Chiang Mai Journal of Science

Print ISSN: 0125-2526 | eISSN : 2465-3845

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Assessment of Genetic Diversity in Rice for Days to Heading and Micronutrient (Zn and Fe) Content using SSR Markers

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 and Untung Susanto*
* Author for corresponding; e-mail address: untu009@brin.go.id, untungsus2011@gmail.com
ORCID ID: https://orcid.org/0000-0002-0992-2349
Volume: Vol.53 No.2 (March 2026)
Research Article
DOI: https://doi.org/10.12982/CMJS.2026.027
Received: 31 August 2025, Revised: 3 January 2026, Accepted: 4 January 2026, Published: -

Citation: Nasution K.Y., Sinaga P.H., Kristamtini, Efendi, Bakar B.A., Azis A., et al., Assessment of genetic diversity in rice for days to heading and micronutrient (Zn and Fe) content using SSR markers. Chiang Mai Journal of Science, 2026; 53(2): e2026027. DOI 10.12982/CMJS.2026.027.

Graphical Abstract

Graphical Abstract

Abstract

     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.

Keywords: genetic diversity, biofortification, early days to heading, rice, local varieties

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