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Indole-3-butyric acid (IBA) is widely used to encourage root development in cuttings of general field crops, vegetables, forest trees, fruit trees, and flowers. However, previous studies reported that IBA inhibited the germination of citrus buds via an unknown molecular mechanism. This study aimed to unravel the regulatory mechanisms underlying this inhibition. Citrus apical buds were sprayed with 100 mg ⋅ L−1 IBA. Subsequently, the plant hormone levels were analyzed, and transcriptomic analysis was performed. The results identified 3325 upregulated genes and 2926 downregulated genes in the citrus apical buds. The gene set enrichment analysis method was used to determine the Gene Ontology related to the treatment. Genes were enriched into 157 sets, including 17 upregulated sets and 140 downregulated sets, after indole butyric acid treatment. The upregulated gene sets were related to glucose import, sugar transmembrane transporter activity, and photosynthesis. The downregulated genes were mainly related to the ribosomal subunit and cell cycle process under butyric acid treatment. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the enrichment of 11 pathways. Of note, genes related to the ribosome and proteasome pathways were significantly downregulated. Only one pathway was significantly upregulated: the autophagy pathway. Overall, these results provided insights into the molecular mechanisms underpinning the IBA-mediated inhibition of citrus bud germination inhibition. Also, the study provided a large transcriptomics dataset that could be used for further research.

The sugars-will-eventually-be-exported-transporters (SWEET) family is a newly characterized group of sugar transporters, which plays an important role in diverse biological processes, including plant growth, development, and response to abiotic and biotic stresses. SWEET family genes, known as SWEETs, have been characterized in many plant species, but a comprehensive analysis has not been performed on citrus. Here, 27 citrus SWEET genes (CitSWEETs) were identified through homology searches. The phylogenetic relationship, transmembrane helices (TMHs), gene distribution, and gene structure were then investigated. Furthermore, the expression patterns of 27 CitSWEETs were examined in several tissues and under different abiotic stresses. The data revealed that CitSWEET1, CitSWEET2, CitSWEET3, CitSWEET4, CitSWEET7, CitSWEET25, and CitSWEET27 were tissue-specific, and others were ubiquitously expressed. Among 27 genes tested, some members were sensitive to abiotic stress or hormone stimuli, and CitSWEET3 transported glucose in EMY4000 yeast strain. In conclusion, we performed the first comprehensive analysis of the CitSWEET gene family in citrus, which can provide useful information to further analyze their potential roles.

The R2R3MYB proteins represent one of the largest families of transcription factors, which play important roles in plant growth and development. Although genome-wide analysis of this family has been conducted in many species, little is known about R2R3MYB genes in citrus, In this study, 101 R2R3MYB genes has been identified in the citrus (Citrus sinesis and Citrus clementina) genomes, which are almost equal to the number of rice. Phylogenetic analysis revealed that they could be subdivided into 21 subgroups. The evolutionary relationships and the intro-exon organizations were also analyzed, revealing strong gene conservation but also the expansions of particular functional genes during the plant evolution. Tissue-specific expression profiles showed that 95 citrus R2R3MYB genes were expressed in at least one tissue and the other 6 genes showed very low expression in all tissues tested, suggesting that citrus R2R3MYB genes play important roles in the development of all citrus organs. The transcript abundance level analysis during abiotic conditions (NaCl, abscisic acid, jasmonic acid, drought and low temperature) identified a group of R2R3MYB genes that responded to one or multiple treatments, which showed a promising for improving citrus adaptation to stresses. Our results provided an essential foundation for the future selection of the citrus R2R3MYB genes for cloning and functional dissection with an aim of uncovering their roles in citrus growth and development.

The nutritional status of citrus leaves is very important to the determining of fertilization plants. The spectrum technique is a quick, un-injured method and is becoming widely used for plant nutrient estimation. The possibility and method of using spectrum technique to estimate the nutrient of citrus leaf was explored in this study. A total amount of 135 leaves from the mature spring shoots of navel orange trees (C. sinensis Osbeck, Newhall) were collected and randomly grouped into two sets of samples. The hyperspectral images were scanned upper and lower side of each leaf and then the total nitrogen (N) and phosphorus (P) contents of each leaf were measured. The raw spectra data were extracted to generate average spectra curves, preprocessed with five different methods, and was used to build N and P content prediction models. The study suggested that the hyperspectral image data from the upper side of the citrus leaves are suitable for nondestructive estimation of nutrient content.

The study aimed to investigate the fast and nondestructive method for detecting carbon and nitrogen content in citrus canopy. The multispectral imagery of Tarocco blood orange (Citrus sinensis L. Osbeck) plant canopy was obtained by a multispectral camera array mounted at an eight-rotor unmanned aerial vehicle (UAV) flying at an altitude of 100 m above the canopy in Wanzhou District of Chongqing Municipality, China. Average spectral reflectance data of the whole canopy, mature leaf areas and young leaves areas were extracted from the imagery. Two spectral pre-processing methods, multiplicative scatter correction (MSC) and standard normal variable (SNV), and two modeling methods, the partial least squares (PLS) and the least squares support vector machine (LS-SVM), were adopted and compared for their prediction accuracy of total content of nitrogen, soluble sugar and starch in the leaves. The results showed that, based on the spectral data extracted from the mature leaves in the multispectral imagery, the PLS model based on the original spectrum obtained a R^sub p^ (correlation coefficient) of 0.6469 and RMSEP (root mean squares error of prediction ) of 0.1296, suggested that it was the best for the prediction of total nitrogen content; the PLS model based on MSC (multiplicative scatter correction) spectrum pre-processing was the best for predicting total soluble sugar content (R^sub p^=0.6398 and RMSEP=8.8891); and the LS-SVM model based on MSC was the best for the starch content prediction (R^sub p^=0.6822 and RMSEP=14.9303). The prediction accuracy for carbon and nitrogen contents based on the spectral data extracted from the whole canopy and the young leaves were lower than that from the mature leaves. The results indicate that it is feasible to estimate the carbon and nitrogen contents by low-altitude airborne multispectral images.

The negative effects of waterlogging can be effectively improved through the use of waterlogging-resistant rootstocks. However, the underlying physiological and molecular mechanisms of Chinese bayberry ( Morella rubra ) rootstock tolerance to waterlogging have not yet been investigated. This study aims to unravel the molecular regulation mechanisms underlying waterlogging-tolerant rootstocks. Two rootstocks, Morella cerifera (tolerant) and Morella rubra (sensitive), were selected for root zone hypoxia treatments, assessments of hormone levels and antioxidant enzyme activity, and transcriptomic analysis. While the contents of abscisic acid (ABA) and brassinosteroid (BR) in the roots of M. rubra decreased significantly after root zone hypoxia treatment, there were no significant changes in M. cerifera . Both the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content increased in M. cerifera but were decreased in M. rubra . Transcriptome sequencing identified 1,925 (928 up- and 997 downregulated) and 733 (278 up- and 455 downregulated) differentially expressed genes (DEGs) in the two rootstocks. The gene set enrichment analysis showed that 84 gene sets were enriched after root zone hypoxia treatment, including 57 (35 up- and 22 downregulated) and 14 (five up- and nine downregulated) gene sets derived from M. cerifera and M. rubra , respectively, while the remaining 13 gene sets were shared. KEGG pathway analysis showed specific enrichment in six pathways in M. cerifera , including the mitogen-activated protein kinase (MAPK), tyrosine metabolism, glycolysis/gluconeogenesis, ribosome, cyanoamino acid metabolism, and plant-pathogen interaction pathways. Overall, these results provide preliminary insights into the molecular mechanisms of Chinese bayberry tolerance to waterlogging.

Citrus, as one of the most economically important fruits worldwide, is adversely affected by salinity stress. However, its molecular mechanisms underlying salinity tolerance are still not clear. In this study, next-generation RNA-seq technology was applied to analyze the gene expression profiling of citrus roots at 3 time points over a 24-h period of salt treatment. A total of 1831 differentially expressed genes (DEGs) were identified. Among them, 1195 and 1090 DEGs were found at 4 and 24 h, of which 454 were overlapped. Based on functional annotation, the salt overly sensitive (SOS) and reactive oxygen species (ROS) signaling pathways were found to be involved. Meanwhile, we found that hormone metabolism and signaling played important roles in salt stress. In addition, a multitude of transcription factors (TFs) including WRKY, NAC, MYB, AP2/ERF, bZIP, GATA, bHLH, ZFP, SPL, CBF, and CAMTA were identified. The genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were also involved in salt stress. Our data not only provided a genetic resource for discovering salt tolerance-related genes, but also furthered our understanding of the molecular mechanisms underlying salt tolerance in citrus.

Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks. GO enrichment analysis revealed that some crucial biological processes related to signal transduction (e.g. ‘MAPK cascade’), hormone-mediated signaling pathways (e.g. abscisic acid- activated signaling pathway’), reactive oxygen species (ROS) metabolic process (e.g. ‘hydrogen peroxide catabolic process’) and transcription factors (e.g., ‘MYB, ZFP and bZIP’) were involved in dehydration and/or salt treatment. The molecular players in response to dehydration and salt treatment were partially overlapping. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-seq and sRNA-seq analysis. This study provides new insights into the molecular mechanisms how citrus roots respond to dehydration and salt treatment.

We analysed the temporal and spatial transcript expression of the panel of 18 putative isoallergens from four gene families ( Pru p 1 – 4 ) in the peach fruit, anther and leaf of two melting cultivars, to gain insight into their expression profiles and to identify the key family members. Genotypic variation of abundantly expressed genes in mature fruit was further screened in nine additional melting cultivars. In the Pru p 1 family, Pru p 1.01 and Pru p 1.06B were predominant and constitutively expressed in all the tissues, with large difference among cultivars observed in mature fruits. Pru p 1.02 was especially abundant only in the leaf. A new member of the Pru p 1 family, Pru p 1.06D , was identified through peach genome mining. In the Pru p 2 family, Pru p 2.01B was predominant in all tissues, whereas Pru p 2.01A was abundant in a few cultivars and undetectable in others. Pru p 3.01 was the most highly expressed member in all tissues except the mesocarp, while the other two members exhibited tissue specificity: Pru p 3.02 was highly expressed in the leaf, and Pru p 3.03 in the anther. Both Pru p 4 isoallergen genes were equally expressed in all tissues of both cultivars. There was high expression variability of Pru p 1 and Pru p 2 members in mature fruits among 11 cultivars, while relative lower for Pru p 3 and Pru p 4 . The location, arrangement and features of peach isoallergen genes on the peach genome scaffolds were illustrated.

Completion of the whole genome sequencing of citrus enabled us to perform genome-wide identification and functional analysis of the gene families involved in agronomic traits and morphological diversity of citrus. In this study, 22 CitARF, 11 CitGH3 and 26 CitAUX/IAA genes were identified in citrus, respectively. Phylogenetic analysis revealed that all the genes of each gene family could be subdivided into three groups and showed strong evolutionary conservation. The GH3 and AUX/IAA gene families shrank and ARF gene family was highly conserved in the citrus genome after speciation from Arabidopsis thaliana. Tissue-specific expression profiles revealed that 54 genes were expressed in at least one tissue while just 5 genes including CitARF07, CitARF20, CitGH3.04, CitAUX/IAA25 and CitAUX/IAA26 with very low expression level in all tissues tested, suggesting that the CitARF, CitGH3 and CitAUX/IAA gene families played important roles in the development of citrus organs. In addition, our data found that the expression of 2 CitARF, 4 CitGH3 and 4 AUX/IAA genes was affected by IAA treatment, and 7 genes including, CitGH3.04, CitGH3.07, CitAUX/IAA03, CitAUX/IAA04, CitAUX/IAA18, CitAUX/IAA19 and CitAUX/IAA23 were related to fruitlet abscission. This study provides a foundation for future studies on elucidating the precise role of citrus ARF, GH3 and AUX/IAA genes in early steps of auxin signal transduction and open up a new opportunity to uncover the molecular mechanism underlying citrus fruitlet abscission.