Search

Pear (Pyrus spp.) belongs to the genus Pyrus, in the family Rosaceae. Some varieties of pear fruit exhibit bulged surface, which seriously affects the quality and commodity value of the pear fruit. In this study, we performed anatomical, physiological, and transcriptomic analysis to explore the mechanism of paclobutrazol (PBZ) on the bulged surface of pear fruit. The vascular bundles of flesh were more evenly distributed, and the fruit cells were more compactly arranged and smaller in size treated with PBZ. However, the auxin (IAA) content of flesh was decreased in the treated group. Furthermore, the GO and KEGG analysis of differentially expressed genes (DEGs) showed that auxin, phenylpropanoid metabolic pathways, and transcriptional factor genes were significantly enriched on the relieved bulged surface of pear fruit. And it was analyzed that some genes contained auxin responded cis-elements from the selected DEGs in the promoter region. We conclude that PBZ plays a negative role in cell division, cell elongation, and vascular bundle development on the bulged surface of pear fruit through the involvement of auxin-related genes. This study will provide a theoretical basis for the regulation of the bulged surface of pear fruit by a growth retardant agent.

BackgroundJujube is one of the characteristic fruit tree species in China. ‘Linhuang No. 1’, a cracking-resistant cultivar, and ‘Muzao’, a cracking-susceptible cultivar, were selected as materials by previous study. Whole-genome re-sequencing and transcriptome of ‘Linhuang No. 1’ and ‘Muzao’ allow the screening out of differently expressed genes with different gene structures between them. It could be helpful in explaining divergence/similarity between the two cultivars. ResultsThere are 664,129 mutation sites between ‘Linhuang No. 1’ and ‘Muzao’ by re-sequencing. To determine the genetic relationship of ‘Linhuang 1’, ‘Muzao’ and reference genome ‘Dongzao’, the characteristic mutation sites were analyzed by principal component analysis. The genetic relationship between ‘Linhuang No. 1’ and ‘Muzao’ was closer than that with ‘Dongzao’. 19 differentially expressed genes were screened by combining the transcriptomics with re-sequencing analysis. LOC107427052 (encoding nitrite reductase) was determined by KEGG enrichment analysis for further study. The large base insertion was not in the domain region of the LOC107427052 gene CDS region. As verified by the finding that the base insertion did not affect protein translation. LOC107427052 gene expression levels, the nitrite reductase activities and the nitrite content of ‘Muzao’ were significantly higher than those of ‘Linhuang No. 1’ at young fruit stage. There was no significant difference in the product ammonia of nitrite reductase between the two varieties. ConclusionsOur study has laid a foundation for the analysis of genetic information and the comparative nitrite metabolism of ‘Linhuang No. 1’ and ‘Muzao’.

Pear (Pyrus spp.) belongs to the genus Pyrus, in the family Rosaceae. Some varieties of pear fruit exhibit bulged surface, which seriously affects the quality and commodity value of the pear fruit. In this study, we performed anatomical, physiological, and transcriptomic analysis to explore the mechanism of paclobutrazol (PBZ) on the bulged surface of pear fruit. The vascular bundles of flesh were more evenly distributed, and the fruit cells were more compactly arranged and smaller in size treated with PBZ. However, the auxin (IAA) content of flesh was decreased in the treated group. Furthermore, the GO and KEGG analysis of differentially expressed genes (DEGs) showed that auxin, phenylpropanoid metabolic pathways, and transcriptional factor genes were significantly enriched on the relieved bulged surface of pear fruit. And it was analyzed that some genes contained auxin responded cis-elements from the selected DEGs in the promoter region. We conclude that PBZ plays a negative role in cell division, cell elongation, and vascular bundle development on the bulged surface of pear fruit through the involvement of auxin-related genes. This study will provide a theoretical basis for the regulation of the bulged surface of pear fruit by a growth retardant agent. SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s12298-021-00929-z) contains supplementary material, which is available to authorized users.

Background: Pear (Pyrus spp.) belongs to the genus Pyrus, in the family Rosaceae. Some varieties of pear fruits exhibit bulged surface, which seriously affect the quality and commodity value. In this study, we performed anatomical, physiological and transcriptomic analysis, to explore the mechanism of paclobutrazol (PBZ) on the bulged surface of pear fruits. Results: The vascular bundles of flesh were more evenly distributed and the cells arranged more compactly with smaller size. However, the auxin (IAA) content of flesh decreased significantly when treated with PBZ. Further, the GO and KEGG analysis of differentially expressed genes (DEGs) showed that auxin, phenylpropanoid metabolic pathways and transcriptional factor genes were significantly enriched on the relieved bulged surface of pear fruits. The promoter region analysis of selected DEGs showed that some genes contained auxin responded cis-elements. Conclusion: We conclude that PBZ might play a negative role in the cell division, cell elongation and vascular bundle development on bulged surface of pear fruits through the involvement of auxin related genes. This study will provide theoretical basis for the regulation of bulged surface of pear fruits by growth retardant agent.

The interactions between hIAPP and the pancreatic β-cells are associated with β-cell death in type II diabetes. Cholesterol modulates hIAPP-membrane interaction and hIAPP aggregation. The molecular mechanism underlying this is not well understood. Here we explore the cholesterol-sensing role of F15 in the interactions of hIAPP and hIAPP1–19 with various compositions of lipids, including DOPC, DPPC and DOPC/DPPC using NMR, CD, ThT fluorescence and dye leakage assays. We show that both hIAPP and hIAPP1–19 are more potent in the disruption to the membranes with cholesterol than they are in the disruption to the membranes without cholesterol. A substitution of F15 by leucine affects the binding and disruption of the peptides to the membranes slightly in the absence of cholesterol, but decreases the activities largely in the presence of cholesterol. F15 also plays a role in accelerating fibrillar assembly of hIAPP, but the function is independent of cholesterol in nature. The promotion of cholesterol to the disruptive potency of hIAPP is more effective in the membrane with raft-like domains than in the membrane with a dispersed distribution of cholesterol. Our results suggest that F15 plays a key role in the cholesterol-sensing binding and disruption of hIAPP to the PC membranes and the distribution of cholesterol in the membranes has an influence on the disruptive activity of hIAPP.

The fruit pericarp wax of jujube accessions with different cracking resistance show differences in morphology and wax chemical content. In this study, transcriptome and genome re-sequencing were used to analyze the differences in wax metabolism between jujube cultivars with different cracking resistance characteristics. The results showed that 431 differentially expressed genes were identified through transcriptome screening between the cracking-resistant cultivar ‘Linhuang No. 1’ and the cracking-susceptible cultivar ‘Muzao’ during the mature stage of fruit development. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis annotated three wax metabolism pathways (involving eight wax metabolism-related genes). Information on gene sequence variation in the eight genes was obtained from genome resequencing, with sequence variation between the two cultivars found in the promoter region of the LOC107415896 gene, which encodes the biotin carboxyl carrier protein of acetyl-CoA carboxylase 2, chloroplastic (BCCP2) protein, where 107 bases were inserted in ‘Linhuang No.1’. As a result, the fatty acid concentration in the wax of ‘Muzao’ was lower than that of ‘Linhuang No. 1’, with the proportion of fatty acids with fewer than 16 C atoms in ‘Muzao’ accounting for a greater proportion of the total fatty acids. This indicated that the expression of the ‘Muzao’ LOC107415896 gene was affected. Our research has laid the foundation for further analysis of the function of jujube wax metabolism in the cracking-resistant fruit phenomenon.

Prunus mume has a unique floral scent feature that can volatilize a large amount of benzyl acetate into the air during flowering. At present, the efficient volatilization mechanism of P. mume floral scent components is still unclear. The volatilization of the key aromatic components in P. mume 'Caizhi Wufen' was explored in different parts of flowers. Our results showed that filaments are the key fragrance-releasing parts of benzyl acetate. Moreover, the volatilization rates of diverse aromatic components were different in several parts. We also identified 130 ABC genes from P. mume, which were divided into eight subfamilies. Among the ABC genes, 55 were PmABCGs, including 24 half-size molecular transporters (white-brown complex, WBC) located on the cell membrane. Combined with RNA sequencing (RNA-seq) analysis, most of the ABCG subfamily genes were specifically expressed in flowers. Importantly, they were also WBC genes and expressed high in filaments. Correlation analysis of volatilization rate and the genes expression of PmABCG showed that the volatilization of benzaldehyde and benzyl alcohol were highly correlated with PmABCG2, 18, 26, and that of benzyl acetate was highly correlated with PmABCG9, 13 and 23. Therefore, the current study would provide a valuable guide for elucidating the transmembrane transport mechanism of benzenoid volatiles and study further a biological function of different fragrance-releasing parts of flowers.

Flower color is an important economic trait of Prunus mume, a famous ornamental plant widely cultivated in East Asia. Anthocyanins, acting as major pigments of flower coloration, are biosynthesized via transcriptional regulation of transcription factors (TFs). Many R2R3-MYB TFs have been identified to regulate anthocyanin biosynthetic pathways. However, very little is known about the role of R2R3-MYB TFs regulating anthocyanin biosynthesis in P. mume. In our study, the first R2R3-MYB TF (PmMYBa1) from P. mume has been isolated and characterized. Sequence analysis revealed that PmMYBa1 contains conserved R2R3 MYB domain and belongs to anthocyanin-related subgroup 6 of R2R3-MYB family. Overexpression of PmMYBa1 in tobacco contributed to anthocyanin accumulation by activating endogenous anthocyanin-relating genes in the flowers and fruits of transgenic lines. Gene expression analysis showed that almost all of the endogenous structural genes of anthocyanin biosynthesis were obviously up-regulated, as well as bHLH TFs An1a and An1b in the flowers and fruits of PmMYBa1-overexpressing tobacco. In contrast, only three structural genes NtCHS, NtF3H, and NtANS were up-regulated in the leaves. In addition, the expression level of PmMYBa1 was higher in the anthocyanin-rich red flowers than in white ones and strongly correlated with anthocyanin content in the developing petals of P. mume. These findings strongly suggest that PmMYBa1 is involved in regulating anthocyanin biosynthesis in P. mume. Moreover, PmDFR and PmANS might be potential target genes regulated by PmMYBa1 in P. mume according to the correlation analysis. Isolation and functional characterization of PmMYBa1 laid a foundation for further exploring the mechanisms of anthocyanin synthesis and provide a potential candidate gene for breeding to manipulate flower colors in P. mume.

Increasing lines of evidence show that the oligomeric intermediates of amyloid peptides/proteins are toxic to biological membranes. However, the structural features of the oligomers that are closely associated with the ability to damage biological membranes are far from understanding. In this study, we constructed two species of oligomers using hIAPP

Prunus mume, a traditional Chinese flower, is the only species of Prunus known to produce a strong floral fragrance, of which eugenol is one of the principal components. To explore the molecular mechanism of eugenol biosynthesis in P. mume, patterns of dynamic, spatial and temporal variation in eugenol were analysed using GC-MS. Coniferyl alcohol acetyltransferase (CFAT), a member of the BAHD acyltransferase family, catalyses the substrate of coniferyl alcohol to coniferyl acetate, which is an important substrate for synthesizing eugenol. In a genome-wide analysis, we found 90 PmBAHD genes that were phylogenetically clustered into five major groups with motif compositions relatively conserved in each cluster. The phylogenetic tree showed that the PmBAHD67-70 proteins were close to the functional CFATs identified in other species, indicating that these four proteins might function as CFATs. In this work, 2 PmCFAT genes, named PmCFAT1 and PmCFAT2, were cloned from P. mume ‘Sanlunyudie’, which has a strong fragrance. Multiple sequences indicated that PmCFAT1 contained two conserved domains, HxxxD and DFGWG, whereas DFGWG in PmCFAT2 was changed to DFGFG. The expression levels of PmCFAT1 and PmCFAT2 were examined in different flower organs and during the flowering stages of P. mume ‘Sanlunyudie’. The results showed that PmCFAT1 was highly expressed in petals and stamens, and this expression increased from the budding stage to the full bloom stage and decreased in the withering stage, consistent with the patterns of eugenol synthesis and emission. However, the peak of gene expression appeared earlier than those of eugenol synthesis and emission. In addition, the expression level of PmCFAT2 was higher in pistils and sepals than in other organs and decreased from the budding stage to the blooming stage and then increased in the withering stage, which was not consistent with eugenol synthesis. Subcellular localization analysis indicated that PmCFAT1 and PmCFAT2 were located in the cytoplasm and nucleus, while enzyme activity assays showed that PmCFAT1 is involved in eugenol biosynthesis in vitro. Overall, the results suggested that PmCFAT1, but not PmCFAT2, contributed to eugenol synthesis in P. mume.

Increasing lines of evidence show that the oligomeric intermediates of amyloid peptides/proteins are toxic to biological membranes. However, the structural features of the oligomers that are closely associated with the ability to damage biological membranes are far from understanding. In this study, we constructed two species of oligomers using hIAPP18-27 peptide and its d,l-alternating isomer, examined the disruptive ability of the oligomers to POPC/POPG 4:1 vesicles by leakage assay and 31P NMR spectroscopy, and characterized the structural features of the oligomers by CD, TEM, 1H NMR and fluorescence quenching experiments. We found that the d,l-alternating peptide oligomers are more disruptive than the all-L peptide oligomers to the lipid membrane. The characterization of the secondary structure revealed that the d,l-alternating peptide adopts an extended polyproline type-II (PPII) conformation, while the all-L peptide adopts a random coil conformation in oligomers. Compared with the all-L peptide oligomers, the d,l-alternating peptide oligomers are less compact and keep more hydrophobic groups water exposed. Both the changes from PPII to α-sheet in the structure of d,l-alternating peptide and from random coil to β-sheet in the structure of all-L peptide reduce the ability of the peptide oligomers to disrupt the lipid membrane. Our results suggest that an oligomer with extended peptide chains could be more potent in membrane disruption than an oligomer with folded peptide chains and an increase in peptide-peptide interaction could decrease the disruptive ability of oligomer.

Class I sirtuin genes including SIRT1, SIRT2 and SIRT3, are members of the nicotinamide adenine dinucleotide (NAD)-dependent family of histone deacetylases, and play essential roles in senescence, metabolism, and apoptosis. This study was conducted to detect potential polymorphisms of the bovine class I sirtuin genes and explore their relationships with ultrasound carcass traits in Qinchuan cattle. Four non-coding mutations in the 3'UTR (SIRT1: g.25751AC, SIRT1: g.25846AG, SIRT2: g.19676GA and SIRT3: g. 25702CT) and three mutations in exons (SIRT2: g.4062CT; SIRT2: g.4406CT and SIRT3: g.25557AG) were identified in 468 individuals of Qinchuan cattle. Chi-square tests showed that g.25751AC, g.19676GA, and g.25702CT were in Hardy-Weinberg disequilibrium (χ(2)χ0.05(2)). The statistical analyses indicated that six SNPs were significantly associated with the ultrasound carcass traits (P0.05) except g.4062CT (SIRT2) (P0.05). These results indicate that the variations in the class I sirtuin genes and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.

The aim of this study was to determine the protective effects of the combination of ascorbic acid (Vc) and vitamin E (VE) on antioxidant enzyme activity, sperm motility, viability, and acrosome integrity of Qinchuan bulls after freeze-thaw. In this study, we determined the effects of Vc and VE on the activity of the antioxidant enzyme defense system comprising glutathione peroxidase (GSH-Px), glutathione reductase (GR), catalase (CAT), and superoxide dismutase (SOD). The combination of Vc and VE had protective effects on sperm motility and viability. With respect to acrosome integrity and the activity of GR and SOD, differences were observed between the experimental groups with added Vc (7 mg/mL) and VE (0.12 IU/mL) and the control group. The activity of GSH-Px in the experimental group (1400 IU/mL Vc and 0.12 IU/mL VE) was not different (P > 0.05) compared with that in the control group, while the activity of CAT showed a significant difference between the 2 groups (P < 0.05). Therefore, we inferred that the combination of Vc (1400 IU/mL) and VE (0.12 IU/mL) protected the sperm quality in the freeze-thaw process.

In order to investigate the difference in their characteristic floral scents between Prunus mume Siebold & Zucc. and the related Prunus species, their headspace volatiles and endogenous extraction were analyzed by gas chromatography–mass spectrometry. The efficiency of substrate utilization of the flowers was studied by incubating them with different alcohol substrates. Our results indicated that benzyl acetate is a dominant compound influencing the characteristic floral scent of P. mume. An alcohol substrate concentration of 4 mmol L−1 and a reaction time of 2 h were constituted the reaction condition for catalysis of exogenous alcohol substrates by the flowers. Under these conditions, Prunus sibirica exhibited the highest utilization efficiency for benzyl alcohol substrate while the utilization efficiency of Prunus persica was the lowest. Comparative analysis of several alcohol substrates indicated that the flowers of the tested species had selective specificity for benzyl alcohol substrates.

Prunus mume is the only species of Prunus known to produce a strong floral fragrance. Most interspecific hybrids between P. mume and other species of Prunus lack the fragrance. The analysis of variations in emitted and endogenous compounds among genetically close cultivars is a powerful approach for revealing the mechanisms underlying floral scent emission. Compounds emitted by flowers from five cultivars were collected using the static headspace method, and endogenous compounds in the flowers were extracted with ethyl acetate. Samples were analysed quantitatively and qualitatively using gas chromatography-mass spectrometry. The result showed that benzenoids were the dominant compounds, of which benzyl acetate was the principal component contributing to the floral scent of P. mume. A clustering analysis of the floral volatiles from the different cultivars suggested that the scent traits of hybrids are related to the taxonomic relationship between their parents. The correlations between the amount of the endogenous and emitted compounds revealed that benzyl acetate had a stronger tendency to be volatile than the other compounds and the volatilisation rate of volatile compounds varied greatly among different cultivars. The importance of the biosynthetic pathway and the function of benzaldehyde are discussed.

Mei (Prunus mume) is widely cultivated in eastern Asia owing to its favored ornamental characteristics and its tolerance for low temperatures. Reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used method for gene expression analysis, requiring carefully selected reference genes to ensure data reliability. The aim of this study was to identify and evaluate reference genes for qRT-PCR in mei. Ten candidate reference genes were chosen, and their expression levels were assessed by qRT-PCR in four sample sets: 1) flowering mei; 2) mei undergoing abiotic stress; 3) different genotypes of Prunus species; and 4) all mei samples. The stability and suitability of the candidate reference genes were validated using commercially available software. We found that protein phosphatase 2A-1 (PP2A-1) and PP2A-2 were suitable reference genes for flowering with ubiquitin-conjugating enzyme E2 (UBC) also being suitable for different genotypes of Prunus species. UBC and actin (ACT) were most stably expressed under abiotic stress. Finally, the expression of an AGAMOUS homolog of Arabidopsis thaliana (PmAG) and a putative homolog of Group 2 late embryogenesis abundant protein gene in A. thaliana (PmLEA) were assessed to allow comparisons between selected candidate reference genes, highlighting the importance of careful reference gene selection.

The BM2113 locus was amplified in Yunnan mithun (Bos frontalis) from the southwest mountains of China. It showed a high degree of polymorphism with a total of 12 alleles. The 121-bp polymorphic allele of the BM2113 locus that accounted for 37.1% of homozygotes was the predominant allele with a frequency of 58.57%, identified as mithun-specific for Bos species in Yunnan mithun. The polymorphism information content value was high with a mean of 0.6170, the expected and observed heterozygosity was moderate with values of 0.6427 and 0.6000, respectively, and the BM2113 locus was under Hardy-Weinberg equilibrium (P = 0.2897) in the Yunnan mithun population. This study elucidated the genetic diversity, multi-origin, specific alleles, and characterization of mithun.

Adipogenin (ADIG) is an adipocyte-specific membrane protein highly expressed in adipose tissues and is increased during the adipocyte differentiation. However, the roles and mechanisms of ADIG on fat accumulation and adipocyte differentiation in ex vivo still largely unknown. In this study, we isolated bovine myosatellite cells based on adhesion characteristics to investigate whether ADIG overexpression could promote trans-differentiation and increase fat accumulation in myosatellite cells. Immunofluorescence labeling was then used for the phenotypic characteristics of myosatellite. Our results showed that, after induction of differentiation, adenovirus mediated ADIG overexpression could upregulate expression level of PPARγ, and Oil Red O staining showed larger lipid drops compared to control groups. In consistent, key components of Hh signaling pathway were down regulated when infected with ADIG adenovirus, even though treated with inhibitor of Hh signaling pathway together could not induce further decrease. In addition, bioinformatics analysis of ADIG was also performed for its structure and function.

The APETALA 2/ethylene-responsive element binding factor (AP2/ERF) transcription factors play important roles in plant development and responses to stress. Although the entire genomes of four Rosaceae species have been fully sequenced, no genome-wide analysis of AP2/ERF gene family has yet been reported in the Rosaceae family. In this study, 116 AP2/ERF genes were identified from Chinese plum (Prunus mume). Based on the number of AP2/ERF domains, these PmAP2/ERF genes were classified into three families (AP2, ERF, and RAV) along with a single member. The ERF family was subdivided into 11 groups. Of those, 22 and 41 PmAP2/ERF genes were involved in segmental and tandem duplications, respectively. Putative orthologs in Arabidopsis were identified for 73 PmAP2/ERF genes following synteny analysis. Transcriptome sequencing analysis showed that expression of PmAP2/ERF genes was widely variable.

Longissimus dorsi muscle (LD) proteomics provides a novel opportunity to reveal the molecular mechanism behind intramuscular fat deposition. Unfortunately, the vast amounts of lipids and nucleic acids in this tissue hampered LD proteomics analysis. Trichloroacetic acid (TCA)/acetone precipitation is a widely used method to remove contaminants from protein samples. However, the high speed centrifugation employed in this method produces hard precipitates, which restrict contaminant elimination and protein re-dissolution. To address the problem, the centrifugation precipitates were first grinded with a glass tissue grinder and then washed with 90% acetone (TCA/acetone-G-W) in the present study. According to our result, the treatment for solid precipitate facilitated non-protein contaminant removal and protein re-dissolution, ultimately improving two-dimensional gel electrophoresis (2-DE) analysis. Additionally, we also evaluated the effect of sample drying on 2-DE profile as well as protein yield. It was found that 30 min air-drying did not result in significant protein loss, but reduced horizontal streaking and smearing on 2-DE gel compared to 10 min. In summary, we developed an optimized TCA/acetone precipitation method for protein extraction of LD, in which the modifications improved the effectiveness of TCA/acetone method.

Prunus mume (mei), which was domesticated in China more than 3,000 years ago as ornamental plant and fruit, is one of the first genomes among Prunus subfamilies of Rosaceae been sequenced. Here, we assemble a 280M genome by combining 101-fold next-generation sequencing and optical mapping data. We further anchor 83.9% of scaffolds to eight chromosomes with genetic map constructed by restriction-site-associated DNA sequencing. Combining P. mume genome with available data, we succeed in reconstructing nine ancestral chromosomes of Rosaceae family, as well as depicting chromosome fusion, fission and duplication history in three major subfamilies. We sequence the transcriptome of various tissues and perform genome-wide analysis to reveal the characteristics of P. mume, including its regulation of early blooming in endodormancy, immune response against bacterial infection and biosynthesis of flower scent. The P. mume genome sequence adds to our understanding of Rosaceae evolution and provides important data for improvement of fruit trees., The Prunus mume was domesticated in China over 3,000 years ago and is an important ornamental plant and fruit. Here Qixiang Zhang et al. obtain the first assembly of its genome with a combination of next-generation sequencing, whole-genome mapping and restriction-site-associated DNA.