Xiaodong Chen

Reliable reference genes (RGs) are of great significance for the normalization of quantitative data. RGs are often used as a reference to ensure the accuracy of experimental results to detect gene expression levels by reverse transcription–quantitative real-time PCR (RT-qPCR). To evaluate the normalized RGs that are suitable for studying the expression of genes during the process of radish stele enlargement, based on the functional annotations and fragment per kilobase of transcript per million mapped reads (FPKM) values in the transcriptome data, three traditional RGs (GAPDH, 18SrRNA, and ACTIN7) and seven commonly used RGs (UBQ11, TUA6, TUB6, EF-1b1, EF-1a2, PP2A11, and SAND) were obtained. In the study, the results of geNorm, NormFinder, and BestKeeper from RefFinder comprehensively analyzed the stability ranking of candidate RGs. The results showed that compared with the traditional RGs, the common RGs show higher and more stable expression. Among the seven commonly used RGs, PP2A11 is recommended as the optimal RG for studying cherry radish stele enlargement. This research provides a useful and reliable RG resource for the accurate study of gene expression during root enlargement in cherry radishes and facilitates the functional genomics research on root enlargement.

Background: Water spinach (Ipomoea aquatica) is an important heat-resistant leafy vegetable that can survive under long-time heat stress condition. However, the physiological characteristics and molecular changes in its response to heat stress are poorly understood. Results: In this study the selected water spinach cultivars with different thermo resistance and their physiological response to heat stress were examined. Under prolonged heat stress, plant growth was inhibited in all tested cultivars. This inhibition was accompanied by the reduction of photosynthetic performance. The reactive oxygen species system in terms of superoxide and hydrogen peroxide contents, as well as antioxidant polyphenols, were evaluated. The results showed that prolonged heat stress caused reduced antioxidant capacity, but the role of antioxidant capacity in a prolonged thermotolerance was not predominant. Transcriptomic analysis of the water spinach subjected to heat stress revealed that 4145 transcripts were specifically expressed with 2420 up-regulated and 1725 down-regulated in heat-sensitive and heat-tolerant cultivars treated with 42 °C for 15 days. Enrichment analysis of these differentially expressed genes showed that the main metabolic differences between heat-sensitive and heat-tolerant cultivars were the carbohydrate metabolism and phenylpropanoid biosynthesis. The results of carbohydrate profiles and RT-qPCR also suggested that heat stress altered carbohydrate metabolism and associated changes in transcriptional level of genes involved in sugar transport and metabolic transition. Conclusions: The prolonged heat stress resulted in a reduced antioxidant capacity while the role of antioxidant capacity in a prolonged thermotolerance of water spinach was not predominant. Transcriptome analysis and the measurement of carbohydrates as well as the gene expression evaluation indicated that the response of the metabolic pathway such as carbohydrate and phenylpropanoid biosynthesis to heat stress may be a key player in thermo resistance.

Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperature. To investigate the link of GS biosynthesis with heat stress response in Chinese kale, global transcription profiles of high-GS line (HG), low-GS line (LG), high-GS line under heat stress (HGT) and low-GS line under heat stress (LGT) were analyzed. Based on three biological replicates of each RNA sequencing data, 3901, 4062 and 2396 differentially expressed genes in HG vs HGT, LG vs LGT and HGT vs LGT were obtained, respectively. GO annotation, KEGG pathway analysis and a comprehensive analysis of DEGs showed a strong correlation between the GS biosynthesis and heat stress response. It was noticed that 11 differentially expressed genes tied to the GS biosynthesis were down-regulated, 23 heat shock transcription factors and 61 heat shock proteins were up-regulated upon the heat treatment. Another two Chinese kale varieties Cuibao and Shunbao with high- and low- GS content respectively, were used to validate the relationship of GS content and heat-response, and the results showed that high-GS content variety were more thermotolerant than the low-GS content one although GS significantly decreased in both varieties under heat stress. In addition, HSP100/ClpB, HSP90, HSP70 and sHSPs were differentially expressed in high- and low-GS varieties. Notably, HSP90 and sHSPs showed an obviously early response to heat stress than other related genes. The higher heat resistance of high-GS Chinese kale and the sharp decrease of glucosinolate content under heat stress indicated a strong relationship of GS accumulation and heat stress response. Combined with the previous report on the low expression of HSP90 at elevated temperatures in GS-deficient mutant TU8 of Arabidopsis, the differential expression pattern of HSP90 in high- and low- GS varieties and its early heat response implied it might be a key regulator in GS metabolism and heat-resistance in Chinese kale.