Nirmala Friyanti Devy1, Sri Widyaningsih1, Farida Yulianti1, Eriyanto Yusnawan2, Agus Sugiyatno1, Siti Subandiyah3, Hardiyanto1*
1Research Center for Horticulture, Research Organization for Agriculture and Food, National Research and Innovation Agency of Indonesia. Cibinong Science Center (BRIN), Jalan Raya Bogor, KM. 46, Cibinong, West Java, Indonesia
2Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency of Indonesia. Cibinong Science Center (BRIN), Jalan Raya Bogor, KM. 46, Cibinong, West Java, Indonesia
3Department of Entomology and Plant Pathology, Universitas Gadjah Mada (UGM), Yogyakarta, Indonesia
*Corresponding author’s email: hardiyanto85@yahoo.com
Received: 11 February 2026 / Revised: 05 May 2026 / Accepted: 19 May 2026 / Published Online: 06 June 2026
Abstract
Citrus rootstock selection is usually based on physiological or anatomical characteristics, which restricts integrative knowledge and lowers the efficacy of selection techniques. The lack of cross-organ metabolic evidence further constrains the use of metabolomics in practical rootstock evaluation. This study determined whether coordinated root and leaf metabolomic profiles distinguish five citrus rootstocks and explain variation in leaf anatomy and vegetative growth of Citrus reticulata Blanco cv. Keprok Batu 55 (KB) and Citrus sinensis L. cv. Manis Pacitan (MP) under highland conditions. Untargeted GC–MS metabolomics, combined with multivariate analysis, anatomical traits, and growth measurements, showed that rootstock identity was the dominant source of variation, with PC1 explaining ~40–45% of the total metabolic variance across organs. Salam and Cleopatra mandarin were enriched in terpenoids, coumarins, and phenylpropanoid-related metabolites, reflecting a defense-associated metabolic profile, whereas Volkameriana and Rough Lemon had a higher relative abundance of intermediates of carbohydrate metabolism, NAD-related compounds, and antioxidants, consistent with a growth-associated profile. Those metabolic configurations are correlated with footsteps in lamina thickness, palisade development, stomatal density, and vegetative growth, all significant at p < 0.05. This study is novel in showing root-leaf metabolomic coordination associated with anatomical plasticity and growth variation, and in providing systematic evidence of rootstock-defined metabolic syndromes co-modulated between roots and leaves in tropical citrus systems. These findings highlight the potential of metabolome-informed approaches to support early rootstock pre-selection, pending validation with replicated metabolomic designs.
Keywords: Citrus, Rootstock–scion interaction, Metabolomics, Metabolic syndromes, Leaf anatomy, Growth–defense trade-off
