Comprehensive Transcriptome Analysis of Tea Crabapple (Malus hupehensis Rehd.) Roots Subjected to Mixed Saline–Alkali Stress

Soil salinization–alkalization is a major hindrance to agricultural development globally. Tea crabapple is widely used in China. However, little remains known regarding the molecular mechanisms used to withstand mixed saline–alkali stress (MSAS). Herein, we exposed tea crabapple seedlings to MSAS, and RNA-seq was performed for the transcriptome analysis of roots. Between 43.26 million and 43.37 million clean reads were thus obtained. In comparison with the control group (day 0), 2931, 2335, and 3746 genes were differentially expressed at day 1, day 3, and day 6 of MSAS exposure, respectively, and 1022 genes were common in the three comparison groups. On functional annotation, we observed that numerous differentially expressed genes were involved in “global and overview maps”; “carbohydrate metabolism”; “folding, sorting, and degradation”; “biosynthesis of other secondary metabolites”; “environmental adaptation”; and “signal transduction.” Heat shock proteins, cytochrome P450s, disease-resistant proteins, non-specific lipid-transfer proteins, pectate lyase, and beta-glucosidases were also induced in response to MSAS, in addition to nitrogen, phosphorus, and potassium absorption and metabolism-related genes. Transcription factor-coding genes appear to regulate the response of tea crabapple roots to MSAS by participating in, for example, plant hormone signal transduction and heat shock response. We also performed quantitative real-time PCR to validate the expression of six differentially expressed genes. Our findings provide new insights into the molecular mechanisms used by tea crabapple to cope with MSAS.