Hardiyanto¹, Nirmala F. Devy^1*, Farida Yulianti¹, Agus Sugiyatno¹, Anang Triwiratno¹, Mutia Erti Dwiastuti¹, Mizu Istianto¹, Agus Sutanto¹, Sukartini¹

¹Research Center for Horticulture, National Research and Innovation Agency of Indonesia. Cibinong Science Center, Jalan Raya Bogor, KM. 46, Cibinong, West Java, Indonesia

 

*Corresponding author’s email: nfdevy@gmail.com

Received: 30 August 2025 / Revised: 23 November 2025 / Accepted: 09 December 2025 / Published Online: 23 December 2025

 

Abstract

 

Climate change intensifies microclimatic variability in tropical highlands, posing a serious challenge to apple (Malus domestica Borkh) cultivation in Indonesia. An integrative analysis combining leaf anatomy, exploratory metabolomic profiling, and gene expression was conducted to identify two tropical cultivar-specific adaptive mechanisms in contrasting highland sites: Bumiaji (1123 m asl, 18.5°C) and Tutur (1325 m asl, 22.2°C). Leaf anatomical traits showed strong genotype × environment interactions, with Anna–Tutur having the thickest palisade (116.0 µm) and spongy mesophyll (112.6 µm), and the highest stomatal density (381 stomata/mm²). Metabolomic profiling revealed that Anna was enriched in fatty acid derivatives, including tetracosanoic and cis-eicosenoic acids. In contrast, Manalagi reprogrammed sugar and antioxidant pathways, particularly in Bumiaji, with a specific focus on fructose/mannose metabolism (p = 0.0002). Gene expression analysis of six MADS-box genes showed consistent induction of AP1, AP3, and SOC1 in Manalagi, contrasting with the site-dependent plasticity observed in Anna. Fruit quality also diverged: Manalagi accumulated higher soluble solids (11.7 °Brix) and vitamin C (44.9 mg/100 g), while Anna exhibited higher acidity (2.8%) and firmness (8.2 kgf). These findings suggest that ‘Anna’ employs responsive plasticity suited to variable microclimates, in contrast, ‘Manalagi’ uses constitutive resilience for stable performance, providing evidence-based guidance for cultivar deployment in tropical highland production systems under climate change.

 

Keywords: Gene expression, Malus domestica, Multi-omics integration, Phenotypic plasticity, Tropical apple

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