain yield formation was closely associated with sink and source relationships, whereas canopy photosynthetic characteristics may contribute to grain quality. Substituting 30% of chemical N with organic fertilizer was associated with a slower decline in canopy photosynthetic performance and mitigated source supply limitations induced by N fertilizer reduction. Consequently, high photosynthetic capacity during the late grain-filling stage was maintained, and source-sink capacity and activity were substantially enhanced, thereby achieving a synergistic optimization of high yield and superior quality in foxtail millet.

The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net ), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.

Branching is a crucial ornamental trait in chrysanthemum (Chrysanthemum morifolium), directly determining its cultivation methods, ornamental quality, and production costs. The AP2 transcription factor family governs diverse aspects of growth and development in plant; however, the role of these genes in plant branching remains unclear. In this study, we identified a novel AP2 protein, CmAP2, which interacts with CmRAX2—a chrysanthemum homolog of RAX2 that functions as a positive regulator of branching. This interaction was confirmed through yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), dual-luciferase complementation assay (LCA), and co-immunoprecipitation (Co-IP) experiments. Furthermore, heterologous overexpression of CmAP2 in Arabidopsis thaliana significantly enhanced branching and induced a late-flowering phenotype. Consistently, in chrysanthemum, overexpression of CmAP2 promoted axillary bud outgrowth, increased axillary bud number, and enhanced plant height. Moreover, CmRAX2 and CmAP2 were rapidly induced by decapitation, and the expression trends were similarly. RNA-seq analysis further revealed significant differential expression of genes associated with cytokinin biosynthesis and signaling pathways in transgenic lines. Collectively, our findings demonstrate that CmAP2 interacts with CmRAX2 and positively regulates branching while concomitantly altering the expression of cytokinin-related genes.

Certain tree species can reach ages of centuries, whereas lifespan of species like apple are markedly shorter. The latter is caused by negative plant-soil feedback that results in microbiome changes. We hypothesized that tree species with a long lifespan will be able to avoid such negative feedback and their root-associated microbiomes will be similar in trees of different ages. To test this, we used Chinese chestnut (Castanea mollissima) trees, ranging from 8 to 830 years old from a Ming orchard at the Great Wall. Their root-associated microbiomes were analysed by using meta-amplicon sequencing analysis. Their root-associated bacterial microbiomes were rather similar although based on linear regression models we cannot exclude that age has a weak correlation with microbiome compositions. When chestnut seedlings were grown for 3 months in soil associated with young or old trees, the plants were healthy and their growth was similar. This strongly supported that negative feedback had not occurred. Pseudomonas OTU1, a member of the core microbiome and representing >50 % of the rhizosphere community, strongly inhibited growth of chestnut pathogens and stimulated plant growth. Such properties of the microbiome, in combination with a high number of resistance genes can contribute to longevity of chestnut.

Chinese chestnut (Castanea mollissima [C. mollissima] Blume), an important nut crop with recalcitrant seeds and contributor to forest ecosystem services, faces challenges due to seed abortion, which seriously influences yield. In this study, stark microstructural and ultrastructural differences were observed between fertile and abortive seeds, with the abortive seeds exhibiting abnormal cell wall shapes and irregular thickening. Immunohistochemical labelling revealed that the content of demethylesterified homogalacturonan (HG) pectin in the cell wall of abortive seeds was significantly lower than fertile seeds. Through a genome-wide analysis, a total of 16 Pectate Lyase-Like (PLL) genes were identified in C. mollissima. Based on the qRT-PCR analysis and subcellular localization observation, CmPLL16a and CmPLL16b were found to be highly expressed in abortive seeds and localized to the cell wall. Silencing of CmPLL16a and CmPLL16b led to an increase in demethylesterified HG pectin concentrations, thereby enhancing somatic embryogenesis in the RNAi lines. In contrast, overexpression of CmPLL16a and CmPLL16b resulted in reduced demethylesterified HG pectin concentrations and decreased embryo production in calli. This study pioneers gene knockdown in Chinese chestnut somatic embryos to analyze gene function, achieving a key technical breakthrough. These findings reveal CmPLLs' roles and provide genetic targets for enhancing somatic embryogenesis in C. mollissima.

Protein S-acyl transferases (PATs) are a family of enzymes that catalyze protein S-acylation, a post-translational lipid modification involved in protein membrane targeting, trafficking, stability, and protein–protein interaction. S-acylation plays important roles in plant growth, development, and stress responses. Here, we report the genome-wide analysis of the PAT family genes in the woodland strawberry (Fragaria vesca), a model plant for studying the economically important Rosaceae family. In total, 21 ‘Asp-His-His-Cys’ Cys Rich Domain (DHHC-CRD)-containing sequences were identified, named here as FvPAT1-21. Expression profiling by reverse transcription quantitative PCR (RT-qPCR) showed that all the 21 FvPATs were expressed ubiquitously in seedlings and different tissues from adult plants, with notably high levels present in vegetative tissues and young fruits. Treating seedlings with hormones indole-3-acetic acid (IAA), abscisic acid (ABA), and salicylic acid (SA) rapidly increased the transcription of most FvPATs. A complementation assay in yeast PAT mutant akr1 and auto-S-acylation assay of one FvPAT (FvPAT19) confirmed its enzyme activity where the Cys in the DHHC motif was required. An AlphaFold prediction of the DHHC and the mutated DHHC155S of FvPAT19 provided further proof of the importance of C155 in fatty acid binding. Together, our data clearly demonstrated that S-acylation catalyzed by FvPATs plays important roles in growth, development, and stress signaling in strawberries. These preliminary results could contribute to further research to understand S-acylation in strawberries and plants in general.

Strawberry fruit size is critical for its marketability. However, organ size control is a complex process regulated by various signalling pathways. In animals, the Hippo signalling pathway acts as a negative regulator of organ size, with Ste20 kinase being a key component. Mutation in Ste20 causes excessive cell proliferation and enlarged organs. In this study, FvM4K1, a Ste20-like kinase from woodland strawberry (Fragaria vesca), is identified. FvM4K1 partially restores defects in a yeast Ste20 mutant ste20Δ and fully rescues growth in Arabidopsis mutant atsik1-4 lacking its Ste20 homologue, AtSIK1, underscoring its functional conservation. Downregulation of FvM4K1 by RNAi in woodland strawberry leads to smaller plants and fruits resulting from reduced cell size and number, while overexpression increases organ size, indicating a positive role in organ size control which contrasts with the negative role of Ste20 in other organisms. FvM4K1 autophosphorylates, with Lys269 and Thr396 being critical for its function. FvM4K1 interacts with FvMOB1A and FvMOB1B, components of the Hippo signalling pathway, and phosphorylates them at Thr35 and Thr36, respectively. These findings provide novel insights into the mechanisms underlying fruit and organ size control in woodland strawberry and contribute to our understanding of the Hippo signalling pathway in higher plants, a pathway that remains largely unexplored. It also opens new avenues for exploring the regulatory function of the Hippo pathway in plant development and potentially informs biotechnological strategies for crop improvement.

Sorghum (Sorghum bicolor) is an important food and feed crop. Root-lesion nematodes (Pratylenchus spp.) are a group of pathogenic nematodes that cause severe economic losses in various food and cash crops. This study identified diseased sorghum plants with stunted growth and brown, rotting roots in sorghum fields in Shanxi Province, China. A species of root-lesion nematode was isolated by modified Baermann funnel method and named the GL-1 population. Afterward, the GL-1 population of root-lesion nematodes was identified as P. coffeae through a combination of morphological, rDNA-ITS and rDNA-28 S D2-D3 region techniques for molecular biological identification. We also conducted greenhouse experiments to assess the parasitism and pathogenicity of GL-1 and four other P. coffeae populations on sorghum through pot inoculation. At 60 days after inoculation, the results indicated that all five populations of P. coffeae were capable of infecting and causing damage to the sorghum plants. Sorghum is a suitable host for P. coffeae (with a reproduction factor > 1). Moreover, compared with those in the control group, the aboveground fresh weights and root fresh weights of sorghum in the five inoculation groups were significantly lower, and brown spots or even necrotic rot appeared on the roots. All five populations were highly pathogenic to sorghum, but there were significant differences in pathogenicity among the populations. This study provides a scientific basis for identifying and detecting root-lesion nematodes in sorghum.

Chinese chestnut is an important economic forest tree species with enormous application value in the wood, medical, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly restricts research on the genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38 Mb-1. Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were ultimately obtained. To verify the capability of the developed SSR for identification, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient Chinese chestnut resources from the Yanshan Mountains. The results showed that only six pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have good potential for identification. We then evaluated the inter-specific universality and polymorphism of these markers using 91 Castanea plants of three different species. The molecular markers amplified 94% of the interspecies with a polymorphic information content (PIC) value of 0.859. Cluster analysis revealed that the resources can be well differentiated using these developed markers, and these markers can be widely used to identify interspecific boundaries. The results of this study proved that the developed molecular markers have the potential for assessing genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, the selection of good products, and the construction of core germplasm resources of chestnut and even chestnut plants. Also these markers provide a solid foundation for the molecular design of hybrids, improved breeding and development of germplasm resources.

Lily is a famous ornamental flower all over the world. In the process of cultivation and production, it usually faces a variety of stresses that influence its growth. While small heat shock proteins (sHSPs) enhance stress tolerance in Lilium regale, their regulatory mechanisms remain poorly defined. Here, we identified LrWRKY16 as a novel transcriptional activator of LrHSP17.2 that conferred dual thermotolerance and drought tolerance, a functionally distinct role not previously characterized in lily. LrWRKY16 directly bound the LrHSP17.2 promoter, activating its expression to maintain cellular homeostasis and enhance ROS scavenging under stress. Overexpression of LrWRKY16 in Arabidopsis significantly elevated both heat and drought tolerance and upregulated stress-responsive genes. Critically, LrWRKY16 orchestrated a unique regulatory module with LrHSP17.2 to co-optimize protein protection and oxidative stress mitigation. Taken together, this study revealed the evidence of a WRKY-sHSP axis mediating dual abiotic stress adaptation in Lilium regale, providing a strategic target for molecular breeding of lily.

Castanea species have enormous potential for broad applications in the biomedical sciences and chemical wood industries. Due to the occurrence of fungal diseases, especially chestnut blight, the survival status of Castanea plants is seriously threatened. Castanea plants in China have natural tolerance to chestnut blight. This study investigated the genetic diversity and chestnut blight resistance of Castanea plants in China and searched for germplasm with high tolerance resistance. Cluster and population structure analysis revealed that wild Castanea plants in China could be divided into three groups with significant interspecific boundary, C. henryi var. omeiensis is located between C. mollissima and C. henryi var. henryi. The ABBA-BBAA test showed that significant gene introgression occurred between C. mollissima and C. henryi in Mount Emei, supporting the conclusion that C. henryi var. omeiensis as a natural hybrid resource. The results of disease resistance evaluation showed that the tolerance of wild C. mollissima to chestnut blight was the highest and significantly higher than that of wild C. henryi and C. seguinii. In particular, there is a strong association between disease tolerance in C. henryi var. omeiensis and the level of genetic introgression from C. mollissima. Then, the rIBD fragments of C. henryi var. omeiensis derived from C. mollissima were analyzed to reveal the source of disease resistance using whole genome resequencing data. A total of 203 rIBD segments containing 435 genes were identified. Finally, 41 candidate genes for chestnut blight resistance were selected through multiple omics. In conclusion, this study investigated a type of interspecific disease-resistant hybrid resources, identified a set of candidate genes for chestnut blight resistance, and provided new strategies for disease-resistant breeding of chestnut resources in the future.

As an important part of heat shock response module, heat shock proteins (HSP) play an important role in plant defense response against heat stress; however, the involvement of the majority of the HSP family members against other abiotic stresses remains poorly understood. In the present study, LrHSP17.2 was identified and its function against abiotic stress was analyzed. The expression level of LrHSP17.2 was significantly induced by heat. Heterologous transgenes of LrHSP17.2 showed that LrHSP17.2 can increase the activity of catalase, peroxidase, superoxide dismutase to removes excess reactive oxygen species (ROS), maintain the stability of the membrane structure, and regulate genes related to antioxidant enzymes and defense under abiotic stress. In addition, LrHSP17.2 could be regulated by exogenous abscisic acid and melatonin, and the related hormone synthesis genes of transgenic plants were significantly up-regulated under heat stress. Taken together, our results revealed that LrHSP17.2 is involved in regulating abiotic stress responses by regulating ROS scavenging and stress-related genes in Lilium regale.

Chrysanthemum(Chrysanthemum x morifolium) branching is an important ornamental trait, which directly determines its ornamental quality and production. In this study, CmPP2C1 and CmPP2C2 were identified as interacting proteins of DgLsL and its function in branches was analyzed. Yeast two-hybrid assay (Y2H) and Luciferase complementation imaging assay (LCA) were used to demonstrate the interaction. The expression of CmPP2C1 and CmPP2C2 were significantly increased after decapitation. In addition, CmPP2C1 overexpression led to a significant decrease in endogenous abscisic acid (ABA) content and expression of related synthetic genes. This implies that CmPP2C1 and DgLsL may regulate chrysanthemum branching by participating in the ABA pathway. Taken together, our results revealed that protein phosphatases type 2C regulate branches by interacting with DgLsL and regulating Abscisic acid synthesis in Chrysanthemum x morifolium 'Jinba', which provides an important theoretical basis for the molecular breeding and production of the chrysanthemum.

The Chinese chestnut (Castanea mollissima Blume) is a dioecious plant in which the number of male inflorescences far exceeds that of female inflorescences. Therefore, it is of interest to study the differentiation of male flowers in C. mollissima. In this study, the male inflorescences of ‘Yanshanhongli’ C. mollissima were observed. Then, the main components of the cell wall were stained by fluorescence and immunofluorescence labeling techniques to examine the changes in cell wall components. The results showed that the development of the male inflorescence of C. mollissima had different transverse elongation and longitudinal elongation. In addition, the development of male inflorescences and anthers were divided into five and four major stages, respectively, according to the microstructural changes. Immunostaining indicated that the fluorescence intensity of cellulose increased with the development of male inflorescences of C. mollissima. The fluorescence intensity of low-esterified homogalacturonan (HG) was stronger in the early stage, while the fluorescence intensity of high-esterified HG was stronger thereafter. This research provides new insights into the changes in cell wall components during the growth and development of male inflorescences of C. mollissima and important clues for exploring the growth and development mechanism of male inflorescences of C. mollissima.

Context Well-organised leaf architecture produces compact canopies and allows for greater sunlight penetration, higher photosynthetic rates, and thus greater yields. Breeding for enhanced leaf architecture of sorghum (Sorghum bicolor L.), a key food source in semi-arid regions, benefits its overall production. Aims The study focuses on selecting useful genotypes with excellent leaf architecture for grain sorghum improvement. Methods In total, 185 sorghum genotypes were subjected to multi-environment trials. Leaf flagging-point length, leaf length, leaf width, leaf angle and leaf orientation value (LOV) were characterised under field conditions. Genotype + genotype × environment interaction (GGE) biplot analysis was used to identify the most stable genotypes with the highest LOV. Key results Statistical analysis showed significant effects of genotype × environment interaction (P < 0.001), and high broad-sense heritability for the traits. Correlation analysis demonstrated negative correlations (P < 0.001) between LOV and its components. Singular value decomposition of LOVs in the first two principal components explained 89.19% of the total variation. GGE biplot analysis identified G55 as the ideotype with the highest and most stable LOV. Conclusions Leaf architecture optimisation should be given greater attention. This study has identified a genotype with optimal and stable leaf architecture, laying the foundation for improvement in breeding to increase overall yields of sorghum. Implications Genotype G55 can be utilised as a parent with other parents that display economically important characteristics in breeding programs to produce offspring that can be planted densely to increase population yields. Genotypes identified with loose leaf architecture are useful in dissecting genes controlling leaf architecture by crossing with G55 to construct genetic mapping populations.

There are many factors that affect the yield of Chinese chestnut (Castanea mollissima), with single nut weight (SNW) being one of the most important. Leaf length is also related to Chinese chestnut yield. However, the genetic architecture and gene function associated with Chinese chestnut nut yield have not been fully explored. In this study, we performed genotyping by sequencing 151 Chinese chestnut cultivars, followed by a genome-wide association study (GWAS) on six horticultural traits. First, we analyzed the phylogeny of the Chinese chestnut and found that the Chinese chestnut cultivars divided into two ecotypes, a northern and southern cultivar group. Differences between the cultivated populations were found in the pathways of plant growth and adaptation to the environment. In the selected regions, we also found interesting tandemly arrayed genes that may influence Chinese chestnut traits and environmental adaptability. To further investigate which horticultural traits were selected, we performed a GWAS using six horticultural traits from 151 cultivars. Forty-five loci that strongly associated with horticultural traits were identified, and six genes highly associated with these traits were screened. In addition, a candidate gene associated with SNW, APETALA2 (CmAP2), and another candidate gene associated with leaf length (LL), CRYPTOCHROME INTERACTING BASIC HELIX-LOOP-HELIX 1 (CmCIB1), were verified in Chinese chestnut and Arabidopsis (Arabidopsis thaliana). Our results showed that CmAP2 affected SNW by negatively regulating cell size. CmCIB1 regulated the elongation of new shoots and leaves by inducing cell elongation, potentially affecting photosynthesis. This study provided valuable information and insights for Chinese chestnut breeding research.

Small molecular heat shock proteins (sHSPs) belong to the HSP family of molecular chaperones. Under high-temperature stress, they can prevent the aggregation of irreversible proteins and maintain the folding of denatured proteins to enhance heat resistance. In this study, the CmHSP17.9-1 and CmHSP17.9-2 genes, which were cloned from chrysanthemum (Chrysanthemum×morifolium ‘Jinba’) by homologous cloning, had a complete open reading frame of 480 bp each, encoding 159 amino acids. The protein subcellular localization analysis showed that CmHSP17.9-1 and CmHSP17.9-2 were located in the cytoplasm and mostly aggregated in granules, especially around the nucleus. Real-time quantitative PCR (qRT-PCR) analysis showed that the relative expression level of the CmHSP17.9-1 and CmHSP17.9-2 genes was highest in the terminal buds of the chrysanthemum, followed by the leaves. CmHSP17.9-1 and CmHSP17.9-2 overex-pression vectors were constructed and used to transform the chrysanthemum; overexpression of these genes led to the chrysanthemum phenotypes being less affected by high-temperature, and the antioxidant capacity was enhanced. The results showed that chrysanthemum with overex-pression of the CmHSP17.9-1 and CmHSP17.9-2 genes had stronger tolerance than the wild type chrysanthemum after high-temperature treatment or some degree of heat exercise, and overex-pression of the CmHSP17.9-1 gene led to stronger heat resistance than that of the CmHSP17.9-2 gene, providing an important theoretical basis for the subsequent molecular breeding and pro-duction applications of chrysanthemum.

Chinese chestnut (Castanea mollissima Blume.) ovary contains 12-18 ovules, but only one can develop and grow normally, which indicates that the abortive rate of ovules can go as high as 94 %. In this study, we observed the developmental characteristics and cytological changes of abortive ovules and fertile ovules during development. Morphological analysis showed it would take about 15 similar to 20 days from globular to cotyledon embryo in fertile ovules, which is accompanied with the formation and apoptosis of endosperm. But there were stark differences in the nutrient transport, microstructure and ultrastructure of fertile and abortive ovules. The fluorescence disodium fluorescein and FDA indicated that all ovules were viable at early stages, but some ovules became inactive at different times as the ovary developed. Fluorescence labelling and ultrastructure showed cell nuclei of abortive ovules were disintegrated at 25 days after anthesis (DAA). Compared with the fertile ovules, starch grains were synthesized at earlier periods, but disappeared immediately, and the cells were usually irregular in shape, and had folded cell membranes in the abortive ovules. Furthermore, the Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was carried out to assess programmed cell death in fertile and abortive ovules, results showed that DNA fragmentation was occurred in the cells of abortive ovules. In short, these results provide new insights into ovule abortion in the angiosperm.