Transcriptome and metabolome analysis reveal the mechanisms of iron absorption differences in apple rootstocks under alkaline condition

Abstract Iron (Fe) is an essential micronutrient for plant growth and development. Fe deficiency leads to growth restriction, developmental disorders, chlorosis, and yield loss of fruit trees. This study investigated the molecular and biochemical mechanisms underlying the differences in Fe absorption among various apple rootstocks under alkaline conditions. Results showed that ‘Oregon Spur II’ grafted onto Qingzhen No.2 (OS/Q2) exhibited foliage etiolation, while ‘Oregon Spur II’ grafted onto Qingzhen No.1 (OS/Q1) did not display such etiolation under alkaline conditions. Physiological experiments revealed that total Fe, ferrous Fe, and chlorophyll content in OS/Q2 were significantly lower than those in OS/Q1, whereas the Fe reductase activity in OS/Q2 was higher than that in OS/Q1. Additionally, a total of 7,025 and 9,102 differentially expressed genes (DEGs), including 488 transcription factors (TFs), were identified in OS/Q1L vs. OS/Q2L and OS/Q1R vs. OS/Q2R, respectively. Subsequently, the pathways associated with “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “hydrogen ion export across plasma membrane”, “heme binding”, and “iron binding” were identified as critical for responding to Fe deficiency under alkaline conditions. Furthermore, a total of 244 differentially accumulated metabolites (DAMs) were identified in OS/Q1R vs. OS/Q2R. A combined analysis of the transcriptome and metabolome revealed that “ABC transporters”, “biosynthesis of amino acids”, and “carbon fixation in photosynthetic organisms” were significantly overrepresented in the KEGG pathways of both DEGs and DAMs. These newly acquired genes and metabolites involved in Fe metabolism will enhance our capacity to employ genetic engineering technologies to maintain Fe homeostasis in plants in the future.