Identification of the ERF gene family of Mangifera indica and the defense response of MiERF4 to Xanthomonas campestris pv. mangiferaeindicae.

An important regulatory role for ethylene-responsive transcription factors (ERFs) is in plant growth and development, stress response, and hormone signaling. However, AP2/ERF family genes in mango have not been systematically studied. In this study, a total of 113 AP2/ERF family genes were identified from the mango genome and phylogenetically classified into five subfamilies: AP2 (28 genes), DREB (42 genes), ERF (33 genes), RAV (6 genes), and Soloist (4 genes). Of these, the ERF family, in conjunction with Arabidopsis and rice, forms a phylogenetic tree divided into seven groups, five of which have MiERF members. Analysis of gene structure and cis-elements showed that each MiERF gene contains only one AP2 structural domain, and that MiERF genes contain a large number of cis-elements associated with hormone signaling and stress response. Collinearity tests revealed a high degree of homology between MiERFs and CsERFs. Tissue-specific and stress-responsive expression profiling revealed that MiERF genes are primarily involved in the regulation of reproductive growth and are differentially and positively expressed in response to external hormones and pathogenic bacteria. Physiological results from a gain-of-function analysis of MiERF4 transiently overexpressed in tobacco and mango showed that transient expression of MiERF4 resulted in decreased colony count and callose deposition, as well as varying degrees of response to hormonal signals such as ETH, JA, and SA. Thus, MiERF4 may be involved in the JA/ETH signaling pathway to enhance plant defense against pathogenic bacteria. This study provides a basis for further research on the function and regulation of MiERF genes and lays a foundation for the selection of disease-resistant genes in mango.

Abnormal functional connectivity of the core olfactory network in patients with chronic rhinosinusitis accompanied by olfactory dysfunction.

Objective: To review and analyze the functional connectivity (FC) abnormalities in the brain olfactory network (ON) of patients with chronic rhinosinusitis with olfactory dysfunction (CRSwOD) and explore the relationship between these FC abnormalities and olfactory dysfunction, providing clues to the neurophysiological mechanisms underlying CRSwOD. Methods: FC analysis on the ON of patients with CRSwOD and patients with chronic rhinosinusitis without olfactory dysfunction (CRSsOD) identified the regions of the ON with abnormal FC in CRSwOD patients, and the correlation between abnormal FC and clinical scales for chronic rhinosinusitis was analyzed. Results: (1) Compared with the CRSsOD group, CRSwOD patients showed decreased FC between the bilateral orbitofrontal cortex (OFC) and the right middle frontal gyrus, (2) Receiver operating characteristic (ROC) curve analysis revealed that the FC value between the right middle frontal gyrus and the left OFC (area under the curve (AUC) = 0.852, sensitivity: 0.821, specificity: 0.800, p < 0.001) was more capable of distinguishing whether CRS patients may have olfactory dysfunction than the FC value between the right middle frontal gyrus and the right OFC (AUC = 0.827, sensitivity: 0.893, specificity: 0.667, p < 0.001), and (3) Lund-Kennedy scores were positively correlated with the FC values between the right middle frontal gyrus and the left OFC (r = 0.443, p < 0.018). Lund-Mackay scores were also positively correlated with the FC values between the right middle frontal gyrus and the left OFC (r = 0.468, p < 0.012). Questionnaire of Olfactory Disorders-Negative Statements scores were negatively correlated with the FC values between the right middle frontal gyrus and the left OFC (r = -0.481, p < 0.001). Conclusion: Persistent nasal inflammation affects the FC between the middle frontal gyrus and the OFC, which may serve as a potential imaging marker for identifying CRSwOD. The severity of nasal inflammation and olfactory damage is closely related to the FC between the middle frontal gyrus and OFC, and the abnormal changes in this FC can be used to explain the neurophysiological mechanisms behind the occurrence of olfactory dysfunction in patients.

MiMYB10 transcription factor regulates biosynthesis and accumulation of carotenoid involved genes in mango fruit.

Carotenoids are essential and beneficial substances for both plant and human health. Identifying the regulatory network of these pigments is necessary for improving fruit quality and commodity value. In this study, we performed integrative analyses of transcriptome data from two different type fruits, ripening peel color at green ('Neelum' mango) and red ('Irwin' mango). Specifically, we found that MiMYB10 transcription level was highly associated with mango peel color. Further, silencing MiMYB10 homologous gene in tomato fruits resulted in lower carotenoid and anthocyanin content. Electrophoretic mobility shift assays and dual-luciferase clarified that MiMYB10 regulates the carotenoid biosynthesis gene MiPDS (phytoene desaturase gene) in a direct manner. On the other hand, MiMYB10 activates the expression of carotenoid biosynthesis genes (PSY, Z-ISO, CRTISO, LCYE) and chlorophyll degradation gene (SGR1), promoting the accumulation of carotenoid, accelerating chlorophyll degradation, and controlling peel color. In summary, this study identified important roles of MiMYB10 in pigment regulatory and provided new options for breeding strategies aiming to improve fruit quality.

Chlorate-induced molecular floral transition revealed by transcriptomes.

Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.

Combined transcriptome and metabolome analysis reveal that the white and yellow mango pulp colors are associated with carotenoid and flavonoid accumulation, and phytohormone signaling.

Mango (Mangifera indica L.) is a widely appreciated tropical fruit for its rich color and nutrition. However, knowledge on the molecular basis of color variation is limited. Here, we studied HY3 (yellowish-white pulp) and YX4 (yellow pulp), reaped with 24 h gap from the standard harvesting time. The carotenoids and total flavonoids increased with the advance of harvest time (YX4 > HY34). Transcriptome sequencing showed that higher expressions of the core carotenoid biosynthesis genes and flavonoid biosynthesis genes are correlated to their respective contents. The endogenous indole-3-acetic acid and jasmonic acid contents decreased but abscisic acid and ethylene contents increased with an increase in harvesting time (YX4 > HY34). Similar trends were observed for the corresponding genes. Our results indicate that the color differences are related to carotenoid and flavonoid contents, which in turn are influenced by phytohormone accumulation and signaling.

Greater functional connectivity between the ventral frontal cortex and occipital cortex in herpes zoster patients than post-herpetic neuralgia patients.

OBJECTIVE: This study aimed to compare whole brain network between herpes zoster (HZ) patients and post-herpetic neuralgia (PHN) patients, as well as to investigate the associations between whole brain network changes and pain intensity and the accuracy of classifying between different types of pain. METHODS: PHN patients (n = 50) and HZ patients (n = 50) and healthy controls (HCs) (n = 50) underwent resting-state functional magnetic resonance imaging (rs-fMRI). Functional connectivity and global and local graph theory metrics were calculated by using Dosenbach-160 atlas. The relationship between neuroimaging indicators and clinical scales was evaluated using correlation analysis, and receiver operating characteristic (ROC) curves evaluated the feasibility of classifying PHN and HZ patients using specific neuroimaging indicators. RESULTS: (1) 10 greater average connectivities were found in HZ group among the default mode, frontoparietal, cingulo-opercular, sensorimotor, occipital networks (ONs), and cerebellum (p < 0.001). (2) HZ patients exhibited higher global efficiency than those in the PHN and HCs (t = 2.178, p = 0.038). (3) Multiple linear regression analyses indicated that functional connectivity between the ventral frontal cortex in the cingulo-opercular network and the occipital gyrus in the ON influenced the visual analog score pain scores (ß = 4.273; p = 0.004). CONCLUSION: The variation of functional connectivity between ventral frontal cortex in the cingulo-opercular network and occipital gyrus in the ON may be a robust neuroimaging marker of the transition from HZ to PHN patients. ADVANCES IN KNOWLEDGE: Whole-brain network analysis may be effective in distinguishing HZ and PHN patients and predicting pain intensity.

Natural Fermentation Quality and Bacterial Community of 12 Pennisetum sinese Varieties in Southern China.

This study investigated the fermentation quality of 12 varieties of Pennisetum sinese grown in different regions of Southern China. Following the production of silage from the natural fermentation of P. sinese, the interplay between the chemical composition, fermentation characteristics, environmental factors, and microbiome was examined to understand the influence of these factors on the fermentation quality of silage. The silage quality produced by most of the P. sinese was low; the pH value of the silage was high (4.26-4.86), whilst the lactic acid content was low (10.7-24.1 g/kg DM), with V-scores between 57.9 and 78.3. The bacterial alpha diversities of the 12 P. sinese silages were distinct. There was a predominance of undesirable bacteria (Pseudomonas, Massilia, and Raoultella), which likely caused the poor fermentation quality. The chemical composition and fermentation characteristics of the silage were closely correlated with the composition of the bacterial community. Furthermore, environmental factors (precipitation, temperature, humidity, location) were found to significantly influence the microbiome of the silage. The results confirmed that silage produced from the natural fermentation of 12 different P. sinese varieties had significant variation in their bacterial communities. The difference in environmental factors, due to the P. sinese being grown in various locations across south china, greatly affected the bacterial community found in the silage and thus the fermentation quality. The specific cultivar used for the silage and the environment in which the cultivar is grown must therefore be considered before the initiation of production of silage in order to ensure a higher quality product.

Effects of Citric Acid and Lactobacillus plantarum on Silage Quality and Bacterial Diversity of King Grass Silage.

To better understand the mechanism underlying the citric acid (CA)-regulated silage fermentation, we investigated the bacterial community and fermentation quality of king grass (KG) ensiled without (CK) or with Lactobacillus plantarum (L), CA and the combination of L and CA (CAL). The bacterial community was characterized by using the 16Sr DNA sequencing technology. The L and CA treatments altered the silage bacterial community of KG, showing reduced bacterial diversity, while the abundance of desirable genus Lactobacillus was increased, and the abundances of undesirable genus Dysgonomonas and Pseudomonas were decreased. The additives also significantly raised the lactic acid content, dropped the pH, and reduced the contents of acetic acid, propionic acid, and ammonia-N in ensiled KG (P < 0.01). Besides, the combination treatment was more effective on silage fermentation with the highest pH and lactic acid content, while the contents of acetic acid, propionic acid, and ammonia-N were the lowest (P < 0.01). Moreover, CAL treatment exerted a notable influence on the bacterial community, with the lowest operational taxonomic unit (OTU) number and highest abundance of Lactobacillus. Furthermore, the bacterial community was significantly correlated with fermentation characteristics. These results proved that L and CA enhanced the KG silage quality, and the combination had a beneficial synergistic effect.

The genome evolution and domestication of tropical fruit mango.

BACKGROUND: Mango is one of the world's most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. RESULTS: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. CONCLUSIONS: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces.

Genetic Diversity in Various Accessions of Pineapple [Ananas comosus (L.) Merr.] Using ISSR and SSR Markers.

Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei's gene diversity (h = 0.28), Shannon's information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.

Influence of irrigation during the growth stage on yield and quality in mango (Mangifera indica L).

Although being one of the few drought-tolerant plants, mango trees are irrigated to ensure optimum and consistent productivity in China. In order to better understand the effects of soil water content on mango yield and fruit quality at fruit growth stage, irrigation experiments were investigated and the object was to determine the soil water content criteria at which growth and quality of mango would be optimal based on soil water measured by RHD-JS water-saving irrigation system through micro-sprinkling irrigation. Five soil water content treatments (relative to the percentage of field water capacity) for irrigation (T1:79%-82%, T2:75%-78%, T3:71%-74%, T4: 65%-70%, T5:63%-66%) were compared in 2013. Amount of applied irrigation water for different treatments varied from 2.93m3 to 1.08 m3. The results showed that mango fruit production and quality at fruit growth stage were significantly affected under different irrigation water amounts. Variation in soil water content not only had effects on fruit size, but also on fruit yield. The highest fruit yield and irrigation water use efficiency were obtained from the T4 treatment. Irrigation water amount also affected fruit quality parameters like fruit total soluble solids, soluble sugar, starch, titratable acid and vitamin C content. Comprehensive evaluation of the effect of indexs of correlation on irrigation treatment by subordinate function showed that when the soil moisture content were controlled at about 65-70% of the field water moisture capacity, water demand in the growth and development of mango could be ensured, and maximum production efficiency of irrigation and the best quality of fruit could be achieved. In conclusion, treatment T4 was the optimum irrigation schedule for growing mango, thus achieving efficient production of mango in consideration of the compromise among mango yield, fruit quality and water use efficiency.

Molecular Cloning, Characterization, and Expression of MiSOC1: A Homolog of the Flowering Gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from Mango (Mangifera indica L).

MADS-box transcription factor plays a crucial role in plant development, especially controlling the formation and development of floral organs. Mango (Mangifera indica L) is an economically important fruit crop, but its molecular control of flowering is largely unknown. To better understand the molecular basis of flowering regulation in mango, we isolated and characterized the MiSOC1, a putative mango orthologs for the Arabidopsis SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1/AGAMOUS-LIKE 20 (SOC1/AGL20) with homology-based cloning and RACE. The full-length cDNA (GenBank accession No.: KP404094) is 945 bp in length including a 74 bp long 5' UTR and a 189 bp long 3' UTR and the open reading frame was 733 bps, encoding 223 amino acids with molecular weight 25.6 kD. Both sequence alignment and phylogenetic analysis all indicated that deduced protein contained a conservative MADS-box and semi-conservative K domain and belonged to the SOC1/TM3 subfamily of the MADS-box family. Quantitative real-time PCR was performed to investigate the expression profiles of MiSOC1 gene in different tissues/organs including root, stem, leaves, flower bud, and flower. The result indicated MiSOC1 was widely expressed at different levels in both vegetative and reproductive tissues/organs with the highest expression level in the stems' leaves and inflorescences, low expression in roots and flowers. The expression of MiSOC1 in different flower developmental stages was different while same tissue -specific pattern among different varieties. In addition, MiSOC1 gene expression was affect by ethephon while high concentration ethephon inhibit the expression of MiSOC1. Overexpression of MiSOC1 resulted in early flowering in Arabidopsis. In conclusion, these results suggest that MiSOC1 may act as induce flower function in mango.

Development of pineapple microsatellite markers and germplasm genetic diversity analysis.

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

[Development and application of EST-derived SSR markers for bananas (Musa nana Lour.)].

A total of 2,284 banana unigene sequences were mined, resulting in the identification of 122 SSRs in 110 sequences. Among them, there were 37 motifs the overall average length of SSRs was 20 bp. The trinucleotide repeats appeared to be the most abundant SSRs (47.6%), followed by dinucleotide repeats (33.1%), whereas the tetranucleotide repeats were less abundant. The rich repeats AG and AGG were predominant, accounting for 75.7% and 36% in dri- and tri-nucleotide repeats respectively. A total of 63 primer pairs were designed and tested against genomic DNA of Brazil. Forty-one primers could be validated as usable markers. Nineteen of these primers revealed moderate to high polymorphism information content (PIC) across 49 accessions. The polymorphic bands were ranged from 4 to 12, averagely 7.58. The mean PIC value was 0.7324, ranging from 0.3572 to 0.8744. Forty-nine banana varieties were separated into two major clusters closely corresponding with the genome composition by UPGMA analysis. The results showed that the EST-SSR markers were of great value in evaluation of banana germplasms.