Genome-wide transcriptional profiling for elucidating the effects of brassinosteroids on Glycine max during early vegetative development

CRISPR/Cas9-mediated editing of GmDWF1 brassinosteroid biosynthetic gene induces dwarfism in soybean

KEY MESSAGE

The study on the GmDWF1-deficient mutant dwf1 showed that GmDWF1 plays a crucial role in determining soybean plant height and yield by influencing the biosynthesis of brassinosteroids. Soybean has not adopted the Green Revolution, such as reduced height for increased planting density, which have proven beneficial for cereal crops. Our research identified the soybean genes GmDWF1a and GmDWF1b, homologous to Arabidopsis AtDWF1, and found that they are widely expressed, especially in leaves, and linked to the cellular transport system, predominantly within the endoplasmic reticulum and intracellular vesicles. These genes are essential for the synthesis of brassinosteroids (BR). Single mutants of GmDWF1a and GmDWF1b, as well as double mutants of both genes generated through CRISPR/Cas9 genome editing, exhibit a dwarf phenotype. The single-gene mutant exhibits moderate dwarfism, while the double mutant shows more pronounced dwarfism. Despite the reduced stature, all types of mutants preserve their node count. Notably, field tests have shown that the single GmDWF1a mutant produced significantly more pods than wild-type plants. Spraying exogenous brassinolide (BL) can compensate for the loss in plant height induced by the decrease in endogenous BRs. Comparing transcriptome analyses of the GmDWF1a mutant and wild-type plants revealed a significant impact on the expression of many genes that influence soybean growth. Identifying the GmDWF1a and GmDWF1b genes could aid in the development of compact, densely planted soybean varieties, potentially boosting productivity.

Transcriptome Analysis Reveals an Essential Role of Exogenous Brassinolide on the Alkaloid Biosynthesis Pathway in Pinellia Ternata

Pinellia ternata (Thunb.) Druce is a traditional medicinal plant containing a variety of alkaloids, which are important active ingredients. Brassinolide (BR) is a plant hormone that regulates plant response to environmental stress and promotes the accumulation of secondary metabolites in plants. However, the regulatory mechanism of BR-induced alkaloid accumulation in P. ternata is not clear. In this study, we investigated the effects of BR and BR biosynthesis inhibitor (propiconazole, Pcz) treatments on alkaloid biosynthesis in the bulbil of P. ternata. The results showed that total alkaloid content and bulbil yield was enhanced by 90.87% and 29.67% under BR treatment, respectively, compared to the control. We identified 818 (476 up-regulated and 342 down-regulated) and 697 (389 up-regulated and 308 down-regulated) DEGs in the BR-treated and Pcz-treated groups, respectively. Through this annotated data and the Kyoto encyclopedia of genes and genomes (KEGG), the expression patterns of unigenes involved in the ephedrine alkaloid, tropane, piperidine, pyridine alkaloid, indole alkaloid, and isoquinoline alkaloid biosynthesis were observed under BR and Pcz treatments. We identified 11, 8, 2, and 13 unigenes in the ephedrine alkaloid, tropane, piperidine, and pyridine alkaloid, indole alkaloid, and isoquinoline alkaloid biosynthesis, respectively. The expression levels of these unigenes were increased by BR treatment and were decreased by Pcz treatment, compared to the control. The results provided molecular insight into the study of the molecular mechanism of BR-promoted alkaloid biosynthesis.

Exogenous genistein enhances soybean resistance to Xanthomonas axonopodis pv. glycines

BACKGROUND

Xanthomonas axonopodis pv. glycines (Xag) is the causal agent of bacterial pustule disease and results in enormous losses in soybean production. Although isoflavones are known to be involved in soybean resistance against pathogen infection, the effects of exogenous isoflavones on soybean plants remain unexplored.

RESULTS

Irrigation of soybean plants with isoflavone genistein inhibited plant growth for short periods, probably by inhibiting the tyrosine (brassinosteroids) kinase pathway, and increased disease resistance against Xag. The number of lesions was reduced by 59%-63% when applying 50 μg ml-1 genistein. The effects on disease resistance were observed for 15 days after treatment. Genistein also enhanced the disease resistance of soybean against the fungal pathogen Sclerotinia sclerotiorum. Exogenous genistein increased antioxidant capacity, decreased H2 O2 level and promoted the accumulation of phenolics in Xag-infected soybean leaves. Exogenous genistein reduced the amounts of endogenous daidzein, genistein and glycitein and increased the concentration of genistin, which was found to show strong antibacterial activity against the pathogen and to reduce the expression of virulence factor yapH, and flagella formation gene flgK. The expression of several soybean defense genes, such as chalcone isomerase, glutathione S-transferase and 1-aminocyclopropane-1-carboxylate oxidase 1, was upregulated after genistein treatment.

CONCLUSIONS

The effects of exogenous genistein on soybean plants were examined for the first time, revealing new insights into the roles of isoflavones in soybean defense and demonstrating that irrigation with genistein can be a suitable method to induce disease resistance in soybean plants. © 2022 Society of Chemical Industry.

Exogenous brassinolide improves the antioxidant capacity of Pinellia ternata by enhancing the enzymatic and nonenzymatic defense systems under non-stress conditions

Brassinolide (BR) improves the antioxidant capacity of plants under various abiotic stresses. However, it is not clear about the effect of BR on the antioxidant capacity in plants under non-stress conditions. In the present study, the antioxidant defense response of Pinellia ternata was to be assessed by applying BR and propiconazole (Pcz) under non-stress conditions. BR treatment enhanced the flavonoid content, peroxidase, and ascorbate peroxidase (APX) activity by 12.31, 30.62, and 25.08% and led to an increase in 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity by 4.31% and a decrease in malondialdehyde content by 1.04%. Exogenous application of BR improved the expression levels of PAL, CHS, CHI, and DFR genes by 3. 18-, 3. 39-, 2. 21-, and 0.87-fold in flavonoid biosynthesis, PGI, PMI, and GME genes by 6. 60-, 1437. 79-, and 3.11-fold in ascorbic acid (ASA), biosynthesis, and γECs and GSHS genes by 6.08- and 2.61-fold in glutathione (GSH) biosynthesis pathway, and the expression of these genes were inhibited by Pcz treatment. In addition, BR treatment promoted the ASA-GSH cycle by enhancing the expression of APX, DHAR, and MDHAR genes, which were enhanced by 3. 33-, 157. 85-, and 154.91-fold, respectively. These results provided novel insights into the effect of BR on the antioxidant capacity in bulbil of P. ternata under non-stress conditions and useful knowledge of applying BR to enhance the antioxidant capacity of plants.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.

Regulation Mechanism of Exogenous Brassinolide on Bulbil Formation and Development in Pinellia ternata

The bulbil is the propagative organ of the P. ternata, which has a great effect on the yield of P. ternata. It is well known that plant hormones play important roles in bulbil formation and development. However, there is not clear about brassinolide (BR) regulation on bulbil formation and development. In this study, we revealed the effects of BR and BR biosynthesis inhibitors (propiconazole, Pcz) application on the histological observation, starch and sucrose metabolism, photosynthesis pathway, and hormone signaling pathway of P. ternata. The results showed that BR treatment reduced starch catabolism to maltodextrin and maltose in bulbil by decreasing BAM and ISA genes expression and increased cellulose catabolism to D-glucose in bulbil by enhancing edg and BGL genes expression. BR treatment enhanced the photosynthetic pigment content and potential maximum photosynthetic capacity and improved the photoprotection ability of P. ternata by increasing the dissipation of excess light energy to heat, thus reduced the photodamage in the PSII center. BR treatment increased the GA and BR content in bulbil of P. ternata, and decreased the ABA content in bulbil of P. ternata. Pcz treatment increased the level of GA, SL, ABA, and IAA in bulbil of P. ternata. BR regulated the signal transduction of BR, IAA, and ABA to regulate the formation and development of bulbil in P. ternata. These results provide molecular insight into BR regulation on bulbil formation and development.

Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata

The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.

Engineered Nanomaterials Suppress the Soft Rot Disease (Rhizopus stolonifer) and Slow Down the Loss of Nutrient in Sweet Potato

About 45% of the world’s fruit and vegetables are wasted, resulting in postharvest losses and contributing to economic losses ranging from $10 billion to $100 billion worldwide. Soft rot disease caused by Rhizopus stolonifer leads to postharvest storage losses of sweet potatoes. Nanoscience stands as a new tool in our arsenal against these mounting challenges that will restrict efforts to achieve and maintain global food security. In this study, three nanomaterials (NMs) namely C₆₀, CuO, and TiO₂ were evaluated for their potential application in the restriction of Rhizopus soft rot disease in two cultivars of sweet potato (Y25, J26). CuO NM exhibited a better antifungal effect than C₆₀ and TiO₂ NMs. The contents of three important hormones, indolepropionic acid (IPA), gibberellic acid 3 (GA-3), and indole-3-acetic acid (IAA) in the infected J26 sweet potato treated with 50 mg/L CuO NM were significantly higher than those of the control by 14.5%, 10.8%, and 24.1%. CuO and C₆₀ NMs promoted antioxidants in both cultivars of sweet potato. Overall, CuO NM at 50 mg/L exhibited the best antifungal properties, followed by TiO₂ NM and C₆₀ NM, and these results were further confirmed through scanning electron microscope (SEM) analysis. The use of CuO NMs as an antifungal agent in the prevention of Rhizopus stolonifer infections in sweet potatoes could greatly reduce postharvest storage and delivery losses.

Optimal Brassinosteroid Levels Are Required for Soybean Growth and Mineral Nutrient Homeostasis

Brassinosteroids (BRs) are steroid phytohormones that are known to regulate plant growth and nutrient uptake and distribution. However, how BRs regulate nutrient uptake and balance in legume species is not fully understood. Here, we show that optimal BR levels are required for soybean (Glycine max L.) seedling growth, as treatments with both 24-epicastasterone (24-epiCS) and the BR biosynthesis inhibitor propiconazole (PPZ) inhibit root growth, including primary root elongation and lateral root formation and elongation. Specifically, 24-epiCS and PPZ reduced the total phosphorus and potassium levels in the shoot and affected several minor nutrients, such as magnesium, iron, manganese, and molybdenum. A genome-wide transcriptome analysis identified 3774 and 4273 differentially expressed genes in the root tip after brassinolide and PPZ treatments, respectively. The gene ontology (GO) analysis suggested that genes related to "DNA-replication", "microtubule-based movement", and "plant-type cell wall organization" were highly responsive to the brassinolide and PPZ treatments. Furthermore, consistent with the effects on the nutrient concentrations, corresponding mineral transporters were found to be regulated by BR levels, including the GmPHT1s, GmKTs, GmVIT2, GmZIPs, and GmMOT1 genes. Our study demonstrates that optimal BR levels are important for growth and mineral nutrient homeostasis in soybean seedlings.

Lactation Associated Genes Revealed in Holstein Dairy Cows by Weighted Gene Co-Expression Network Analysis (WGCNA)

Simple Summary

Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In the past few years, studies on the gene expression changes of dairy cow mammary glands were only based on transcriptome comparisons between two lactation stages. Few studies focused on the relationships between gene expression of the dairy mammary gland and lactation stage or milk composition in a lactation cycle. In this study, we detected milk yield and composition in a lactation cycle. For the first time, we constructed a gene coexpression network using WGCNA on the basis of 18 gene expression profiles during six stages of a lactation cycle by transcriptome sequencing, generating 10 specific modules. Genes in each module were performed with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Module–trait relationship analysis showed a series of potential candidates related to milk yield and composition. The current study provides an important theoretical basis for the further molecular breeding of dairy cows.

Abstract

Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In this study, the milk yield, lactose, fat, and protein of Holstein dairy cows were detected in a lactation cycle. Meanwhile, a total of 18 gene expression profiles were detected using mammary glands from six lactation stages (day 7 to calving, −7 d; day 30 post-calving, 30 d; day 90 post-calving, 90 d; day 180 post-calving, 180 d; day 270 post-calving, 270 d; day 315 post-calving, 315 d). On the basis of the 18 profiles, WGCNA identified for the first time 10 significant modules that may be related to lactation stage, milk yield, and the main milk composition content. Genes in the 10 significant modules were examined with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results revealed that the galactose metabolism pathway was a potential candidate for milk yield and milk lactose synthesis. In −7 d, ion transportation was more frequent and cell proliferation related terms became active. In late lactation, the suppressor of cytokine signaling 3 (SOCS3) might play a role in apoptosis. The sphingolipid signaling pathway was a potential candidate for milk fat synthesis. Dairy cows at 315 d were in a period of cell proliferation. Another notable phenomenon was that nonlactating dairy cows had a more regular circadian rhythm after a cycle of lactation. The results provide an important theoretical basis for the further molecular breeding of dairy cows.