Khairul Yusuf Nasution, Parlin Halomoan Sinaga, Kristamtini, Efendi, Basri Abu Bakar, Abdul Azis, June Mellawati, Tri Retno Dyah Larasati, Aryanti, Swisci Margaret, Yuni Widyastuti, Puput Melati, Joko Prasetiyono, Tasliah, Azri Kusuma Dewi, Ita Dwimahyani, Sobrizal, Untung Susanto
Biofortification of rice with iron (Fe) and zinc (Zn) offers a promising strategy to combat micronutrient deficiencies, particularly in developing countries, and selecting early-maturing rice cultivars is essential for maximizing the efficiency of multiple plantings per year. This study assessed 40 Indonesian local rice genotypes from three agroecological zones, upland (Aceh), swampy lowland (Riau), and irrigated lowland (Java), to evaluate their genetic diversity, population structure, and marker-trait associations for days to heading (DTH), grain Fe, and Zn content. Phenotypic data were collected for these traits, and genotyping was performed using 14 polymorphic simple sequence repeat (SSR) markers. STRUCTURE analysis, principal coordinate analysis (PCoA), and phylogenetic clustering consistently grouped the genotypes into two main clusters. Molecular diversity analysis revealed moderate to high polymorphism (average PIC = 0.57), with substantial genetic variation within populations. Marker– trait association analysis identified SSR markers RM12276 as significantly linked to high Fe content, collectively explaining 33.45% of phenotypic variation. Favorable alleles associated with this trait was also identified, offering valuable tools for marker-assisted selection. The integration of phenotypic and molecular data in this study supports the breeding of early-maturing, micronutrient-rich rice varieties suitable for diverse growing environments. © 2026 Author (s).
Research Center for Food Crops, National Research and Innovation Agency, Cibinong Science Center, Jalan Raya Jakarta-Bogor Km 46, Bogor, 16911, Indonesia; Aceh Rice Research Institute, Universitas Syiah Kuala, Jalan Brokoli No. 7 Kopelma Darussalam, Banda Aceh, 23111, Indonesia; Research Center for Safety, Metrology, and Nuclear Quality Technology, National Research and Innovation Agency, BJ Habibie Science and Technology Park, South Tangerang, 15314, Indonesia; Research Center for Radiation Process Technology, National Research and Innovation Agency, BJ Habibie Science and Technology Park, South Tangerang, 15314, Indonesia; Directorate of Laboratory Management, Research Facilities, and Science and Technology Area, National Research and Innovation Agency, Cibinong Science Center, Jalan Raya Jakarta-Bogor Km 46, Bogor, 16911, Indonesia; Research Center for Applied Botany, National Research and Innovation Agency, Cibinong Science Center, Jalan Raya Jakarta-Bogor Km 46, Bogor, 16911, Indonesia
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