Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress.

Saline-alkali stress is a severely adverse abiotic stress limiting plant growth. Malus halliana Koehne is an apple rootstock that is tolerant to saline-alkali stress. To understand the molecular mechanisms underlying the tolerance of M. halliana to saline-alkali stress, an integrated metabolomic and proteomic approach was used to analyze the plant pathways involved in the stress response of the plant and its regulatory mechanisms. A total of 179 differentially expressed proteins (DEPs) and 140 differentially expressed metabolites (DEMs) were identified. We found that two metabolite-related enzymes (PPD and PAO) were associated with senescence and involved in porphyrin and chlorophyll metabolism; six photosynthesis proteins (PSAH2, PSAK, PSBO2, PSBP1, and PSBQ2) were significantly upregulated, especially PSBO2, and could act as regulators of photosystem II (PSII) repair. Sucrose, acting as a signaling molecule, directly mediated the accumulation of D-phenylalanine, tryptophan, and alkaloid (vindoline and ecgonine) and the expression of proteins related to aspartate and glutamate (ASP3, ASN1, NIT4, and GLN1-1). These responses play a central role in maintaining osmotic balance and removing reactive oxygen species (ROS). In addition, sucrose signaling induced flavonoid biosynthesis by activating the expression of CYP75B1 to regulate the homeostasis of ROS and promoted auxin signaling by activating the expression of T31B5_170 to enhance the resistance of M. halliana to saline-alkali stress. The decrease in peroxidase superfamily protein (PER) and ALDH2C4 during lignin synthesis further triggered a plant saline-alkali response. Overall, this study provides an important starting point for improving saline-alkali tolerance in M. halliana via genetic engineering.

Transcriptome analysis in Malus halliana roots in response to iron deficiency reveals insight into sugar regulation.

Iron (Fe) deficiency is a frequent nutritional problem limiting apple production in calcareous soils. The utilization of rootstock that is resistant to Fe deficiency is an effective way to solve this problem. Malus halliana is an Fe deficiency-tolerant rootstock; however, few molecular studies have been conducted on M. halliana. In the present work, a transcriptome analysis was combined with qRT-PCR and sugar measurements to investigate Fe deficiency responses in M. halliana roots at 0 h (T1), 12 h (T2) and 72 h (T3) after Fe deficiency stress. Total of 2473, 661, and 776 differentially expressed genes (DEGs) were identified in the pairs of T2 vs. T1, T3 vs. T1, and T3 vs. T2, respectively. Several DEGs were enriched in the photosynthesis, glycolysis and gluconeogenesis, tyrosine metabolism and fatty acid degradation pathways. The glycolysis and photosynthesis pathways were upregulated under Fe deficiency. In this experiment, sucrose accumulated in Fe-deficient roots and leaves. However, the glucose content significantly decreased in the roots, while the fructose content significantly decreased in the leaves. Additionally, 15 genes related to glycolysis and sugar synthesis and sugar transport were selected to validate the accuracy of the transcriptome data by qRT-PCR. Overall, these results indicated that sugar synthesis and metabolism in the roots were affected by Fe deficiency. Sugar regulation is a way by which M. halliana responds to Fe deficiency stress.

Transcriptional and physiological analyses of short-term Iron deficiency response in apple seedlings provide insight into the regulation involved in photosynthesis.

BACKGROUND: Iron (Fe) is an essential micronutrient for plants. Utilization of Fe deficiency-tolerant rootstock is an effective strategy to prevent Fe deficiency problems in fruit trees production. Malus halliana is an apple rootstock that is resistant to Fe deficiency; however, few molecular studies have been conducted on M. halliana. RESULTS: To evaluate short-term molecular response of M. halliana leaves under Fe deficiency condition, RNA sequencing (RNA-Seq) analyses were conducted at 0 (T1), 0.5 (T2) and 3 d (T3) after Fe-deficiency stress, and the timepoints were determined with a preliminary physiological experiment. In all, 6907, 5328, and 3593 differentially expressed genes (DEGs) were identified in pairs of T2 vs. T1, T3 vs. T1, and T3 vs. T2. Several of the enriched DEGs were related to heme binding, Fe ion binding, thylakoid membranes, photosystem II, photosynthesis-antenna protein, porphyrin and chlorophyll metabolism and carotenoid biosynthesis under Fe deficiency, which suggests that Fe deficiency mainly affects the photosynthesis of M. halliana. Additionally, we found that Fe deficiency induced significant down-regulation in genes involved in photosynthesis at T2 when seedlings were treated with Fe-deficient solution for 0.5 d, indicating that there was a rapid response of M. halliana to Fe deficiency. A strong up-regulation of photosynthesis genes was detected at T3, which suggested that M. halliana was able to recover photosynthesis after prolonged Fe starvation. A similar expression pattern was found in pigment regulation, including genes for coding chlorophyllide a oxygenase (CAO), ß-carotene hydroxylase (ß-OHase), zeaxanthin epoxidase (ZEP) and 9-cis-epoxycarotenoid dioxygenase (NCED). Our results suggest that pigment regulation plays an important role in the Fe deficiency response. In addition, we verified sixteen genes related to photosynthesis-antenna protein, porphyrin and chlorophyll metabolism and carotenoid biosynthesis pathways using quantitative real-time PCR (qRT-PCR) to ensure the accuracy of transcriptome data. Photosynthetic parameters, Chl fluorescence parameters and the activity of Chlase were also determined. CONCLUSIONS: This study broadly characterizes a molecular mechanism in which pigment and photosynthesis-related regulations play indispensable roles in the response of M. halliana to short-term Fe deficiency and provides a basis for future analyses of the key genes involved in the tolerance of Fe deficiency.