Guo-Fei Tan

High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response

BackgroundMicroRNAs (miRNAs) are small, non-coding RNAs of 20 to 24 nucleotides that regulate gene expression and responses to biotic and abiotic stress. Till now, no reports have previously been published concerning miRNAs in celery.ResultsTwo small RNAs libraries were constructed from two celery varieties, ‘Jinnan Shiqin’ and ‘Ventura’, and characterized by deep sequencing. A total of 431 (418 known and 13 novel) and 346 (341 known and five novel) miRNAs were identified in celery varieties ‘Jinnan Shiqin’ and ‘Ventura’, respectively. Potential miRNA-target genes were predicted and annotated by screening diverse protein databases, including Gene Ontology, Cluster of Orthologous Groups and Kyoto Encyclopedia of Genes and Genomes. Significant differential expression between the two varieties was seen for 221 miRNAs. qRT-PCR was used to analyze the abundance of six miRNAs under cold and heat stress conditions. The results showed that miRNAs may have important functions in controlling temperature stress in celery.ConclusionA large number of miRNAs were identified in celery, and their target genes, functional annotations, and gene expression patterns have been explored.These findings provide the first information on celery miRNAs and enhance understanding of celery miRNA regulatory mechanisms under extreme temperature stress.

Selection of suitable reference genes for qPCR normalization under abiotic stresses in Oenanthe javanica (BI.) DC.

Accurate normalization of gene expression data is an absolute prerequisite to obtain reliable results in qPCR analysis. Oenanthe javanica, an aquatic perennial herb, belongs to the Oenanthe genus in Apiaceae family, with known medicinal properties. In the current study, O. javanica was subjected to hormone stimuli (gibberellin, salicylic acid, methyl jasmonate, and abscisic acid) and abiotic stresses (heat, cold, salt, and drought), and the expression of nine candidate reference genes (eIF-4α, ACT7, TIP41, GAPDH, SAND, EF-1α, PP2A, TBP, and TUB) was evaluated. Stability of the genes was assessed using geNorm, NormFinder and BestKeeper. All the genes presented distinct expression profiles under the experimental conditions analyzed. Under abiotic stress conditions, ACT7 and PP2A genes displayed the maximum stability; PP2A and SAND were the most stable genes under hormone stimuli. Even though PP2A gene was most stable across all the samples, individual analysis revealed changes in expression profile. To further validate the suitability of the reference genes identified in this study, the expression level of M6PR gene under salt treatment was studied. Based on our data, we propose that it is essential to normalize the target gene expression with specific reference genes under different experimental conditions for most accurate results. To our knowledge, this is the first systematic analysis for reference genes under abiotic stress and hormone stimuli conditions in O. javanica. This will be beneficial for future studies on O. javanica and other plants in Apiaceae family at molecular level.

Regulation of ascorbic acid biosynthesis and recycling during root development in carrot (Daucus carota L.).

Ascorbic acid (AsA), also known as vitamin C, is an essential nutrient in fruits and vegetables. The fleshy root of carrot (Daucus carota L.) is a good source of AsA for humans. However, the metabolic pathways and molecular mechanisms involved in the control of AsA content during root development in carrot have not been elucidated. To gain insights into the regulation of AsA accumulation and to identify the key genes involved in the AsA metabolism, we cloned and analyzed the expression of 21 related genes during carrot root development. The results indicate that AsA accumulation in the carrot root is regulated by intricate pathways, of which the l-galactose pathway may be the major pathway for AsA biosynthesis. Transcript levels of the genes encoding l-galactose-1-phosphate phosphatase and l-galactono-1,4-lactone dehydrogenase were strongly correlated with AsA levels during root development. Data from this research may be used to assist breeding for improved nutrition, quality, and stress tolerance in carrots.

Genome-wide analysis of HSF family transcription factors and their responses to abiotic stresses in two Chinese cabbage varieties

Key messageHSF family transcription factors were analyzed in genome of Chinese cabbage. Chromosomal locations showed that duplication might result in expansion. Response to abiotic stresses was elucidated in Chinese cabbage varieties.AbstractThe major heat shock factors regulating the heat stress response are heat shock transcription factors (HSFs), which interact with heat shock elements. In this study, Chinese cabbage (Brassica rapa L. ssp. pekinensis) HSFs were comprehensively analyzed. A total of 52 HSF family genes were identified for phylogenetic relationships and motif analysis based on the genome sequence of Chinese cabbage. All HSFs were divided into classes A, B, and C. The chromosomal locations and gene duplications of these HSFs were also presented. Nine potential duplication events were found in Chinese cabbage chromosomes. Expression of three HSF genes in two varieties of Chinese cabbage using quantitative real-time PCR revealed that BraHSF039 and BraHSF043 were up-regulated under temperature and salt stresses treatments, and only BraHSF043 gene was also down-regulated under salt stress in ‘Lubaisanhao’. BraHSF001 gene was down-regulated in the ‘Lubaisanhao’ variety under heat and cold stresses, under drought stress in ‘Qingdao 87-114’. These results can serve as a foundation for further studies on HSFs in Brassica.

Advances in the research of celery, an important Apiaceae vegetable crop

Abstract Celery (Apium graveolens L.), one of the most important vegetables in Apiaceae family, is cultivated worldwide and utilized in food and cosmetic industries because it is an excellent source of vitamins, phenolic compounds, volatile oils and other nutrients. Celery extracts possess various medicinal properties, such as antibacterial, anti-inflammatory and lowering blood glucose and serum lipid levels. With the rapid advancements in molecular biology and sequencing technology, studies on celery have been performed. Numerous molecular markers and regulatory genes have been discovered and applied to improve celery. Research advances, including genetic breeding, genomics research, function genes and chemical composition, regarding celery are reviewed in this paper. Further exploration and application trends are briefly described. This review provides a reference for basic and applied research on celery, an important Apiaceae vegetable crop.

Distinct transcription profile of genes involved in carotenoid biosynthesis among six different color carrot (Daucus carota L.) cultivars

Carotenoid, a group of lipophilic molecules, is widely distributed in nature, and is important for plant photosynthesis and photoprotection. In carrot taproot, different types of dominant carotenoid accumulation lead to yellow, orange, and red colors. In this study, six different carrot cultivars were used to simultaneously analyze carotenoid contents by high performance liquid chromatography. The expression levels of genes involved in carotenoid biosynthesis of carrot were also detected by real-time quantitative PCR. It was found that genes involved in xanthophyll formation were expressed at high levels in yellow carrot cultivars. However, these genes were expressed at low levels in orange carrot cultivars. The contents of α- and β-carotene accounted for a large proportion in total carotenoid contents in orange carrot cultivars. These results indicate that α-carotene accumulation and xanthophyll formation may be related to the expression levels of carotene hydroxylase genes in carrot.

Different lengths, copies and expression levels of the mitochondrial atp6 gene in male sterile and fertile lines of carrot (Daucus carota L.)

Abstract The male-sterile carrot is an effective material for carrot breeding. The atp6 gene is involved in carrot fertility. However, the differences in lengths, copies, and expression profiles of the atp6 gene in fertile and male-sterile lines of carrot are unclear. In this study, one copy atp6 gene was found in the mtDNAs of ‘Kuroda’ (fertility, 954 bp) and ‘Wuye-BY’ (male sterility, 819 bp) carrot lines, while two copies atp6 genes (Wuye-L and Wuye-D, 954 bp and 819 bp, respectively) were found in the mtDNA of ‘Wuye’ (fertility). Two putative conserved domains have been detected in the carrot atp6 protein. Evolutionary analysis showed that the atp6 protein sequences of Wuye-L and Kuroda were clustered in the same branch, while Wuye-D and Wuye-BY were clustered in the same branch. The atp6 gene was higher expressed in the flowers of ‘Kuroda’ and ‘Wuye’ (Wuye-L), while lower expressed in ‘Wuye-BY’ and ‘Wuye’ (Wuye-D).

Effects of dark treatment and regular light recovery on the growth characteristics and regulation of chlorophyll in water dropwort

Water dropwort is one of Apiaceae vegetables. Dark treatment could help to promote the degradation of chlorophyll and improve exterior quality and flavor of vegetable crops. Previous studies showed that the chlorophylls content would dramatically reduce in the dark, while the chlorophylls content would be promoted after regular light recovery. However, the understanding of the metabolic mechanism is limited in water dropwort. We treated the water dropwort under the dark at 0, 4, 8, 12, 16, 20 and 25 days, then, recovered with regular light for 2 and 4 days, respectively. The total of chlorophylls content gradually degraded and the chlorophyll a content decreased faster than chlorophyll b content during dark treatment in water dropwort. After regular light recovery, the expression levels of the genes related to chlorophyll synthesis and transformation were increased, while the expression levels of PPH and PAO degradation-related genes decreased gradually. The water dropwort sprouted a large amount of newborn petioles and leaf blades after 16 days dark treatment. After regular light recovery, chlorophyll content and gene expression level both increased slowly. The plants would maintain lower chlorophyll content for a long time and have a longer shelf-life after 16 days dark treatment. Taken together, the results suggested that the best time of blanching culture for water dropwort is 16 days. This study could help to elucidate the chlorophyll metabolism in water dropwort during blanching culture and provide new perspectives for screening the best time of dark treatment for water dropwort.