Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic characterization of North Sulawesi local rice varieties, super win and Burungan

Abstract

Background and Objective: The genetic character of North Sulawesi's local rice cultivated by local communities has not been extensively explored. Genetic character can be used as tool for rice varieties identification to complement the morphological characters. This study aimed at developing genetic character of North Sulawesi's local rice varieties Burungan and Super Win using SSR and SNP molecular markers. Materials and Methods: Two local North Sulawesi varieties of rice from Bolaang Mongondow Regency, namely Super Win (Tropical Japonica) and Burungan (Japonica), were used. Control varieties included in this research were IR64 (Indica), Nipponbare (Japonica), Super Win Aromatik (Tropical Japonica) and Leukat Hitam (Tropical Japonica). The significant markers associated with agro-morphological characters were used, such as flowering date, panicle length, flag leaf corner, leaf length, panicle branches and the number of productive tillers. The SSR and SNP 384-chip which are mapped in the entire rice genome were employed. Results: The study showed that Burungan has alleles' size range 108.7-148.8 with a mean size of alleles 118.97. The frequency of this allele is 33.33%. Alleles' size range of Super Win is 109.2-148.8 with a mean size of alleles 119.50. The frequency of this allele is 22.22%. This diversity variation of allele size cannot be used as a genetic identifier for both varieties. The genetic distance between Burungan and Super Win varieties was quite high (0.461). It was due to they came from different sub species, Burungan was from Japonica while Super Win was from Tropical Japonica. Conclusion: Burungan and Super Win varieties are not a local rice of North Sulawesi.