The ECERIFERUM (CER) gene family plays an important role in wax biosynthesis. However, little is known about the CER gene family in jujube (Ziziphus jujuba Mill.). We identified 29 CER genes in the Z. jujuba genome and named them ZjCER1 to ZjCER29 according to their chromosomal locations. We then investigated the chemical characteristics, gene structures, and evolutionary relationships of these ZjCER genes. The genes were classified into three clades according to their phylogenetic relationship with Arabidopsis thaliana and Malus domestica. One pair of syntenic orthologous CER genes was matched between Z. jujuba and M. domestica. Analysis of conserved gene motifs revealed similar motifs within clades; 27 ZjCER genes had two or more introns. Twelve representative ZjCER genes showed different expression patterns in two Z. jujuba cultivars with contrasting cracking-resistant character. To further analyze the potential roles of ZjCER genes in response to various circumstances, we examined a 2.0 kb promoter region of the candidate ZjCER genes. All ZjCER genes except ZjCER28 shared a light-responsive element, and most shared hormone-related cis-elements. Our results provide rich resources for studying CER genes and potential clues for genetic improvement of jujube wax biosynthesis for improvement of cracking in Z. jujuba fruit.

Real-time quantitative PCR (RT-qPCR) has become a widely used method for exploring plant gene expression level. The method requires using some stably expressed genes as a reference to accurately normalize the RT-qPCR data. However, under various stresses and hormone treatments, the levels of most reference genes vary. Environmental variations also influence their expression levels. The lack of validated, stably expressed reference genes can mislead the study of gene function in pears. “Huangguan” pears have recently become the focus of research on stress resistance mechanisms, such as high resistance. Therefore, the aim of this study was to select the optimal reference genes in Huangguan pears, and we analyzed the expression of the genes EF1α, ACT, SKD1, YLS8, UBQ, GAPDH, TUB, and WDP in a series of pear leaf sets under various stresses and hormone treatments. Using different statistical algorithms, we found that under various treatments, the WDP gene had more stable expression, ACT was the most stable under MeJA treatment, YLS8 was the most valuable reference gene under ABA hormone and heat stress conditions, and GAPDH showed worst results compared to other housekeeping genes, except under heat stress. These results will supply valuable and updated information for the selection of housekeeping genes in pears under biotic and abiotic stresses in the future.

Background: Jujube is a typical fruit tree species from China. ‘Muzao’, a cracking-susceptible cultivar, and ‘Linhuang No. 1’, a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of ‘Linhuang No. 1’ and ‘Muzao’ allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars. Results: Resequencing identified 664,129 polymorphic variable sites between ‘Linhuang No. 1’ and ‘Muzao’. To determine the genetic relationship among ‘Linhuang No. 1’, ‘Muzao’ and the jujube genome reference cultivar ‘Dongzao’, the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between ‘Linhuang No. 1’ and ‘Muzao’ was closer than that of either variety and ‘Dongzao’. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of ‘Muzao’ were significantly higher than the corresponding values of ‘Linhuang No. 1’ at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars. Conclusions: The present study was the first to explore the differences between different jujube cultivars (‘Linhuang No. 1’ and ‘Muzao’) by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars ‘Linhuang No. 1’ and ‘Muzao’.