Genome-wide identification and expression analysis of brassinosteroid biosynthesis and metabolism genes regulating apple tree shoot and lateral root growth

Integration of mRNA-miRNA Reveals the Possible Role of PyCYCD3 in Increasing Branches Through Bud-Notching in Pear (Pyrus bretschneideri Rehd.)

Bud-notching in pear varieties with weak-branches enhances branch development, hormone distribution, and germination, promoting healthier growth and improving early yield. To examine the regulatory mechanisms of endogenous hormones on lateral bud germination in Pyrus spp. (cv. 'Huangguan') (Pyrus bretschneideri Rehd.), juvenile buds were collected from 2-year-old pear trees. Then, a comprehensive study, including assessments of endogenous hormones, germination and branching rates, RNA-seq analysis, and gene function analysis in these lateral buds was conducted. The results showed that there was no significant difference in germination rate between the control and bud-notching pear trees, but the long branch rate was significantly increased in bud-notching pear trees compared to the control (p < 0.05). After bud-notching, there was a remarkable increase in IAA and BR levels in the pruned section of shoots, specifically by 141% and 93%, respectively. However, the content of ABA in the lateral buds after bud-notching was not significantly different from the control. Based on RNA-seq analysis, a notable proportion of the differentially expressed genes (DEGs) were linked to the plant hormone signal transduction pathway. Notably, the brassinosteroid signaling pathway seemed to have the closest connection with the branching ability of pear with the related genes encoding BRI1 and CYCD3, which showed significant differences between lateral buds. Finally, the heterologous expression of PyCYCD3 has a positive regulatory effect on the increased Arabidopsis growth and branching numbers. Therefore, the PyCYCD3 was identified as an up-regulated gene that is induced via brassinosteroid (BR) and could act as a conduit, transforming bud-notching cues into proliferative signals, thereby governing lateral branching mechanisms in pear trees.

Brassinosteroids biosynthetic gene MdBR6OX2 regulates salt stress tolerance in both apple and Arabidopsis

Salt stress is a critical limiting factor for fruit yield and quality of apples. Brassinosteroids (BRs) play an important role in response to abiotic stresses. In the present study, application of 2,4- Epicastasterone on seedlings of Malus 'M9T337' and Malus domestica 'Gala3' alleviated the physiological effects, such as growth inhibition and leaf yellowing, induced by salt stress. Further analysis revealed that treatment with NaCl induced expression of genes involved in BR biosynthesis in 'M9T337' and 'Gala3'. Among which, the expression of BR biosynthetic gene MdBR6OX2 showed a three-fold upregulation upon salt treatment, suggesting its potential role in response to salt stress in apple. MdBR6OX2, belonging to the CYP450 family, contains a signal peptide region and a P450 domain. Expression patterns analysis showed that the expression of MdBR6OX2 can be significantly induced by different abiotic stresses. Overexpressing MdBR6OX2 enhanced the tolerance of apple callis to salt stress, and the contents of endogenous BR-related compounds, such as Typhastero (TY), Castasterone (CS) and Brassinolide (BL) were significantly increased in transgenic calli compared with that of wild-type. Extopic expression of MdBR6OX2 enhanced tolerance to salt stress in Arabidopsis. Genes associated with salt stress were significantly up-regulated, and the contents of BR-related compounds were significantly elevated under salt stress. Our data revealed that BR-biosynthetic gene MdBR6OX2 positively regulates salt stress tolerance in both apple calli and Arabidopsis.

Genomic Analysis of Brassinosteroid Biosynthesis Gene Family Reveals Its Roles in Cotton Development across Gossypium Species

Cotton is a globally significant economic crop. Brassinosteroids (BRs) are crucial to cotton development. This study systematically analyzed the BR synthase gene family in four cotton species and identified 60 BR genes: 20 in Gossypium hirsutum (GhBRs), 20 in G. barbadense (GbBRs), 10 in G. arboreum (GaBRs), and 10 in G. raimondii (GrBRs). The analysis was extended to chromosomal localization, evolutionary relationships, domain features, and cis-regulatory elements in the promoter regions of BR synthase genes. The results showed that the BR synthase genes were evenly distributed across different subgenomes and chromosomes. Bioinformatics analyses revealed high conservation of amino acid sequences, secondary structures, and conserved domains among the subfamily members, which is closely linked to their pivotal roles in the BR biosynthesis pathway. Cis-element distribution analysis of the BR synthase genes further underscored the complexity of BR gene expression regulation, which is influenced by multiple factors, including plant hormones, abiotic stress, and transcription factors. Expression profiling of GhBRs genes in various cotton tissues and developmental stages highlighted the key roles of GhROT3-1 and GhDET2-1 in fiber elongation and initiation, respectively. Protein-protein interactions and transcription factor analyses further elucidated the regulatory mechanisms of GhROT3-1 and GhDET2-1 in cotton growth and development. This study lays a theoretical foundation for understanding the role of the BR signaling pathway in cotton development, facilitating molecular breeding.

The cytochrome P450 gene, MdCYP716B1, is involved in regulating plant growth and anthracnose resistance in apple

Apple is one of the main cultivated fruit trees worldwide. Both biotic and abiotic stresses, especially fungal diseases, have serious effects on the growth and fruit quality of apples. Cytochrome P450, the largest protein family in plants, is critical for plant growth and stress responses. However, the function of apple P450 remains poorly understood. In our previous study, 'Hanfu' autotetraploid showed dwarfism and fungal resistance phenotypes compared to 'Hanfu' diploid. Digital gene expression sequencing analysis revealed that the transcript level of MdCYP716B1 was significantly downregulated in the autotetraploid apple cultivar 'Hanfu'. In this study, we identified and cloned the MdCYP716B1 gene from 'Hanfu' apples. The MdCYP716B1 protein fused to a green fluorescent protein was localized in the cytoplasm. We constructed the plant overexpression vector and RNAi vector of MdCYP716B1, and the apple 'GL-3' was transformed by Agrobacterium-mediated transformation to obtain transgenic plants. Overexpressing and RNAi silencing transgenic plants exhibited an increase and decrease in plant height to 'GL-3', respectively. RNAi silencing transgenic plants displayed increased resistance to Colletotrichum gloeosporioides, whereas overexpression transgenic plants were more sensitive to C. gloeosporioides. According to transcriptome analysis, the transcript levels of gibberellin biosynthesis genes were upregulated in MdCYP716B1-overexpression plants. In contrast with 'GL-3', GA3 accumulation was rose in MdCYP716B1-OE lines and impaired in MdCYP716B1-RNAi lines. Collectively, our data indicate that MdCYP716B1 regulates plant growth and resistance to fungal stress.

BvCPD promotes parenchyma cell and vascular bundle development in sugar beet (Beta vulgaris L.) taproot

Constitutive photomorpogenic dwarf (CPD) is a pivotal enzyme gene for brassinolide (BR) synthesis and plays an important role in plant growth, including increasing plant biomass and plant height, elongating cells, and promoting xylem differentiation. However, little is known about the function of the CPD gene in sugar beet. In the current study, we isolated CPD from Beta vulgaris L. (BvCPD), which encodes protein localized in the nucleus, cell membrane, and cell wall. BvCPD was strongly expressed in parenchyma cells and vascular bundles. The transgenic sugar beet overexpressing BvCPD exhibited larger diameter than that of the wild type (WT), which mainly owing to the increased number and size of parenchyma cells, the enlarged lumen and area of vessel in the xylem. Additionally, overexpression of BvCPD increased the synthesis of endogenous BR, causing changes in the content of endogenous auxin (IAA) and gibberellin (GA) and accumulation of cellulose and lignin in cambium 1-4 rings of the taproot. These results suggest that BvCPD can promote the biosynthesis of endogenous BR, improve cell wall components, promote the development of parenchyma cells and vascular bundle, thereby playing an important role in promoting the growth and development of sugar beet taproot.

Exogenous brassinosteroids increases tolerance to shading by altering stress responses in mung bean (Vigna radiata L.)

Plant steroidal hormones, brassinosteroids, play a key role in various developmental processes of plants and the adaptation to various environmental stresses. The purpose of this research was to evaluate the effect of exogenous 24-epibrassinolide (EBR) application on the morphology, photosynthetic characteristics, chlorophyll fluorescence parameters, photosynthetic enzymes activities, and endogenous hormone content of mung bean (Vigna radiata L.) leaves under shading stress environment. Two mung bean cultivars, Xilv 1 and Yulv 1, were tested. The results showed that all of the investigated data were significantly affected by shading stress; however, foliar application of EBR increased the net photosynthetic rate, transpiration rate, stomatal conductance, and decreased intercellular CO₂ concentration of mung bean leaves under shading condition. Increased photosynthetic capacity in EBR-treated leaves was accompanied by improvement in higher photosynthetic enzymes activities. EBR-treated leaves exhibited more quantum yield of PSII electron transport and efficiency of energy capture than the control, which was mainly due to clearer leaf anatomical structure such as palisade tissues and spongy tissues, further resulting in altered plant morphological characteristics. Moreover, the treatment with EBL regulated the endogenous hormone content, including the decreased gibberellins and increased brassinolide, although to different levels. Combined with the morphological and physiological responses, we concluded that exogenous EBR treatment is beneficial to enhancing plant tolerance to shading stress and mitigating injure from weak light. The modifications of the physiological metabolism through EBR application may be a potential strategy to weaken shading stress in the future sustainable agricultural production.

Genome-wide identification of Gramineae histone modification genes and their potential roles in regulating wheat and maize growth and stress responses

BACKGROUND

In plants, histone modification (HM) genes participate in various developmental and defense processes. Gramineae plants (e.g., Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Setaria italica, Setaria viridis, and Zea mays) are important crop species worldwide. However, little information on HM genes is in Gramineae species.

RESULTS

Here, we identified 245 TaHMs, 72 HvHMs, 84 SbHMs, 93 SvHMs, 90 SiHMs, and 90 ZmHMs in the above six Gramineae species, respectively. Detailed information on their chromosome locations, conserved domains, phylogenetic trees, synteny, promoter elements, and gene structures were determined. Among the HMs, most motifs were conserved, but several unique motifs were also identified. Our results also suggested that gene and genome duplications potentially impacted the evolution and expansion of HMs in wheat. The number of orthologous gene pairs between rice (Oryza sativa) and each Gramineae species was much greater than that between Arabidopsis and each Gramineae species, indicating that the dicotyledons shared common ancestors. Moreover, all identified HM gene pairs likely underwent purifying selection based on to their non-synonymous (Ka)/synonymous (Ks) nucleotide substitutions. Using published transcriptome data, changes in TaHM gene expression in developing wheat grains treated with brassinosteroid, brassinazole, or activated charcoal were investigated. In addition, the transcription models of ZmHMs in developing maize seeds and after gibberellin treatment were also identified. We also examined plant stress responses and found that heat, drought, salt, insect feeding, nitrogen, and cadmium stress influenced many TaHMs, and drought altered the expression of several ZmHMs. Thus, these findings indicate their important functions in plant growth and stress adaptations.

CONCLUSIONS

Based on a comprehensive analysis of Gramineae HMs, we found that TaHMs play potential roles in grain development, brassinosteroid- and brassinazole-mediated root growth, activated charcoal-mediated root and leaf growth, and biotic and abiotic adaptations. Furthermore, ZmHMs likely participate in seed development, gibberellin-mediated leaf growth, and drought adaptation.

MdBZR1 regulates ABA response by modulating the expression of MdABI5 in apple

MdBZR1 directly binds to the promoter of MdABI5 and suppresses its expression to mediate ABA response. The plant hormones brassinosteroids (BRs) and abscisic acid (ABA) antagonistically regulate various aspects of plant growth and development. However, the association between BR and ABA signaling is less clear. Here, we identified MdBZR1 in apple (Malus domestica) and demonstrated that it was activated by BRs and could respond to ABA treatment. Overexpression of MdBZR1 in apple calli and Arabidopsis reduced ABA-hypersensitive phenotypes, suggesting that MdBZR1 negatively regulates ABA signaling. Subsequently, we found that MdBZR1 directly bound to the promoter region of MdABI5 and suppressed its expression. MdABI5 was significantly induced by ABA treatment. And overexpression of MdABI5 in apple calli increased sensitivity to ABA. Ectopic expression of MdABI5 in Arabidopsis inhibited seed germination and seedling growth. In addition, overexpression of MdBZR1 partially attenuated MdABI5-mediated ABA sensitivity. Taken together, our data indicate that MdBZR1 directly binds to the promoter of MdABI5 and suppresses its expression to antagonistically mediate ABA response. Our work contributes to the functional studies of BZR1 and further broadens the insight into the between BR and ABA signaling.

Exogenous application of brassinosteroids regulates tobacco leaf size and expansion via modulation of endogenous hormones content and gene expression

Brassinosteroids (BR) play diverse roles in the regulation of plant growth and development. BR promotes plant growth by triggering cell division and expansion. However, the effect of exogenous BR application on the leaf size and expansion of tobacco is unknown. Tobacco seedlings are treated with different concentrations of exogenous 2,4-epibrassinolide (EBL) [control (CK, 0 mol L^-1), T1 (0.5 × 10^-7 mol L^-1), and T2 (0.5 × 10^-4 mol L^-1)]. The results show that T1 has 17.29% and T2 has 25.99% more leaf area than control. The epidermal cell area is increased by 24.40% and 17.13% while the number of epidermal cells is 7.06% and 21.06% higher in T1 and T2, respectively, relative to control. So the exogenous EBL application improves the leaf area by increasing cell numbers and cell area. The endogenous BR (7.5 times and 68.4 times), auxin (IAA) (4.03% and 25.29%), and gibberellin (GA₃) contents (84.42% and 91.76%) are higher in T1 and T2, respectively, in comparison with control. Additionally, NtBRI1, NtBIN2, and NtBES1 are upregulated showing that the brassinosteroid signaling pathway is activated. Furthermore, the expression of the key biosynthesis-related genes of BR (NtDWF4), IAA (NtYUCCA6), and GA₃ (NtGA3ox-2) are all upregulated under EBL application. Finally, the exogenous EBL application also upregulated the expression of cell growth-related genes (NtCYCD3;1, NtARGOS, NtGRF5, NtGRF8, and NtXTH). The results reveal that the EBL application increases the leaf size and expansion by promoting the cell expansion and division through higher BR, IAA, and GA₃ contents along with the upregulation of cell growth-related genes. The results of the study provide a scientific basis for the effect of EBL on tobacco leaf growth at morphological, anatomical, biochemical, and molecular levels.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00971-x.

Genome-Wide Identification of Brassinosteroid Signaling Downstream Genes in Nine Rosaceae Species and Analyses of Their Roles in Stem Growth and Stress Response in Apple

Brassinosteroid signaling downstream genes regulate many important agronomic traits in rice. However, information on such genes is limited in Arabidopsis and Rosaceae species. We identified these genes in Arabidopsis and nine Rosaceae species. They were, respectively, named based on chromosomal locations. Segmental duplication and whole-genome duplication under purifying selection, as determined by Ka/Ks analysis, likely contributed to Rosaceae gene expansion. Apple (Malus domestica), Arabidopsis, and rice genes were generally similar, while several Rosaceae genes differed from their rice homologs in various characteristics, such as gene length, subcellular localization, transmembrane topology, conserved domains, secondary structures, and responses to external signals. The brassinosteroid downstream genes in apple were, respectively, induced or repressed by five phytohormones. Furthermore, these apple downstream genes were differentially expressed in different apple grafting combinations (“Nagafu No. 2”/“Malling 9” and “Nagafu No. 2”/“Nagafu No. 2”) and long–short shoot varieties (“Yanfu No. 6” and “Nagafu No. 2”). Responses of the MdBZR genes to diverse stress signals were examined and candidate hub genes were identified. These findings indicated that several brassinosteroid signaling downstream genes in Rosaceae functionally differed from their rice homologs, and certain apple genes may play roles in plant height and stress responses. This study provided valuable information and presented enriched biological theories on brassinosteroid signaling downstream genes in apple. Identification of such genes serve to help expand apple breeding and growth. This study provides useful information for brassinosteroid signaling downstream genes.

Exogenous 6-benzyladenine application affects root morphology by altering hormone status and gene expression of developing lateral roots in Malus hupehensis

Malus hupehensis is an extensively used apple rootstock in China. In the current study, M. hupehensis seedlings were treated with exogenous 2.2 µm 6-benzyladenine (6-BA) so as to investigate the mechanism by which 6-BA affects lateral root development. The results indicate that 6-BA treatment promotes elongation and thickening of both root and shoot in M. hupehensis, but reduces the number of lateral roots, as well as reducing the auxin level after 6-BA treatment. Moreover, MhAHK4, MhRR1 and MhRR2 were also significantly up-regulated in response to 6-BA treatment. Expression levels of auxin synthesis- and transport-related genes, such as MhYUCCA6, MhYUCCA10, MhPIN1 and MhPIN2, were down-regulated, which corresponds with lower auxin levels in the 6-BA-treated seedlings. A negative regulator of auxin, MhIAA3, was induced by 6-BA treatment, leading to reduced expression of MhARF7 and MhARF19 in 6-BA-treated seedlings. As a result, expression of MhWOX11, MhWOX5, MhLBD16 and MhLBD29 was blocked, which in turn inhibited lateral root initiation. In addition, a lower auxin level decreased expression of MhRR7 and MhRR15, which repressed expression of key transcription factors associated with root development, thus inhibiting lateral root development. In contrast, 6-BA treatment promoted secondary growth (thickening) of the root by inducing expression of MhCYCD3;1 and MhCYCD3;2. Collectively, the changes in hormone levels and gene expression resulted in a reduced number of lateral roots and thicker roots in 6-BA-treated plants.

Transcriptome Analysis Reveals New Insights into MdBAK1-Mediated Plant Growth in Malus domestica

BAK1 effects on plant stress responses have been well documented, but little is known regarding its effects on plant growth. In this study, we functionally characterized MdBAK1. Overexpressing MdBAK1 in Arabidopsis thaliana and apple trees promoted growth. Longitudinal stem cells were longer in transgenic plants than in wild-type plants. The size and number of cells and the area of the transverse stem were greater in the transgenic lines than in the wild-type plants. Moreover, transgenic A. thaliana and apple plants were more sensitive to an exogenous brassinosteroid. A transcriptome analysis of wild-type and transgenic apple revealed that MdBAK1 overexpression activated the brassinosteroid and ethylene signals, xylem production, and stress responses. Trend and Venn analyses indicated that carbohydrate, energy, and hormone metabolic activities were greater in transgenic plants during different periods. Moreover, a weighted gene coexpression network analysis proved that carbohydrate, hormone, and xylem metabolism as well as cell growth may be critical for MdBAK1-mediated apple tree growth and development. Compared with the corresponding levels in wild-type plants, the endogenous brassinosteroid, cytokinin, starch, sucrose, trehalose, glucose, fructose, and total sugar contents were considerably different in transgenic plants. Our results imply that MdBAK1 helps to regulate the growth of apple tree through the above-mentioned pathways. These findings provide new information regarding the effects of MdBAK1 onplant growth and development.

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.