Allelic variation of BBX24 is a dominant determinant controlling red coloration and dwarfism in pear.

Variation in anthocyanin biosynthesis in pear fruit provides genetic germplasm resources for breeding, while dwarfing is an important agronomic trait, which is beneficial to reduce the management costs and allow for the implementation of high-density cultivation. Here, we combined bulked segregant analysis (BSA), quantitative trait loci (QTL), and structural variation (SV) analysis to identify a 14-bp deletion which caused a frame shift mutation and resulted in the premature translation termination of a B-box (BBX) family of zinc transcription factor, PyBBX24, and its allelic variation termed PyBBX24ΔN14. PyBBX24ΔN14 overexpression promotes anthocyanin biosynthesis in pear, strawberry, Arabidopsis, tobacco, and tomato, while that of PyBBX24 did not. PyBBX24ΔN14 directly activates the transcription of PyUFGT and PyMYB10 through interaction with PyHY5. Moreover, stable overexpression of PyBBX24ΔN14 exhibits a dwarfing phenotype in Arabidopsis, tobacco, and tomato plants. PyBBX24ΔN14 can activate the expression of PyGA2ox8 via directly binding to its promoter, thereby deactivating bioactive GAs and reducing the plant height. However, the nuclear localization signal (NLS) and Valine-Proline (VP) motifs in the C-terminus of PyBBX24 reverse these effects. Interestingly, mutations leading to premature termination of PyBBX24 were also identified in red sports of un-related European pear varieties. We conclude that mutations in PyBBX24 gene link both an increase in pigmentation and a decrease in plant height.

Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution.

Previously released pear genomes contain a plethora of gaps and unanchored genetic regions. Here, we report a telomere-to-telomere (T2T) gap-free genome for the red-skinned pear, 'Yunhong No. 1' (YH1; Pyrus pyrifolia), which is mainly cultivated in Yunnan Province (southwest China), the pear's primary region of origin. The YH1 genome is 501.20 Mb long with a contig N50 length of 29.26 Mb. All 17 chromosomes were assembled to the T2T level with 34 characterized telomeres. The 17 centromeres were predicted and mainly consist of centromeric-specific monomers (CEN198) and long terminal repeat (LTR) Gypsy elements (≥74.73%). By filling all unclosed gaps, the integrity of YH1 is markedly improved over previous P. pyrifolia genomes ('Cuiguan' and 'Nijisseiki'). A total of 1531 segmental duplication (SD) driven duplicated genes were identified and enriched in stress response pathways. Intrachromosomal SDs drove the expansion of disease resistance genes, suggesting the potential of SDs in adaptive pear evolution. A large proportion of duplicated gene pairs exhibit dosage effects or sub-/neo-functionalization, which may affect agronomic traits like stone cell content, sugar content, and fruit skin russet. Furthermore, as core regulators of anthocyanin biosynthesis, we found that MYB10 and MYB114 underwent various gene duplication events. Multiple copies of MYB10 and MYB114 displayed obvious dosage effects, indicating role differentiation in the formation of red-skinned pear fruit. In summary, the T2T gap-free pear genome provides invaluable resources for genome evolution and functional genomics.

The pear genomics database (PGDB): a comprehensive multi-omics research platform for Pyrus spp.

BACKGROUND: Pears are among the most important temperate fruit trees in the world, with significant research efforts increasing over the last years. However, available omics data for pear cannot be easily and quickly retrieved to enable further studies using these biological data. DESCRIPTION: Here, we present a publicly accessible multi-omics pear resource platform, the Pear Genomics Database (PGDB). We collected and collated data on genomic sequences, genome structure, functional annotation, transcription factor predictions, comparative genomics, and transcriptomics. We provide user-friendly functional modules to facilitate querying, browsing and usage of these data. The platform also includes basic and useful tools, including JBrowse, BLAST, phylogenetic tree building, and additional resources providing the possibility for bulk data download and quick usage guide services. CONCLUSIONS: The Pear Genomics Database (PGDB, http://pyrusgdb.sdau.edu.cn ) is an online data analysis and query resource that integrates comprehensive multi-omics data for pear. This database is equipped with user-friendly interactive functional modules and data visualization tools, and constitutes a convenient platform for integrated research on pear.

Auxin inhibits lignin and cellulose biosynthesis in stone cells of pear fruit via the PbrARF13-PbrNSC-PbrMYB132 transcriptional regulatory cascade.

Stone cells are often present in pear fruit, and they can seriously affect the fruit quality when present in large numbers. The plant growth regulator NAA, a synthetic auxin, is known to play an active role in fruit development regulation. However, the genetic mechanisms of NAA regulation of stone cell formation are still unclear. Here, we demonstrated that exogenous application of 200 µM NAA reduced stone cell content and also significantly decreased the expression level of PbrNSC encoding a transcriptional regulator. PbrNSC was shown to bind to an auxin response factor, PbrARF13. Overexpression of PbrARF13 decreased stone cell content in pear fruit and secondary cell wall (SCW) thickness in transgenic Arabidopsis plants. In contrast, knocking down PbrARF13 expression using virus-induced gene silencing had the opposite effect. PbrARF13 was subsequently shown to inhibit PbrNSC expression by directly binding to its promoter, and further to reduce stone cell content. Furthermore, PbrNSC was identified as a positive regulator of PbrMYB132 through analyses of co-expression network of stone cell formation-related genes. PbrMYB132 activated the expression of gene encoding cellulose synthase (PbrCESA4b/7a/8a) and lignin laccase (PbrLAC5) binding to their promotors. As expected, overexpression or knockdown of PbrMYB132 increased or decreased stone cell content in pear fruit and SCW thickness in Arabidopsis transgenic plants. In conclusion, our study shows that the 'PbrARF13-PbrNSC-PbrMYB132' regulatory cascade mediates the biosynthesis of lignin and cellulose in stone cells of pear fruit in response to auxin signals and also provides new insights into plant SCW formation.

The transcription factor PbrMYB24 regulates lignin and cellulose biosynthesis in stone cells of pear fruits.

Lignified stone cell content is a key factor used to evaluate fruit quality, influencing the economic value of pear (Pyrus pyrifolia) fruits. However, our understanding of the regulatory networks of stone cell formation is limited due to the complex secondary metabolic pathway. In this study, we used a combination of co-expression network analysis, gene expression profiles, and transcriptome analysis in different pear cultivars with varied stone cell content to identify a hub MYB gene, PbrMYB24. The relative expression of PbrMYB24 in fruit flesh was significantly correlated with the contents of stone cells, lignin, and cellulose. We then verified the function of PbrMYB24 in regulating lignin and cellulose formation via genetic transformation in homologous and heterologous systems. We constructed a high-efficiency verification system for lignin and cellulose biosynthesis genes in pear callus. PbrMYB24 transcriptionally activated multiple target genes involved in stone cell formation. On the one hand, PbrMYB24 activated the transcription of lignin and cellulose biosynthesis genes by binding to different cis-elements [AC-I (ACCTACC) element, AC-II (ACCAACC) element and MYB-binding sites (MBS)]. On the other hand, PbrMYB24 bound directly to the promoters of PbrMYB169 and NAC STONE CELL PROMOTING FACTOR (PbrNSC), activating the gene expression. Moreover, both PbrMYB169 and PbrNSC activated the promoter of PbrMYB24, enhancing gene expression. This study improves our understanding of lignin and cellulose synthesis regulation in pear fruits through identifying a regulator and establishing a regulatory network. This knowledge will be useful for reducing the stone cell content in pears via molecular breeding.

MdBAK1 overexpression in apple enhanced resistance to replant disease as well as to the causative pathogen Fusarium oxysporum.

Apple replant disease (ARD) is a complex syndrome caused by various biotic and abiotic stresses contained in replanted soil, leading to reduced plant growth and fruit yields and causing serious economic loss. Breeding disease-resistant varieties is an effective and practical method to control ARD. Effective plant defense depends in part on the plant immune responses induced by the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). BAK1 participates in the regulation of plant immunity as an important PRR-binding protein. In this study, MdBAK1 overexpression activated indeterminate immune responses in tissue-cultured apple plants. MdBAK1-overexpressing rooted apple plants exhibited enhanced resistance to ARD, as the inhibition of plant growth was significantly alleviated during the replanted soil treatment. In addition, MdBAK1-overexpressing apple plants showed abolished growth inhibition, wilting and root rot induced by Fusarium oxysporum, which is the main pathogen that causes ARD in China. MdBAK1 overexpression changed the microbial community structure in the rhizosphere soil, as reflected by the increase in bacterial content and the decrease in fungal content, and the root exudates of MdBAK1-overexpressing plants inhibited F. oxysporum spore germination compared with that of wild-type plants. Furthermore, the constitutive immunity and cell necrosis induced by the upregulation of MdBAK1 expression were involved in the inhibition of colonization and expansion of F. oxysporum in host plants. In short, MdBAK1 plays an important role in the regulation of apple resistance to ARD, suggesting that MdBAK1 may be a valuable gene for molecular breeding of ARD resistance.

An emerging chemical fumigant: two-sided effects of dazomet on soil microbial environment and plant response.

Methyl bromide has been banned worldwide because it causes damage to the ozone layer and the environment. To find a substitute for methyl bromide, the relationships among fumigation, plant growth, and the microbial community in replant soil require further study. We performed pot and field experiments to investigate the effects of dazomet fumigation on soil properties and plant performance. Changes in soil microbial community structure and diversity were assessed using high-throughput sequencing, and plant physiological performance and soil physicochemical properties were also measured. Dazomet fumigation enhanced photosynthesis and promoted plant growth in replant soil; it altered soil physical and chemical properties and reduced soil enzyme activities, although these parameters gradually recovered over time. After dazomet fumigation, the dominant soil phyla changed, microbial diversity decreased significantly, the relative abundance of biocontrol bacteria such as Mortierella increased, and the relative abundance of pathogenic bacteria such as Fusarium decreased. Over the course of the experiment, the soil microbial flora changed dynamically, and soil enzyme activities and other physical and chemical properties also recovered to a certain extent. This result suggested that the effect of dazomet on soil microorganisms was temporary. However, fumigation also led to an increase in some resistant pathogens, such as Trichosporon, that affect soil function and health. Therefore, it is necessary to consider potential negative impacts of dazomet on the soil environment and to perform active environmental risk management in China.

[Effects of dazomet fumigation on growth, biological characteristics of Malus hupehensis seedlings and soil environment]. / 棉隆熏蒸处理对平邑甜茶幼苗生长和生物学特性及土壤环境的影响.

In this study, we examined the effects of dazomet fumigation with different concentrations (0, 0.1, 0.2, 0.4 g·kg-1) on the microbial characteristics of continuous cropping soil and growth of Malus hupehensis seedling in greenhouse and open-field pot. The results showed that all the treatment of dazomet fumigation could promote the growth of M. hupehensis seedlings in continuous cropping soil, with 0.2 g·kg-1 treatment showing the strongest effect. Compared to the control, plant height, stem diameter, dry weight of M. hupehensis seedlings in 0.2 g·kg-1 dazomet fumigation were increased by 192.9% and 91.8%, 72.8% and 60.1%, 196.8% and 195.0%, 138.5% and 130.7%, respectively in greenhouse and open-field. The root related indices (root length, root area, root volume, root respiration rate) were significantly promoted. The activities of SOD, POD, CAT in roots were increased by 114.6% and 118.5%, 123.5% and 107.6%, 164.6% and 175.6% respectively compared with the control, whereas the content of malondialdehyde was significantly lowered. Soil bacterial content, fungal content, copy number of Fusarium oxysporum gene and soil enzyme activity were significantly decreased with the increasing dazomet concentrations. In conclusion, 0.2 g·kg-1 dazomet fumigation could increase the biomass of M. hupehensis seedlings in continuous cropping, improve soil environment, and effectively alleviate the continuous cropping obstacle. Therefore, 0.2 g ·kg-1 dazomet fumigation could be given priority during the reconstruction of old apple orchards.

Transcription strategies related to photosynthesis and nitrogen metabolism of wheat in response to nitrogen deficiency.

BACKGROUND: Agricultural yield is closely associated with nitrogen application. Thus, reducing the application of nitrogen without affecting agricultural production remains a challenging task. To understand the metabolic, physiological, and morphological response of wheat (Triticum aestivum) to nitrogen deficiency, it is crucial to identify the genes involved in the activated signaling pathways. RESULTS: We conducted a hydroponic experiment using a complete nutrient solution (N1) and a nutrient solution without nitrogen (N0). Wheat plants under nitrogen-deficient conditions (NDC) showed decreased crop height, leaf area, root volume, photosynthetic rate, crop weight, and increased root length, root surface area, root/shoot ratio. It indicates that nitrogen deficiency altered the phenotype of wheat plants. Furthermore, we performed a comprehensive analysis of the phenotype, transcriptome, GO pathways, and KEGG pathways of DEGs identified in wheat grown under NDC. It showed up-regulation of Exp (24), and Nrt (9) gene family members, which increased the nitrogen absorption and down-regulation of Pet (3), Psb (8), Nar (3), and Nir (1) gene family members hampered photosynthesis and nitrogen metabolism. CONCLUSIONS: We identified 48 candidate genes that were involved in improved photosynthesis and nitrogen metabolism in wheat plants grown under NDC. These genes may serve as molecular markers for genetic breeding of crops.