Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Genome-Wide Analysis and Expression Profiles of AhCOLs Family in Peanut (Arachis hypogaea L.)

The CONSTANS-like (COL) gene family plays critical roles in plant growth, development, stress responses, and light signal transduction. However, its functions in peanut (Arachis hypogaea) remain poorly understood. In this study, we identified 18 AhCOL genes in the peanut genome, all localized in the nucleus. Phylogenetic analysis classified these genes into three subfamilies, with Group I containing eight members and Groups II and III each comprising five. Conserved domain analysis revealed that all AhCOL proteins possess at least one B-box and one CCT domain. Most of the AhCOL members in peanuts contain a large number of ABA and MeJA elements. Additionally, some members have low-temperature response elements, anaerobic induction, circadian control, and defense stress elements. Expression profiling indicated that most AhCOL genes are abundantly expressed in leaves, flowers, and fruit needles. Notably, genes such as AhCOL4, AhCOL8, AhCOL13, and AhCOL14 were upregulated under light induction and mechanical stress, highlighting their involvement in pod development. AhCOL1 interacts with AhNF-YC1, while AhCOL3 interacts with both AhNF-YC1 and AhCOP1 proteins. This study identifies key AhCOL genes implicated in light and mechanical stress responses, offering insights into their potential roles in peanut flowering and abiotic stress tolerance.

Replacing rice straw with peanut vine and Broussonetia papyrifera silage in beef cattle feed reduced the use of soybean meal

The present study investigated whether replacing dietary rice straw with peanut vine (PEV) and Broussonetia papyrifera silage (BPS) reduces the use of soybean meal and explored its effects on the growth performance, blood biochemical indicators, serum metabolomics, and meat quality of fattening bulls. Forty-five Simmental crossbred bulls (initial body weight = 484.29 ± 8.49 kg) were randomly allotted into three dietary treatment groups (n = 15): (1) CON, 5% rice straw (DM basis); (2) PEV, 5% peanut vine (DM basis); and (3) BPS, 5% B. papyrifera silage (DM basis). The remaining roughage for all three treatment groups was supplemented with 25% corn silage (DM basis). The experiment lasted for 123 d, with the first 14 d serving as an adaptive period. Throughout the experiment, dietary BPS decreased the average daily dry matter intake (P < 0.001) and feed cost (P < 0.001). Serum metabolomics analysis showed that PEV affected the phenylalanine, tyrosine, and tryptophan biosynthesis pathways (P = 0.021) and lysine degradation pathway (P = 0.042), whereas BPS affected the phenylalanine, tyrosine and tryptophan biosynthesis pathways (P = 0.004), lysine degradation pathway (P = 0.012), and serotonergic synapse pathway (P < 0.001). Regarding meat quality, the redness (P = 0.025) and hue angle values (P < 0.001) of the longissimus dorsi muscle were lower in the BPS group than in the CON and PEV groups. The yellowness of the longissimus dorsi muscle was lower in the BPS group than in the PEV group (P = 0.024), and the shear force was lower in the PEV group than in the BPS group (P = 0.014). However, lysine content in beef was higher in the BPS group than in the CON group (P = 0.005). In conclusion, replacing rice straw with PEV and BPS reduced the use of soybean meal but had no adverse effects on growth performance. BPS affected the amino acid metabolism of bulls, thus decreasing feed intake and increasing the lysine content in meat. The PEV group showed better meat quality than the BPS group.

Deciphering the Proteome and Phosphoproteome of Peanut (Arachis hypogaea L.) Pegs Penetrating into the Soil

Peanut (Arachis hypogaea L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground. In order to fully understand this phenomenon, we investigated the dynamic proteomic and phosphoproteomic profiling of the pegs aerially and underground in this study. A total of 6859 proteins and 4142 unique phosphoproteins with 10,070 phosphosites were identified. The data were validated and quantified using samples randomly selected from arial pegs (APs) and underground pegs (UPs) by parallel reaction monitoring (PRM). Function analyses of differentially abundant proteins (DAPs) and differentially regulated phosphoproteins (DRPPs) exhibited that they were mainly related to stress response, photosynthesis, and substance metabolism. Once the pegs successfully entered the soil, disease-resistant and stress response proteins, such as glutathione S-transferase, peroxidase, and cytochrome P450, significantly increased in the UP samples in order to adapt to the new soil environment. The increased abundance of photosynthesis-associated proteins in the UP samples provided more abundant photosynthetic products, which provided the preparation for subsequent pod development. Phosphoproteomics reveals the regulatory network of the synthesis of nutrients such as starch, protein, and fatty acid (FA). These results provide new insights into the mechanism, indicating that after the pegs are inserted into the soil, phosphorylation is involved in the rapid elongation of the pegs, accompanied by supplying energy for pod development and preparing for the synthesis of metabolites during pod development following mechanical stimulation and darkness.

Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit

Peanut (Arachis hypogaea L.) is an important leguminous oil and economic crop that produces flowers aboveground and fruits belowground. Subterranean fruit-pod development, which significantly affects peanut production, involves complex molecular mechanisms that likely require the coordinated regulation of multiple genes in different tissues. To investigate the molecular mechanisms that underlie peanut fruit-pod development, we characterized the anatomical features of early fruit-pod development and integrated single-nucleus RNA-sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) data at the single-cell level. We identified distinct cell types, such as meristem, embryo, vascular tissue, cuticular layer, and stele cells within the shell wall. These specific cell types were used to examine potential molecular changes unique to each cell type during pivotal stages of fruit-pod development. snRNA-seq analyses of differentially expressed genes revealed cell-type-specific insights that were not previously obtainable from transcriptome analyses of bulk RNA. For instance, we identified MADS-box genes that contributes to the formation of parenchyma cells and gravity-related genes that are present in the vascular cells, indicating an essential role for the vascular cells in peg gravitropism. Overall, our single-nucleus analysis provides comprehensive and novel information on specific cell types, gene expression, and chromatin accessibility during the early stages of fruit-pod development. This information will enhance our understanding of the mechanisms that underlie fruit-pod development in peanut and contribute to efforts aimed at improving peanut production.

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

Biochar alleviated the toxic effects of microplastics-contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation

BACKGROUND

The accumulation of microplastics in agricultural soil poses a threat to the sustainability of agriculture, impacting crop growth and soil health. Due to the geocarpy feature of peanut, geocarposphere soil environment is critical to pod development and its nutritional quality. While the effects of microplastics in the rhizosphere have been studied, their impact on peanut pod in the geocarposphere remains unknown. Biochar has emerged as a potential soil agent with the ability to remediate soil contamination. However, the mechanisms of biochar in mitigating the toxic effects of microplastics-contaminated geocarposphere soil on peanut pod development remain largely unexplored.

RESULTS

We evaluated the peanut pod performance and microbiome when facing microplastics contamination and biochar amendment in geocarposphere soil. The results showed that microplastics present in geocarposphere soil could directly enter the peanut pod, cause pod developmental disorder and exert adverse effects on nutritional quality. Aberrant expression of key genes associated with amino acid metabolism, lipid synthesis, and auxin and ethylene signaling pathways were the underlying molecular mechanisms of microplastics-induced peanut pod developmental inhibition. However, these expression abnormalities could be reversed by biochar application. In addition, peanut geocarposphere microbiome results showed that biochar application could restore the diversity of microbial communities inhibited by microplastics contamination and promote the relative abundance of bacteria correlated with pathogen resistance and nitrogen cycle of geocarposphere soil, further promoting peanut pod development.

CONCLUSION

This study demonstrated that biochar application is an effective strategy to mitigate the toxic effects of microplastics-contaminated geocarposphere soil on pod development and nutritional quality. © 2023 Society of Chemical Industry.

Comparative analysis of two kinds of garlic seedings: qualities and transcriptional landscape

BACKGROUND

Facility cultivation is widely applied to meet the increasing demand for high yield and quality, with light intensity and light quality being major limiting factors. However, how changes in the light environment affect development and quality are unclear in garlic. When garlic seedlings are grown, they can also be exposed to blanching culture conditions of darkness or low-light intensity to ameliorate their appearance and modify their bioactive compounds and flavor.

RESULTS

In this study, we determined the quality and transcriptomes of 14-day-old garlic and blanched garlic seedlings (green seedlings and blanched seedlings) to explore the mechanisms by which seedlings integrate light signals. The findings revealed that blanched garlic seedlings were taller and heavier in fresh weight compared to green garlic seedlings. In addition, the contents of allicin, cellulose, and soluble sugars were higher in the green seedlings. We also identified 3,872 differentially expressed genes between green and blanched garlic seedlings. The Kyoto Encyclopedia of Genes and Genomes analysis suggested enrichment for plant-pathogen interactions, phytohormone signaling, mitogen-activated protein kinase signaling, and other metabolic processes. In functional annotations, pathways related to the growth and formation of the main compounds included phytohormone signaling, cell wall metabolism, allicin biosynthesis, secondary metabolism and MAPK signaling. Accordingly, we identified multiple types of transcription factor genes involved in plant-pathogen interactions, plant phytohormone signaling, and biosynthesis of secondary metabolites among the differentially expressed genes between green and blanched garlic seedlings.

CONCLUSIONS

Blanching culture is one facility cultivation mode that promotes chlorophyll degradation, thus changing the outward appearance of crops, and improves their flavor. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system. This study increases our understanding of the regulatory network integrating light and darkness signals in garlic seedlings and provides a useful resource for the genetic manipulation and cultivation of blanched garlic seedlings.