Comparative Transcriptomic Analysis of Differentially Expressed Transcripts Associated with Flowering Time of Loquat (Eriobotya japonica Lindl.)

Comparative transcriptome analysis on drought stress-induced floral formation of Curcuma kwangsiensis

The rhizomes and tubers of Curcuma kwangsiensis have extensive medicinal value in China. However, the inflorescences of C. kwangsiensis are rarely known in horticulture, because of its low field flowering rate. In order to improve the flowering rate of C. kwangsiensis, we conducted drought stress treatment on the rhizome of C. kwangsiensis. The flowering rate of rhizome was the highest after 4d of drought stress treatment, and the buds on the rhizome could be obviously swell on the 4th day of rehydration culture. In order to identify the genes regulating the flowering time of Curcuma kwangsiensis, comparative transcriptome analysis was performed on the buds on rhizomes before drought stress treatment, 4 d after drought stress treatment and 4 d after rehydration culture. During this process, a total of 20 DEGs controlling flowering time and 23 DEGs involved in ABA synthesis and signal transduction were identified, which might regulate the flowering of C. kwangsiensis under drought stress. Some floral integration factors, such as SOC1 and FTIP, were up-regulated under drought stress for 4 d, indicating that C. kwangsiensis had flowering trend under drought stress. The results of the present study will provide theoretical support for the application of Curcuma kwangsiensis in gardening.

Cross-Talk between Transcriptome Analysis and Dynamic Changes of Carbohydrates Identifies Stage-Specific Genes during the Flower Bud Differentiation Process of Chinese Cherry (Prunus pseudocerasus L.)

Flower bud differentiation is crucial to reproductive success in plants. In the present study, RNA-Seq and nutrients quantification were used to identify the stage-specific genes for flower bud differentiation with buds which characterize the marked change during flower bud formation from a widely grown Chinese cherry (Prunus pseudocerasus L.) cultivar 'Manaohong'. A KEGG enrichment analysis revealed that the sugar metabolism pathways dynamically changed. The gradually decreasing trend in the contents of total sugar, soluble sugar and protein implies that the differentiation was an energy-consuming process. Changes in the contents of D-glucose and sorbitol were conformed with the gene expression trends of bglX and SORD, respectively, which at least partially reflects a key role of the two substances in the transition from physiological to morphological differentiation. Further, the WRKY and SBP families were also significantly differentially expressed during the vegetative-to-reproductive transition. In addition, floral meristem identity genes, e.g., AP1, AP3, PI, AGL6, SEP1, LFY, and UFO demonstrate involvement in the specification of the petal and stamen primordia, and FPF1 might promote the onset of morphological differentiation. Conclusively, the available evidence justifies the involvement of sugar metabolism in the flower bud differentiation of Chinese cherry, and the uncovered candidate genes are beneficial to further elucidate flower bud differentiation in cherries.

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

Identification and Comparative Analysis of Genes and MicroRNAs Involved in the Floral Transition of the Xinjiang Early-Flowering Walnut (Juglans regia L.)

For tree crops, shortening the juvenile phase is a vital strategy to advance fruit bearing and enhance the breeding efficiency. Walnut (Juglans regia L.) seedlings usually take at least eight to 10 years to flower, but early-flowering (EF) types can flower one or two years after planting. In this study, RNA sequencing (RNA-Seq) and microRNA sequencing (miRNA-Seq) were used for a transcriptome-wide analysis of gene and miRNA expression in hybrids of the Xinjiang EF walnut variety ‘Xinwen 81’ and later-flowering (LF) walnut. Based on a high-quality chromosome-scale reference genome, a total of 3009 differentially expressed genes (DEGs) were identified, of which 933 were upregulated (accounting for 31%) and 2076 were downregulated (accounting for 69%). DEGs were functionally annotated, and the flowering-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), and LEAFY (LFY) showed remarkable upregulation in EF compared with in the LF walnut. In addition, miRNAs associated with floral transition were screened as candidates for flowering time regulation in the walnut. This work provides new insights into walnut floral transition, which may ultimately contribute to genetic improvement of the walnut.

Neglected Potential of Wild Garlic (Allium ursinum L.)—Specialized Metabolites Content and Antioxidant Capacity of Wild Populations in Relation to Location and Plant Phenophase

Wild garlic (Allium ursinum L.) is one of the species widely distributed in Europe and Asia and is often nutritionally neglected, characterized by a high content of various phytochemicals with high therapeutic potential and a range of biological activities. The aim of this study was to determine the content of bioactive compounds in the leaves of wild garlic populations collected from different micro-locations, and to determine the differences in the content of phytochemicals in the vegetative and generative phases. A significant content of different specialized metabolites was detected in all analyzed leaves of wild garlic populations regardless of the different factors (location and phenophase): vitamin C content with the highest determined value of 63.31 mg/100 g fw; total phenolic content with the highest determined value of 186.18 mg GAE/100 g fw (according to gallic acid in fresh sample); and antioxidant capacity with the highest determined value of 2230.66 µmol TE/L (according to Trolox). Significant differences in all the phytochemicals analyzed were observed depending on both the location and phenophase of the plants, with the most pronounced differences depending on the phenophase. Thus, lower levels of polyphenolic compounds and vitamin C were generally observed before the flowering phase, while the trend toward higher levels of pigment compounds was observed during the flowering phase of the plants. The results suggest that the leaves of wild garlic can be considered a valuable source of a variety of specialized metabolites with high antioxidant capacity, and thus have high production potential for various functional products and food supplements of natural origin, which are important for the promotion of human health.