Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (Solanum Lycopersicum L.)

The role of strigolactone analog (GR24) in endogenous hormone metabolism and hormone-related gene expression in tobacco axillary buds

KEY MESSAGE

Strigolactone has the potential to influence hormone metabolism, in addition to having a role in inhibiting axillary bud elongation, which could be regulated by the expression of phytohormones-related genes. The elongation of axillary buds affects the economic benefits of tobacco. In this study, it was investigated the effect of strigolactone (SL) on the elongation of tobacco axillary buds and its endogenous hormone metabolism and related gene expression by applying the artificial analog of SL, GR24, and an inhibitor of SL synthesis, TIS-108, to the axillary buds. The results showed that the elongation of axillary buds was significantly inhibited by GR24 on day 2 and day 9. Ultra-high-performance liquid-chromatography-mass spectrometry results further showed that SL significantly affected the metabolism of endogenous plant hormones, altering both their levels and the ratios between each endogenous hormone. Particularly, the levels of auxin (IAA), trans-zeatin-riboside (tZR), N6-(∆2-isopentenyl) adenine (iP), gibberellin A4 (GA4), jasmonic acid (JA), and jasmonoyl isoleucine (JA-Ile) were decreased after GR24 treatment on day 9, but the levels of 1-aminocyclopropane-1-carboxylic acid (ACC) and gibberellin A1 (GA1) were significantly increased. Further analysis of endogenous hormonal balance revealed that after the treatment with GR24 on day 9, the ratio of IAA to cytokinin (CTK) was markedly increased, but the ratios of IAA to abscisic acid (ABA), salicylic acid (SA), ACC, JAs, and, GAs were notably decreased. In addition, according to RNA-seq analysis, multiple differentially expressed genes were found, such as GH3.1, AUX/IAA, SUAR20, IPT, CKX1, GA2ox1, ACO3, ERF1, PR1, and HCT, which may play critical roles in the biosynthesis, deactivation, signaling pathway of phytohormones, and the biosynthesis of flavonoids to regulate the elongation of axillary buds in tobacco. This work lays the certain theoretical foundation for the application of SL in regulating the elongation of axillary buds of tobacco.

Integrated transcriptomics and metabolomics analysis provide insight into anthocyanin biosynthesis for sepal color formation in Heptacodium miconioides

Heptacodium miconioides Rehd., commonly known as "seven-son flower," is an ornamental species with a beautiful flower pattern and persistent sepals. Its sepals are of horticultural value, turning bright red and elongating in the autumn; however, the molecular mechanisms that cause sepal color change remain unclear. We analyzed the dynamic changes in anthocyanin composition in the sepal of H. miconioides at four developmental stages (S1-S4). A total of 41 anthocyanins were detected and classified into 7 major anthocyanin aglycones. High levels of the pigments cyanidin-3,5-O-diglucoside, cyanidin-3-O-galactoside, cyanidin-3-O-glucoside, and pelargonidin-3-O-glucoside were responsible for sepal reddening. Transcriptome analysis revealed 15 differentially expressed genes involved in anthocyanin biosynthesis that were detected between 2 developmental stages. Of these, the high expression of HmANS was considered critical structural gene related to anthocyanin biosynthesis pathway in the sepal through co-expression analysis with anthocyanin content. In addition, a transcription factor (TF)-metabolite correlation analysis revealed that three HmMYB, two HmbHLH, two HmWRKY, and two HmNAC TFs exhibited a strong positive role in the regulation of the anthocyanin structural genes (Pearson's correlation coefficient > 0.90). Luciferase activity assay showed that HmMYB114, HmbHLH130, HmWRKY6, and HmNAC1 could activate the promoters of HmCHS4 and HmDFR1 genes in vitro. These findings increase our understanding of anthocyanin metabolism in the sepal of H. miconioides and provide a guide for studies involving sepal color conversion and regulation.

Genome-wide identification and expression analysis of metal tolerance protein (MTP) gene family in soybean (Glycine max) under heavy metal stress

AIM

Plant metal tolerance proteins (MTPs) are plant membrane divalent cation transporters that specifically contribute to heavy metal stress resistance and mineral uptake. However, little is known about this family's molecular behaviors and biological activities in soybean.

METHODS AND RESULTS

A total of 20 potential MTP candidate genes were identified and studied in the soybean genome for phylogenetic relationships, chromosomal distributions, gene structures, gene ontology, cis-elements, and previous gene expression. Furthermore, the expression of MTPs has been investigated under different heavy metals treatments. All identified soybean MTPs (GmaMTPs) contain a cation efflux domain or a ZT dimer and are further divided into three primary cation diffusion facilitator (CDF) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The developmental analysis reveals that segmental duplication contributes to the GmaMTP family's expansion. Tissue-specific expression profiling revealed comparative expression profiling in similar groups, although gene expression differed between groups. GmaMTP genes displayed biased responses in either plant leaves or roots when treated with heavy metal. In the leaves and roots, nine and ten GmaMTPs responded to at least one metal ion treatment. Furthermore, in most heavy metal treatments, GmaMTP1.1, GmaMTP1.2, GmaMTP3.1, GmaMTP3.2, GmaMTP4.1, and GmaMTP4.3 exhibited significant expression responses.

CONCLUSION

Our findings provided insight into the evolution of MTPs in soybean. Overall, our findings shed light on the evolution of the MTP gene family in soybean and pave the path for further functional characterization of this gene family.

Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.

Physiological and Comparative Transcriptome Analyses of the High-Tillering Mutant mtn1 Reveal Regulatory Mechanisms in the Tillering of Centipedegrass (Eremochloa ophiuroides (Munro) Hack.)

Tillering is a key factor that determines the reproductive yields of centipedegrass, which is an important perennial warm-season turfgrass. However, the regulatory mechanism of tillering in perennial plants is poorly understood, especially in perennial turfgrasses. In this study, we created and characterised a cold plasma-mutagenised centipedegrass mutant, mtn1 (more tillering number 1). Phenotypic analysis showed that the mtn1 mutant exhibited high tillering, short internodes, long seeds and a heavy 1000-seed weight. Then, a comparative transcriptomic analysis of the mtn1 mutant and wild-type was performed to explore the molecular mechanisms of centipedegrass tillering. The results revealed that plant hormone signalling pathways, as well as starch and sucrose metabolism, might play important roles in centipedegrass tillering. Hormone and soluble sugar content measurements and exogenous treatment results validated that plant hormones and sugars play important roles in centipedegrass tiller development. In particular, the overexpression of the auxin transporter ATP-binding cassette B 11 (EoABCB11) in Arabidopsis resulted in more branches. Single nucleotide polymorphisms (SNPs) were also identified, which will provide a useful resource for molecular marker-assisted breeding in centipedegrass. According to the physiological characteristics and transcriptional expression levels of the related genes, the regulatory mechanism of centipedegrass tillering was systematically revealed. This research provides a new breeding resource for further studies into the molecular mechanism that regulates tillering in perennial plants and for breeding high-tillering centipedegrass varieties.

A MADS-box transcription factor, SlMADS1, interacts with SlMACROCALYX to regulate tomato sepal growth

In flowering plants, sepals play important roles in the development of flowers and fruit, and both processes are regulated by MADS-box (MADS) transcription factors (TFs). SlMADS1 was previously reported to act as a negative regulator of fruit ripening. In this study, expression analysis shown that its transcripts were very highly expressed during the development of sepals. To test the role of SlMADS1, we generated KO-SlMADS1 (knock-out) tomato mutants by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9) technology and over-expression of SlMADS1 (OE-SlMADS1). The sepals and individual cells of KO-SlMADS1 mutants were significantly elongated, compared with the wild type (WT), whereas the sepals of OE-SlMADS1 tomatoes were significantly shorter and their cells were wider. RNA-seq (RNA-sequencing) of sepal samples showed that ethylene-, gibberellin-, auxin-, cytokinin- and cell wall metabolism-related genes were significantly affected in both KO-SlMADS1 and OE-SlMADS1 plants with altered sepal size. Since SlMACROCALYX (MC) is known to regulate the development of tomato sepals, we also studied the relationship between SlMC and SlMADS1 and the result showed that SlMADS1 interacts directly with SlMC. In addition, we also found that manipulating SlMADS1 expression alters the development of tomato plant leaves, roots and plant height. These results enrich our understanding of sepal development and the function of SlMADS1 throughout the plant.

Advances in Understanding and Harnessing the Molecular Regulatory Mechanisms of Vegetable Quality

The quality of vegetables is facing new demands in terms of diversity and nutritional health. Given the improvements in living standards and the quality of consumed products, consumers are looking for vegetable products that maintain their nutrition, taste, and visual qualities. These requirements are directing scientists to focus on vegetable quality in breeding research. Thus, in recent years, research on vegetable quality has been widely carried out, and many applications have been developed via gene manipulation. In general, vegetable quality traits can be divided into three parts. First, commodity quality, which is most related to the commerciality of plants, refers to the appearance of the product. The second is flavor quality, which usually represents the texture and flavor of vegetables. Third, nutritional quality mainly refers to the contents of nutrients and health ingredients such as soluble solids (sugar), vitamin C, and minerals needed by humans. With biotechnological development, researchers can use gene manipulation technologies, such as molecular markers, transgenes and gene editing to improve the quality of vegetables. This review attempts to summarize recent studies on major vegetable crops species, with Brassicaceae, Solanaceae, and Cucurbitaceae as examples, to analyze the present situation of vegetable quality with the development of modern agriculture.

Hormone and carbohydrate metabolism associated genes play important roles in rhizome bud full-year germination of Cephalostachyum pingbianense

Cephalostachyum pingbianense is the only woody bamboo species that can produce bamboo shoots in four seasons under natural conditions. So far, the regulatory mechanism of shoot bud differentiation and development is unknown. In the present study, indole-3-acetic acid (IAA), zeatin riboside (ZR), gibberellin A3 (GA₃ ) and abscisic acid (ABA) contents determination, RNA sequencing and differentially expressed gene analysis were performed on dormant rhizome bud (DR), growing rhizome bud (GR), and germinative bud (GB) in each season. The results showed that the contents of IAA and ZR increased while ABA content decreased, and GA₃ content was stable during bud transition from dormancy to germination in each season. Moreover, rhizome bud germination was cooperatively regulated by multiple pathways such as carbohydrate metabolism, hormone signal transduction, cell wall biogenesis, temperature response, and water transport. The inferred hub genes among these candidates were identified by protein-protein interaction network analyses, most of which were involved in hormone and carbohydrate metabolism, such as HK and BGLU4 in spring, IDH and GH3 in winter, GPI and talA/talB in summer and autumn. It is speculated that dynamic phytohormone changes and differential expression of these genes promote the release of rhizome bud dormancy and contribute to the phenological characteristics of full-year shooting. Moreover, the rhizome buds of C. pingbianense may not suffer from ecodormancy in winter. These findings would help accumulate knowledge on shooting mechanisms in woody bamboos and provide a physiological insight into germplasm conservation and forest management of C. pingbianense.

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)

Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by ⁶⁰Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful information for the understanding of the complex mechanisms of plant hormones in controlling pod size by regulating the cell size in peanuts and will facilitate the improvement of peanut breeding.

Comprehensive genome wide identification and expression analysis of MTP gene family in tomato (Solanum lycopersicum) under multiple heavy metal stress

Plant metal tolerance proteins (MTPs) play major roles in enhancing resistance to heavy metal tolerance and homeostasis. However, the role of MTPs genes in tomato, which is one of the most popular crops, is still largely limited. Hence, we investigated genome-wide study of tomato MTPs, including phylogenetic, duplication, gene structure, gene ontology and previous transcriptomic data analysis. Moreover, the MTPs expression behaviour under various heavy metals stress has rarely been investigated. In the current study, eleven MTP candidate genes were genome-wide identified and classified into three major groups; Mn-cation diffusion facilitators (CDFs), Fe/Zn-CDFs, and Zn-CDFs based on the phylogeny. Structural analysis of SlMTPs showed high gene similarity within the same group with cation_efflux or ZT_dimerdomains. Evolutionary analysis revealed that segmental duplication contributed to the expansion of the SlMTP family. Gene ontology further showed the vital roles of MTPs in metal-related processes. Tissue-specific expression profiling exhibited similar expression patterns in the same group, whereas gene expression varied among groups. The MTPs expression was evaluated after tomato treatments by five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). SlMTP genes displayed differential responses in either plant leaves or roots under heavy metals treatments. Nine and ten SlMTPs responded to at least one metal ion treatment in leaves and roots, respectively. In addition SlMTP1, SlMTP3, SlMTP4, SlMTP8, SlMTP10 and SlMTP11 exhibited the highest expression responses in most of heavy metals treatments. Overall, our findings presented a standpoint on the evolution of MTPs and their evolution in tomato and paved the way for additional functional characterization under heavy metal toxicity.

Exogenous 1',4'-trans-Diol-ABA Induces Stress Tolerance by Affecting the Level of Gene Expression in Tobacco (Nicotiana tabacum L.)

1',4'-trans-diol-ABA is a key precursor of the biosynthesis of abscisic acid (ABA) biosynthesis in fungi. We successfully obtained the pure compound from a mutant of Botrytis cinerea and explored its function and possible mechanism on plants by spraying 2 mg/L 1',4'-trans-diol-ABA on tobacco leaves. Our results showed that this compound enhanced the drought tolerance of tobacco seedlings. A comparative transcriptome analysis showed that a large number of genes responded to the compound, exhibiting 1523 genes that were differentially expressed at 12 h, which increased to 1993 at 24 h and 3074 at 48 h, respectively. The enrichment analysis demonstrated that the differentially expressed genes (DEGs) were primarily enriched in pathways related to hormones and resistance. The DEGs of transcription factors were generally up-regulated and included the bHLH, bZIP, ERF, MYB, NAC, WRKY and HSF families. Moreover, the levels of expression of PYL/PYR, PP2C, SnRK2, and ABF at the ABA signaling pathway responded positively to exogenous 1',4'-trans-diol-ABA. Among them, seven ABF transcripts that were detected were significantly up-regulated. In addition, the genes involved in salicylic acid, ethylene and jasmonic acid pathways, reactive oxygen species scavenging system, and other resistance related genes were primarily induced by 1',4'-trans-diol-ABA. These findings indicated that treatment with 1',4'-trans-diol-ABA could improve tolerance to plant abiotic stress and potential biotic resistance by regulating gene expression, similar to the effects of exogenous ABA.