Pigmented rice (Oryza sativa L.) genotypes are popular for their nutritional and functional benefits; however, exploring their genetic diversity has not received attention in Indonesia. The following study aimed to assess the genetic variation in 15 pigmented rice accessions from East and North Kalimantan using chloroplast DNA barcoding (matK and rbcL) and nuclear inter-simple sequence repeat (ISSR) markers. DNA barcoding revealed no nucleotide polymorphisms, suggesting a common ancestry for rice accessions. The chloroplast genes appeared unsuitable for distinguishing closely related cultivars with the same genetic backgrounds. In contrast, ISSR analysis disclosed substantial nuclear genomic diversity. Eleven primers generated polymorphic profiles that grouped the rice accessions into four distinct clusters based on the 70% genetic similarity threshold. Group I included 10 cultivars from overlapping agroecological regions, while Groups II–IV contained genetically distinct accessions, including a divergent red rice cultivar from Setulang, Indonesia. The results underscore the effectiveness of ISSR markers in detecting intraspecific variation and highlight the genetic richness of pigmented rice. The study highlighted the significant genetic diversity in these pigmented rice cultivars, offering insights for conservation strategies and the development of superior cultivars through breeding programs.

Keywords: Pigmented rice (O. sativa L.), genetic variation, DNA barcoding, genomic analysis, ISSR

Key findings: Chloroplast DNA barcoding using matK and rbcL genes revealed no detectable genetic variation among the pigmented rice (O. sativa L.) accessions. However, ISSR markers detected substantial genomic polymorphism, and highlighting their potential for further improvement through breeding programs.