Transcription-metabolism association analysis of molecular mechanisms in sweet orange plants in response to boron deficiency

Sweet orange (Citrus sinensis) is the most widely grown citrus fruit worldwide, with the highest production and largest cultivated area. Serious problems associated with boron (B) deficiency are emerging in most old production areas, resulting in the lignification of sweet orange flesh and fruit souring. However, the molecular mechanisms through which sweet orange plants react to boron deficiency stress remain unreported in the literature. Through transcriptome analysis and RT-qPCR expression validation, this study revealed that CsBBX11, CsBBX13, and CsBBX14 may play important roles in the response of sweet orange plants to boron deficiency stress. Metabolomic analysis revealed that the contents of quercetin 3-glucoside, taxifolin, and isovitexin all exceeded 1 µg/g, with significant differences in the contents of these metabolites observed before and after treatment. Correlation analysis revealed that CsBBX14 was positively correlated with quercetin 3-glucoside and isovitexin, but negatively correlated with taxifolin. Furthermore, the expression of CsBBX14 was highly significantly correlated with that of 57% of the genes associated with flavonoid biosynthesis and metabolism. Finally, a possible regulatory mechanism for sweet orange resistance to boron deficiencywas proposed in this study. CsBBX14 is likely to interact with the G-box element located in the promoter region of HY5, thereby initiating the expression of genes responsible for flavonoid synthesis. In conclusion, CsBBX14 is likely a key gene involved in the synthesis of flavonoids during stress caused by a lack of B. However, its specific functions in flavonoid synthesis need to be further verified. These findings offer a novel reference point for the molecular breeding of sweet oranges aimed at addressing boron deficiency stress.