Evaluation of molecular markers linked to fragrance and genetic diversity in Indian aromatic rice

DNA-based markers have the potential to improve the efficiency and precision of breeding programs based on marker-assisted selection. In the present study we evaluated the predictive abilities of previously reported PCR-based simple sequence repeat and functional markers related to fragrance in a set of 24 rice genotypes, including traditional basmatis, evolved basmatis, and aromatic indigenous landraces. High-resolution melting analysis with 3 markers was also performed to detect the presence of SNPs and length polymorphism in monomorphic amplicons. All genotypes showed expected marker patterns according to their fragrance classification except 5 fragrant genotypes: Kalanamak 3119, Kasturi Basmati, Basmati LC 74-3, Thurunbhog, and Jeeraga Samba. The genetic diversity analysis based on fragrance locus grouped the genotypes broadly into 2 major clusters representing fragrant and nonfragrant genotypes. Kalanamak 3119, Kasturi Basmati, and Basmati LC 74-3 comprised the fragrant cluster, while Thurunbhog and Jeeraga Samba clustered with nonfragrant genotypes. None of the functional markers could identify these 5 genotypes as fragrant, which supports the assumption of the existence of a second gene for fragrance in rice. Our work validates previously identified markers, namely nksbad2, L06, BADEX7-5, and ESP + IFAP + INSP + EAP, suitable for use in marker-assisted selection programs.